SAXSdb — 1bdm

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1. Protein Identity and Related Structures Protein Identity & Related Structures

MALATE DEHYDROGENASE

Thermus thermophilus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–327 Chain B； UniProt 1–327	Not recorded	NAX BETA-6-HYDROXY-1,4,5,6-TETRHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.80 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1BDM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BMD DETERMINANTS OF PROTEIN THERMOSTABILITY OBSERVED IN THE 1.9 ANGSTROMS CRYSTAL STRUCTURE OF MALATE DEHYDROGENASE FROM THE THERMOPHILIC BACTERIUM THERMUS FLAVUS Deposited 1992-11-10	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–327（327 aa） Chain B 1–327（327 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1IZ9 Crystal Structure of Malate Dehydrogenase from Thermus thermophilus HB8 Deposited 2002-10-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–327（327 aa） Chain B 1–327（327 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；PEG MME 2000, Nickel Chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.226
1WZE Structural basis for alteration of cofactor specificity of Malate dehydrogenase from Thermus flavus Deposited 2005-03-04	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–327（327 aa） Chain B 1–327（327 aa）	Mutation：E41G, I42S, P43E, Q44R, A45S, M46F, K47Q Mutation：E41G, I42S, P43E, Q44R, A45S, M46F, K47Q	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；PEG 4000, dithiothreitol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.228
1WZI Structural basis for alteration of cofactor specificity of Malate dehydrogenase from Thermus flavus Deposited 2005-03-05	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–327（327 aa） Chain B 1–327（327 aa）	Mutation：E41G, I42S, P43E, Q44R, A45S, M46F, K47Q Mutation：E41G, I42S, P43E, Q44R, A45S, M46F, K47Q	NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；PEG 4000, dithiothreitol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.229
1Y7T Crystal structure of NAD(H)-depenent malate dehydrogenase complexed with NADPH Deposited 2004-12-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–327（327 aa） Chain B 1–327（327 aa）	Not recorded	NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.65 Å R-free 0.207
2CVQ Crystal structure of NAD(H)-dependent malate dehydrogenase complexed with NADPH Deposited 2005-06-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–327（327 aa） Chain B 1–327（327 aa）	Not recorded	NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.08 Å R-free 0.247
4KDE Crystal Structure of the Apo Form of Thermus thermophilus Malate Dehydrogenase Deposited 2013-04-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–327（327 aa） Fragment：Malate Dehydrogenase Chain B 1–327（327 aa） Fragment：Malate Dehydrogenase	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；283 K；22.5% PEG 4000, 1.0M Tris-HCl, 0.2M MgCl2, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 283K	Resolution 1.80 Å R-free 0.170
4KDF Crystal Structure of Thermus thermophilus Malate Dehydrogenase in Complex with NAD Deposited 2013-04-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–327（327 aa） Fragment：Malate Dehydrogenase Chain D 1–327（327 aa） Fragment：Malate Dehydrogenase	Not recorded	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；283 K；22.5% PEG 4000, 0.1M Tris-HCl, 0.2M MgCl2, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 283K	Resolution 2.36 Å R-free 0.232
4KDF Crystal Structure of Thermus thermophilus Malate Dehydrogenase in Complex with NAD Deposited 2013-04-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–327（327 aa） Fragment：Malate Dehydrogenase Chain C 1–327（327 aa） Fragment：Malate Dehydrogenase	Not recorded	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；283 K；22.5% PEG 4000, 0.1M Tris-HCl, 0.2M MgCl2, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 283K	Resolution 2.36 Å R-free 0.232

8 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MDH_THETH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–327； UniProt 1–327 Author chain B； PDBConstruct 1–327； UniProt 1–327

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1bdm
Deposition date deposition_date	1993-02-16
Structure title title	THE STRUCTURE AT 1.8 ANGSTROMS RESOLUTION OF A SINGLE SITE MUTANT (T189I) OF MALATE DEHYDROGENASE FROM THERMUS FLAVUS WITH INCREASED ENZYMATIC ACTIVITY
Keywords keywords	OXIDOREDUCTASE(NAD(A)-CHOH(D)); OXIDOREDUCTASE(NAD(A)-CHOH(D))
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	27.10 Å
Radius of gyration Rg (electron density) rg_electron	26.37 Å
Forward intensity I(0) i0	82216500.00
Molecular weight molecular_weight	70860.0 kDa
Excluded volume excluded_volume	88742 Å³
Envelope volume envelope_volume	104740 Å³
Hydration-shell volume shell_volume	32862 Å³
Envelope diameter envelope_diameter	93.3 Å
Shell Rg shell_rg	33.96 Å
Envelope Rg envelope_rg	26.45 Å
Shape Rg shape_rg	26.39 Å
Total Rg total_rg	27.09 Å
Total atoms total_atoms	4975
Residues n_residues	645
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	87.8 Å
Rg (real space) rg_real	27.08 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	8.2220e+07
I(0) uncertainty (real space) i0_real_error	1.1680e+06
Rg (reciprocal space) rg_reciprocal	27.09 Å
I(0) (reciprocal space) i0_reciprocal	82220000.0000
Solution quality estimate total_estimate	0.8186
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.8 Å
Skewness Skewness skewness	0.334
Kurtosis Kurtosis kurtosis	-0.407
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	31900000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.883; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	MALATE DEHYDROGENASE
Molecular weight formula_weight	35464.7 kDa
EC 编号 ec_number	1.1.1.37
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5197

