SAXSdb — 1b74

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

GLUTAMATE RACEMASE

OrganismNot specified

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 1–254	Not recorded	DGN D-GLUTAMINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 2.30 Å R-free 0.286

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 1B74	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B73 GLUTAMATE RACEMASE FROM AQUIFEX PYROPHILUS Deposited 1999-01-26	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–254（254 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.30 Å R-free 0.284

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

View Construct and Data Evidence

UniProt name	MURI_AQUPY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–254； UniProt 1–254

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	1b74
Deposition date deposition_date	1999-01-27
Structure title title	GLUTAMATE RACEMASE FROM AQUIFEX PYROPHILUS
Keywords keywords	RACEMASE, ISOMERASE; ISOMERASE
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	19.66 Å
Radius of gyration Rg (electron density) rg_electron	18.53 Å
Forward intensity I(0) i0	12092500.00
Molecular weight molecular_weight	27834.0 kDa
Excluded volume excluded_volume	35700 Å³
Envelope volume envelope_volume	41165 Å³
Hydration-shell volume shell_volume	18577 Å³
Envelope diameter envelope_diameter	61.7 Å
Shell Rg shell_rg	24.73 Å
Envelope Rg envelope_rg	18.61 Å
Shape Rg shape_rg	18.53 Å
Total Rg total_rg	19.47 Å
Total atoms total_atoms	1962
Residues n_residues	252
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	61.3 Å
Rg (real space) rg_real	19.54 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	1.2090e+07
I(0) uncertainty (real space) i0_real_error	1.5470e+05
Rg (reciprocal space) rg_reciprocal	19.56 Å
I(0) (reciprocal space) i0_reciprocal	12090000.0000
Solution quality estimate total_estimate	0.8266
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	25.0 Å
Skewness Skewness skewness	0.140
Kurtosis Kurtosis kurtosis	-0.496
Angular range angular_range	— – 0.4050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2319000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.918; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; 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)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1b74a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.78 — ATC-like
Superfamily Superfamily superfamily	c.78.2 — Aspartate/glutamate racemase
Family Family family	c.78.2.1 — Aspartate/glutamate racemase

Domain ID domain_id	d1b74a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.78 — ATC-like
Superfamily Superfamily superfamily	c.78.2 — Aspartate/glutamate racemase
Family Family family	c.78.2.1 — Aspartate/glutamate racemase

CATH v4.4 (2 domains)

Domain ID domain_id	1b74A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1860 —

Domain ID domain_id	1b74A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1860 —

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8. Citations (1)

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Unit-cell length a length_a	72.170 Å
Unit-cell length b length_b	72.170 Å
Unit-cell length c length_c	184.990 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.2210
R_free r_free	0.2860

Description description	GLUTAMATE RACEMASE
Molecular weight formula_weight	27978.7 kDa
EC 编号 ec_number	5.1.1.3
Source method src_method	nat
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2066

GLUTAMATE RACEMASE FROM AQUIFEX PYROPHILUS

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

GLUTAMATE RACEMASE

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	D-GLUTAMINE
Molecular weight formula_weight	146.1 kDa
Source method src_method	syn
Copy count entity_count	1

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	104

fit	/app/data/saxs_computation/b7/1b74/1b74.fit
pddf	/app/data/pr_computation/b7/1b74/1b74.pr.out
profile	/app/data/saxs_computation/b7/1b74/1b74.dat