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1vpe

CRYSTALLOGRAPHIC ANALYSIS OF PHOSPHOGLYCERATE KINASE FROM THE HYPERTHERMOPHILIC BACTERIUM THERMOTOGA MARITIMA

Method: X-RAY DIFFRACTION Dmax: 75.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PHOSPHOGLYCERATE KINASE

Thermotoga maritima

UniProt P36204

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 2–398 Not recorded MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 3PG 3-PHOSPHOGLYCERIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions：PEG 3000/8000 Resolution 2.00 Å R-free 0.288

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 1VPE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B9B TRIOSEPHOSPHATE ISOMERASE OF THERMOTOGA MARITIMA Deposited 1999-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–255（255 aa）
Chain B 1–255（255 aa）
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.0
Resolution 2.85 Å R-free 0.249
1B9B TRIOSEPHOSPHATE ISOMERASE OF THERMOTOGA MARITIMA Deposited 1999-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–255（255 aa）
Chain B 1–255（255 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.0
Resolution 2.85 Å R-free 0.249

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

View Construct and Data Evidence
UniProt name PGKT_THEMA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–397； UniProt 2–398

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 1vpe

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1vpe
Deposition date deposition_date1997-05-06
Structure title titleCRYSTALLOGRAPHIC ANALYSIS OF PHOSPHOGLYCERATE KINASE FROM THE HYPERTHERMOPHILIC BACTERIUM THERMOTOGA MARITIMA
Keywords keywordsTRANSFERASE, PHOSPHOGLYCERATE KINASE, THERMOTOGA MARITIMA, HYPERTHERMOSTABILITY, CRYSTAL, AMP-PNP, 3-PGA; TRANSFERASE
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_guinier22.95 Å
Radius of gyration Rg (electron density) rg_electron22.31 Å
Forward intensity I(0) i030630900.00
Molecular weight molecular_weight43697.0 kDa
Excluded volume excluded_volume55314 ų
Envelope volume envelope_volume64223 ų
Hydration-shell volume shell_volume24026 ų
Envelope diameter envelope_diameter75.4 Å
Shell Rg shell_rg29.16 Å
Envelope Rg envelope_rg22.47 Å
Shape Rg shape_rg22.31 Å
Total Rg total_rg23.14 Å
Total atoms total_atoms3069
Residues n_residues398
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 dmax75.1 Å
Rg (real space) rg_real22.94 Å
Rg uncertainty (real space) rg_real_error0.49 Å
I(0) (real space) i0_real3.0630e+07
I(0) uncertainty (real space) i0_real_error4.4650e+05
Rg (reciprocal space) rg_reciprocal22.94 Å
I(0) (reciprocal space) i0_reciprocal30630000.0000
Solution quality estimate total_estimate0.8884
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.4 Å
Skewness Skewness skewness0.369
Kurtosis Kurtosis kurtosis-0.325
Angular range angular_range— – 0.3450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7332000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.854; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.988
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1vpea_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.86 — Phosphoglycerate kinase
Superfamily Superfamily superfamilyc.86.1 — Phosphoglycerate kinase
Family Family familyc.86.1.1 — Phosphoglycerate kinase

CATH v4.4 (2 domains)

Domain ID domain_id1vpeA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1260 — Phosphoglycerate kinase, N-terminal domain
Domain ID domain_id1vpeA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1260 — Phosphoglycerate kinase, N-terminal domain
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8. Citations (2)

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9. Files and Curves (10)