PDB-7by8: Malate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH)

ID or keywords:

Entry

Database: PDB / ID: 7by8

Title

Malate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH)

Components

Malate dehydrogenase

Keywords

OXIDOREDUCTASE / Malate Dehydrogenase

Function / homology

Function and homology information

malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / tricarboxylic acid cycle / nucleotide binding
Similarity search - Function

Biological species

Geobacillus stearothermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.945 Å

Authors

Shimozawa, Y. / Nakamura, T. / Himiyama, T. / Nishiya, Y.

Funding support

Japan, 2items

Citation

Journal: J.Biochem. / Year: 2021
Title: Structural analysis and reaction mechanism of malate dehydrogenase from Geobacillus stearothermophilus.
Authors: Shimozawa, Y. / Himiyama, T. / Nakamura, T. / Nishiya, Y.

History

Deposition	Apr 22, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 24, 2021	Provider: repository / Type: Initial release
Revision 1.1	Feb 16, 2022	Group: Database references / Category: citation / database_2 Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Nov 29, 2023	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	7by8_validation.pdf.gz	460.2 KB	Display	wwPDB validaton report
Full document	7by8_full_validation.pdf.gz	468.3 KB	Display
Data in XML	7by8_validation.xml.gz	42.7 KB	Display
Data in CIF	7by8_validation.cif.gz	61.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/by/7by8 ftp://data.pdbj.org/pub/pdb/validation_reports/by/7by8	HTTPS FTP

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Related structure data

Related structure data	7by9C 7byaC 3tl2S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6jml-1 6j9u-2 1hyh-d 6j9t-1 6j9u-1 4ply-2 6k13-1 4ply-1 2zqz-2 3p7m-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#102 - Jun 2008 Lactate Dehydrogenase similarity (7) #154 - Oct 2012 Citric Acid Cycle similarity (7) #142 - Oct 2011 PDB Pioneers similarity (6)

Deposited unit

A: Malate dehydrogenase

B: Malate dehydrogenase

C: Malate dehydrogenase

D: Malate dehydrogenase

144 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	81.682, 108.679, 146.643
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Malate dehydrogenase Mass: 35932.312 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: mdh / Production host: Escherichia coli (E. coli) / References: UniProt: A0A143T1U9, malate dehydrogenase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.41 Å³/Da / Density % sol: 48.96 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES (pH 7.5), 10 % polyethylene glycol (PEG) 6000, 5 % 2-Methyl-2,4-pentanediol (MPD)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 14, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.945→50 Å / Num. obs: 95978 / % possible obs: 99.7 % / Redundancy: 11.8 % / CC_1/2: 0.998 / R_merge(I) obs: 0.079 / Net I/σ(I): 11.2
Reflection shell	Resolution: 1.95→1.98 Å / R_merge(I) obs: 0.596 / Num. unique obs: 4731 / CC_1/2: 0.835

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3TL2

3tl2

Resolution: 1.945→44.619 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.939 / SU B: 5.224 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.163
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2546	4804	5.009 %
R_work	0.2059	-	-
all	0.208	-	-
obs	-	95909	99.501 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 39.396 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.002 Å²	0 Å²	0 Å²
2-	-	0.011 Å²	-0 Å²
3-	-	-	-0.009 Å²

Refinement step

Cycle: LAST / Resolution: 1.945→44.619 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9290	0	0	268	9558

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	9418
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	9274
X-RAY DIFFRACTION	r_angle_refined_deg	1.515	1.642	12747
X-RAY DIFFRACTION	r_angle_other_deg	1.282	1.576	21494
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.007	5	1219
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.414	23.252	409
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.167	15	1701
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.469	15	48
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	1279
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	10451
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1769
X-RAY DIFFRACTION	r_nbd_refined	0.195	0.2	1921
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.176	0.2	8676
X-RAY DIFFRACTION	r_nbtor_refined	0.156	0.2	4686
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	4407
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.155	0.2	343
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.04	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.165	0.2	5
X-RAY DIFFRACTION	r_nbd_other	0.233	0.2	18
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.132	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	3.124	3.989	4894
X-RAY DIFFRACTION	r_mcbond_other	3.124	3.988	4893
X-RAY DIFFRACTION	r_mcangle_it	4.059	5.969	6107
X-RAY DIFFRACTION	r_mcangle_other	4.059	5.971	6108
X-RAY DIFFRACTION	r_scbond_it	3.535	4.419	4524
X-RAY DIFFRACTION	r_scbond_other	3.533	4.415	4521
X-RAY DIFFRACTION	r_scangle_it	5.281	6.462	6640
X-RAY DIFFRACTION	r_scangle_other	5.282	6.461	6639
X-RAY DIFFRACTION	r_lrange_it	6.35	47.878	10279
X-RAY DIFFRACTION	r_lrange_other	6.356	47.864	10250

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.945-1.995	0.357	358	0.323	6437	X-RAY DIFFRACTION	96.7673
1.995-2.05	0.346	353	0.295	6481	X-RAY DIFFRACTION	99.5484
2.05-2.109	0.346	319	0.272	6320	X-RAY DIFFRACTION	99.8496
2.109-2.174	0.323	328	0.258	6176	X-RAY DIFFRACTION	99.7699
2.174-2.245	0.307	286	0.262	5976	X-RAY DIFFRACTION	99.8565
2.245-2.324	0.312	291	0.256	5822	X-RAY DIFFRACTION	99.9183
2.324-2.411	0.314	290	0.239	5600	X-RAY DIFFRACTION	99.9491
2.411-2.51	0.322	256	0.248	5384	X-RAY DIFFRACTION	99.9646
2.51-2.621	0.292	282	0.233	5196	X-RAY DIFFRACTION	99.9635
2.621-2.748	0.285	269	0.22	4935	X-RAY DIFFRACTION	100
2.748-2.897	0.275	270	0.223	4715	X-RAY DIFFRACTION	99.9799
2.897-3.072	0.305	228	0.222	4469	X-RAY DIFFRACTION	100
3.072-3.283	0.283	249	0.23	4217	X-RAY DIFFRACTION	99.9776
3.283-3.544	0.216	193	0.2	3945	X-RAY DIFFRACTION	99.9758
3.544-3.881	0.227	201	0.191	3643	X-RAY DIFFRACTION	100
3.881-4.335	0.221	167	0.163	3307	X-RAY DIFFRACTION	100
4.335-4.999	0.186	156	0.144	2944	X-RAY DIFFRACTION	99.9355
4.999-6.107	0.223	134	0.173	2522	X-RAY DIFFRACTION	100
6.107-8.57	0.202	107	0.15	1982	X-RAY DIFFRACTION	99.9522
8.57-44.619	0.171	67	0.175	1034	X-RAY DIFFRACTION	87.1734

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