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1b8v

Malate dehydrogenase from Aquaspirillum arcticum

Method: X-RAY DIFFRACTION Dmax: 63.7 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (MALATE DEHYDROGENASE)

OrganismNot specified

UniProt Q9ZF99

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 1–329 Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.0 Resolution 2.10 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 1B8V Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B8P MALATE DEHYDROGENASE FROM AQUASPIRILLUM ARCTICUM Deposited 1999-02-02 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–329（329 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.0
Resolution 1.90 Å R-free 0.178
1B8U MALATE DEHYDROGENASE FROM AQUASPIRILLUM ARCTICUM Deposited 1999-02-02 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–329（329 aa）
Not recorded OAA OXALOACETATE ION × 2 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.0
Resolution 2.50 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MDH_AQUAR
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–329； UniProt 1–329

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1b8v

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1b8v
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1b8v
Deposition date deposition_date1999-02-02
Structure title titleMalate dehydrogenase from Aquaspirillum arcticum
Keywords keywordsDEHYDROGENASE, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.53 Å
Radius of gyration Rg (electron density) rg_electron19.44 Å
Forward intensity I(0) i022547700.00
Molecular weight molecular_weight35709.0 kDa
Excluded volume excluded_volume44523 ų
Envelope volume envelope_volume51335 ų
Hydration-shell volume shell_volume21728 ų
Envelope diameter envelope_diameter66.8 Å
Shell Rg shell_rg26.18 Å
Envelope Rg envelope_rg19.67 Å
Shape Rg shape_rg19.43 Å
Total Rg total_rg20.36 Å
Total atoms total_atoms2505
Residues n_residues327
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax63.7 Å
Rg (real space) rg_real20.42 Å
Rg uncertainty (real space) rg_real_error0.33 Å
I(0) (real space) i0_real2.2550e+07
I(0) uncertainty (real space) i0_real_error2.8580e+05
Rg (reciprocal space) rg_reciprocal20.44 Å
I(0) (reciprocal space) i0_reciprocal22550000.0000
Solution quality estimate total_estimate0.9009
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.9 Å
Skewness Skewness skewness0.193
Kurtosis Kurtosis kurtosis-0.422
Angular range angular_range— – 0.3850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4904000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.985
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1b8va1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.5 — LDH N-terminal domain-like
Domain ID domain_idd1b8va2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.162 — LDH C-terminal domain-like
Superfamily Superfamily superfamilyd.162.1 — LDH C-terminal domain-like
Family Family familyd.162.1.1 — Lactate & malate dehydrogenases, C-terminal domain

CATH v4.4 (2 domains)

Domain ID domain_id1b8vA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id1b8vA02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal
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8. Citations (1)

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9. Files and Curves (10)