MKAPVRVAVTGAAGQIGYSLLFRIAAGEMLGKDQPVILQLLEIPQAMKALEGVVMELEDCAFPLLAGLEATDDPDVAFKDADYALLVGAAPRKAGMERRDLLQVNGKIFTEQGRALAEVAKKDVKVLVVGNPANTNALIAYKNAPGLNPRNFTAMTRLDHNRAKAQLAKKTGTGVDRIRRMTVWGNHSSIMFPDLFHAEVDGRPALELVDMEWYEKVFIPTVAQRGAAIIQARGASSAASAANAAIEHIRDWALGTPEGDWVSMAVPSQGEYGIPEGIVYSFPVTAKDGAYRVVEGLEINEFARKRMEITAQELLDEMEQVKALGLI

来源 Source

来源生物 organism	Thermus thermophilus
NCBI Class编号 ncbi_taxonomy_id	274

Entity 2 Entity 2 non-polymer

Description description	BETA-6-HYDROXY-1,4,5,6-TETRHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
Molecular weight formula_weight	683.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	202

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1bdma1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.5 — LDH N-terminal domain-like

Domain ID domain_id	d1bdma2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.162 — LDH C-terminal domain-like
Superfamily Superfamily superfamily	d.162.1 — LDH C-terminal domain-like
Family Family family	d.162.1.1 — Lactate & malate dehydrogenases, C-terminal domain

Domain ID domain_id	d1bdmb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.5 — LDH N-terminal domain-like

Domain ID domain_id	d1bdmb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.162 — LDH C-terminal domain-like
Superfamily Superfamily superfamily	d.162.1 — LDH C-terminal domain-like
Family Family family	d.162.1.1 — Lactate & malate dehydrogenases, C-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id	1bdmA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1bdmA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal

Domain ID domain_id	1bdmB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1bdmB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal

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8. Citations (7)

;Determinants of protein thermostability observed in the 1.9-A crystal structure of malate dehydrogenase from the thermophilic bacterium Thermus flavus. ;

Biochemistry (1993)

PMID: 8471603 · DOI: 10.1021/bi00066a010 PRIMARY

Preliminary X-Ray Diffraction Analysis of a Crystallizable Mutant of Malate Dehydrogenase from the Thermophile Thermus Flavus

J.Mol.Biol. (1991)

Role of Threonine 190 in Modulating the Catalytic Function of Malate Dehydrogenase from a Thermophile Thermus Flavus

J.Biol.Chem. (1991)

Refined Crystal Structure of Cytoplasmic Malate Dehydrogenase at 2.5-Angstroms Resolution

Biochemistry (1989)

Nucleotide Sequence of the Malate Dehydrogenase Gene of Thermus Flavus and its Mutation Directing an Increase in Enzyme Activity

J.Biol.Chem. (1986)

Chemistry and Solution Conformation of the Pyridine Coenzymes

The Pyridine Nucleotide Coenzymes (1982)

Malate Dehydrogenase

The Enzymes,Third Edition (1975)

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Unit-cell length a length_a	71.750 Å
Unit-cell length b length_b	88.640 Å
Unit-cell length c length_c	118.970 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	0.1690
R_work r_work	0.1690
R_free r_free	—

fit	/app/data/saxs_computation/bd/1bdm/1bdm.fit
pddf	/app/data/pr_computation/bd/1bdm/1bdm.pr.out
profile	/app/data/saxs_computation/bd/1bdm/1bdm.dat

THE STRUCTURE AT 1.8 ANGSTROMS RESOLUTION OF A SINGLE SITE MUTANT (T189I) OF MALATE DEHYDROGENASE FROM THERMUS FLAVUS WITH INCREASED ENZYMATIC ACTIVITY

1. Protein Identity and Related Structures Protein Identity & Related Structures

MALATE DEHYDROGENASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution