6TLK | pdb_00006tlk

Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylorubrum extorquens AM1 in an open conformation containing NADP+ and methylene-H4MPT

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LU9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	281.15	The protein at 25 mg/ml was in 25 mM tris(hydroxymethyl)aminomethane (Tris)/HCl buffer pH 7.5 containing 150 mM NaCl, 5% glycerol and 2 mM dithiothreitol, supplemented with 2.5 mM methenyl-H4MPT and 2 mM NADP. The crystallization solution was 20% w/v polyethylene glycol 3350 and 200 mM magnesium formate. The crystallization drop contained 0.7 ul of protein solution and 0.7 ul crystallization solution

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.923	α = 90
b = 149.267	β = 93.64
c = 78.559	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2017-09-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.97992	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.8	78.401	98.9	0.066	0.066	0.08	0.044	0.99	12.2	3		161189			28.48

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.9	99.5		1.032	1.032	1.247	0.69	0.543	0.8	3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1LU9	1.8	26.35	161135	7909	98.8	0.167	0.166	0.17	0.201	0.21	RANDOM	36.17

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
1.0754		5.0536	-0.6214		-0.454

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	13.72
t_omega_torsion	3.63
t_angle_deg	1.21
t_bond_d	0.009
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	13.72
t_omega_torsion	3.63
t_angle_deg	1.21
t_bond_d	0.009
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12548
Nucleic Acid Atoms
Solvent Atoms	2093
Heterogen Atoms	489

Software

Software
Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.