SAXSdb — 1wzi

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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	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

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 1WZI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BDM THE STRUCTURE AT 1.8 ANGSTROMS RESOLUTION OF A SINGLE SITE MUTANT (T189I) OF MALATE DEHYDROGENASE FROM THERMUS FLAVUS WITH INCREASED ENZYMATIC ACTIVITY Deposited 1993-02-16	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）	Not recorded	NAX BETA-6-HYDROXY-1,4,5,6-TETRHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
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 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）	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 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）	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 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）	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
1Y7T Crystal structure of NAD(H)-depenent malate dehydrogenase complexed with NADPH Deposited 2004-12-10	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）	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 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）	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 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） 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 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） 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 mutation/modification 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	1wzi
Deposition date deposition_date	2005-03-05
Structure title title	Structural basis for alteration of cofactor specificity of Malate dehydrogenase from Thermus flavus
Keywords keywords	Seven amino acid residues mutant, protein-NADPH complex, OXIDOREDUCTASE; OXIDOREDUCTASE
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	26.96 Å
Radius of gyration Rg (electron density) rg_electron	26.20 Å
Forward intensity I(0) i0	86275100.00
Molecular weight molecular_weight	72082.0 kDa
Excluded volume excluded_volume	90062 Å³
Envelope volume envelope_volume	105960 Å³
Hydration-shell volume shell_volume	33280 Å³
Envelope diameter envelope_diameter	90.1 Å
Shell Rg shell_rg	33.97 Å
Envelope Rg envelope_rg	26.29 Å
Shape Rg shape_rg	26.22 Å
Total Rg total_rg	26.94 Å
Total atoms total_atoms	5058
Residues n_residues	654
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	90.7 Å
Rg (real space) rg_real	26.92 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	8.6280e+07
I(0) uncertainty (real space) i0_real_error	1.0710e+06
Rg (reciprocal space) rg_reciprocal	26.93 Å
I(0) (reciprocal space) i0_reciprocal	86280000.0000
Solution quality estimate total_estimate	0.6961
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.8 Å
Skewness Skewness skewness	0.318
Kurtosis Kurtosis kurtosis	-0.426
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	38500000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.825; Stabil: 1.000; Sysdev: 0.199; Positv: 1.000; Valcen: 0.974; Smooth: 0.999

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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	35460.6 kDa
EC 编号 ec_number	1.1.1.37
Mutation mutation	E41G, I42S, P43E, Q44R, A45S, M46F, K47Q
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	5682

MKAPVRVAVTGAAGQIGYSLLFRIAAGEMLGKDQPVILQLLGSERSFQALEGVVMELEDCAFPLLAGLEATDDPKVAFKDADYALLVGAAPRKAGMERRDLLQVNGKIFTEQGRALAEVAKKDVKVLVVGNPANTNALIAYKNAPGLNPRNFTAMTRLDHNRAKAQLAKKTGTGVDRIRRMTVWGNHSSTMFPDLFHAEVDGRPALELVDMEWYEKVFIPTVAQRGAAIIQARGASSAASAANAAIEHIRDWALGTPEGDWVSMAVPSQGEYGIPEGIVYSFPVTAKDGAYRVVEGLEINEFARKRMEITAQELLDEMEQVKALGLI

来源 Source

来源生物 organism	Thermus thermophilus
NCBI Class编号 ncbi_taxonomy_id	274
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Molecular weight formula_weight	745.4 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	624

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1wzia1
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	d1wzia2
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	d1wzib1
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	d1wzib2
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	1wziA01
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	1wziA02
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	1wziB01
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	1wziB02
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)

Structural basis for alteration of cofactor specificity of malate dehydrogenase from Thermus flavus

to be published

PRIMARY

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

Biochemistry (1993)

PMID: 8471603 · DOI: 10.1021/bi00066a010

Preliminary X-ray diffraction analysis of a crystallizable mutant of malate dehydrogenase from the thermophile Thermus flavus

J.Mol.Biol. (1991)

PMID: 1920425 · DOI: 10.1016/0022-2836(91)80060-8

Refined crystal structure of cytoplasmic malate dehydrogenase at 2.5-A resolution

Biochemistry (1989)

PMID: 2775751 · DOI: 10.1021/bi00440a051

Nucleotide sequence of the malate dehydrogenase gene of Thermus flavus and its mutation directing an increase in enzyme activity

J.Biol.Chem. (1986)

PMID: 3771528

;The presence of a histidine-aspartic acid pair in the active site of 2-hydroxyacid dehydrogenases. X-ray refinement of cytoplasmic malate dehydrogenase ;

J.Biol.Chem. (1983)

PMID: 6848515

Malate Dehydrogenases

Enzyme (1975)

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Unit-cell length a length_a	70.310 Å
Unit-cell length b length_b	85.390 Å
Unit-cell length c length_c	117.700 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	2.000 Å
Low-resolution limit resolution_low	28.890 Å
R factor r_factor	0.1960
R_work r_work	0.1960
R_free r_free	0.2290

fit	/app/data/saxs_computation/wz/1wzi/1wzi.fit
pddf	/app/data/pr_computation/wz/1wzi/1wzi.pr.out
profile	/app/data/saxs_computation/wz/1wzi/1wzi.dat

Structural basis for alteration of cofactor specificity of Malate dehydrogenase from Thermus flavus

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

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction