SAXSdb — 1b7b

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

CARBAMATE KINASE

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 1–310 Chain C； UniProt 1–310	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.4；PEG 4000, (NH4)2SO4, SODIUM CACODYLATE, pH 6.4	Resolution 2.80 Å R-free 0.283
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–310 Chain D； UniProt 1–310	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.4；PEG 4000, (NH4)2SO4, SODIUM CACODYLATE, pH 6.4	Resolution 2.80 Å R-free 0.283

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	ARCC1_ENTFC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–310； UniProt 1–310 Author chain B； PDBConstruct 1–310； UniProt 1–310 Author chain C； PDBConstruct 1–310； UniProt 1–310 Author chain D； PDBConstruct 1–310； UniProt 1–310

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	1b7b
Deposition date deposition_date	1999-01-20
Structure title title	Carbamate kinase from Enterococcus faecalis
Keywords keywords	PHOSPHOTRANSFERASE, ARGININE CATABOLISM, ATP SYNTHESYS, ACYLPHOSPHATE-MAKING ENZYMES, OPEN ALPHA/BETA SHEET, TRANSFERASE; TRANSFERASE
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	36.88 Å
Radius of gyration Rg (electron density) rg_electron	36.33 Å
Forward intensity I(0) i0	258395000.00
Molecular weight molecular_weight	130540.0 kDa
Excluded volume excluded_volume	163860 Å³
Envelope volume envelope_volume	216390 Å³
Hydration-shell volume shell_volume	48842 Å³
Envelope diameter envelope_diameter	131.7 Å
Shell Rg shell_rg	43.05 Å
Envelope Rg envelope_rg	36.02 Å
Shape Rg shape_rg	36.35 Å
Total Rg total_rg	36.72 Å
Total atoms total_atoms	9444
Residues n_residues	1228
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	120.7 Å
Rg (real space) rg_real	36.85 Å
Rg uncertainty (real space) rg_real_error	1.06 Å
I(0) (real space) i0_real	2.5840e+08
I(0) uncertainty (real space) i0_real_error	4.9100e+06
Rg (reciprocal space) rg_reciprocal	36.87 Å
I(0) (reciprocal space) i0_reciprocal	258400000.0000
Solution quality estimate total_estimate	0.8926
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	36.5 Å
Skewness Skewness skewness	0.254
Kurtosis Kurtosis kurtosis	-0.569
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	129500000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.925

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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	CARBAMATE KINASE
Molecular weight formula_weight	32958.6 kDa
EC 编号 ec_number	2.7.2.2
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9512

MGKKMVVALGGNAILSNDASAHAQQQALVQTSAYLVHLIKQGHRLIVSHGNGPQVGNLLLQQQAADSEKNPAMPLDTCVAMTQGSIGYWLSNALNQELNKAGIKKQVATVLTQVVVDPADEAFKNPTKPIGPFLTEAEAKEAMQAGAIFKEDAGRGWRKVVPSPKPIDIHEAETINTLIKNDIITISCGGGGIPVVGQELKGVEAVIDKDFASEKLAELVDADALVILTGVDYVCINYGKPDEKQLTNVTVAELEEYKQAGHFAPGSMLPKIEAAIQFVESQPNKQAIITSLENLGSMSGDEIVGTVVTK

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	68

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1b7ba_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.73 — Carbamate kinase-like
Superfamily Superfamily superfamily	c.73.1 — Carbamate kinase-like
Family Family family	c.73.1.1 — Carbamate kinase

Domain ID domain_id	d1b7bb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.73 — Carbamate kinase-like
Superfamily Superfamily superfamily	c.73.1 — Carbamate kinase-like
Family Family family	c.73.1.1 — Carbamate kinase

Domain ID domain_id	d1b7bc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.73 — Carbamate kinase-like
Superfamily Superfamily superfamily	c.73.1 — Carbamate kinase-like
Family Family family	c.73.1.1 — Carbamate kinase

Domain ID domain_id	d1b7bd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.73 — Carbamate kinase-like
Superfamily Superfamily superfamily	c.73.1 — Carbamate kinase-like
Family Family family	c.73.1.1 — Carbamate kinase

CATH v4.4 (4 domains)

Domain ID domain_id	1b7bA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

Domain ID domain_id	1b7bB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

Domain ID domain_id	1b7bC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

Domain ID domain_id	1b7bD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

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8. Citations (1)

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Unit-cell length a length_a	80.860 Å
Unit-cell length b length_b	172.920 Å
Unit-cell length c length_c	98.790 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	16

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	—
R_work r_work	0.2240
R_free r_free	0.2830

fit	/app/data/saxs_computation/b7/1b7b/1b7b.fit
pddf	/app/data/pr_computation/b7/1b7b/1b7b.pr.out
profile	/app/data/saxs_computation/b7/1b7b/1b7b.dat

Carbamate kinase from Enterococcus faecalis

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

CARBAMATE KINASE

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