SAXSdb — 1fvo

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

ORNITHINE TRANSCARBAMYLASE

Homo sapiens

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 34–354	Not recorded	CP PHOSPHORIC ACID MONO(FORMAMIDE)ESTER × 3	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 6.5；291 K；Mes, PEG 8000, pH 6.5, EVAPORATION, temperature 291.0K	Resolution 2.60 Å R-free 0.236
2	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 34–354	Not recorded	CP PHOSPHORIC ACID MONO(FORMAMIDE)ESTER × 3	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 6.5；291 K；Mes, PEG 8000, pH 6.5, EVAPORATION, temperature 291.0K	Resolution 2.60 Å R-free 0.236

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 1FVO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C9Y HUMAN ORNITHINE TRANSCARBAMYLASE: CRYSTALLOGRAPHIC INSIGHTS INTO SUBSTRATE RECOGNITION AND CATALYTIC MECHANISM Deposited 1999-08-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 34–354（321 aa）	Not recorded	NVA NORVALINE × 3 CP PHOSPHORIC ACID MONO(FORMAMIDE)ESTER × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；PEG 400, AMMONIUM SULFATE, POTASSIUM CHLORIDE, EDTA, TRIS ACETATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.90 Å R-free 0.208
1EP9 HUMAN ORNITHINE TRANSCARBAMYLASE: CRYSTALLOGRAPHIC INSIGHTS INTO SUBSTRATE RECOGNITION AND CONFORMATIONAL CHANGE Deposited 2000-03-28	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 34–354（321 aa）	Not recorded	CP PHOSPHORIC ACID MONO(FORMAMIDE)ESTER × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；20 MM TRISAC, 2MM EDTA, 20MM KCL, 4MM PALO, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.40 Å R-free 0.223
1FB5 LOW RESOLUTION STRUCTURE OF OVINE ORNITHINE TRANSCARBMOYLASE IN THE UNLIGANDED STATE Deposited 2000-07-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 35–354（320 aa）	Not recorded	NVA NORVALINE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；8% PEG 4000, 0.1 M Na acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298.K	Resolution 3.50 Å R-free 0.252
1OTH CRYSTAL STRUCTURE OF HUMAN ORNITHINE TRANSCARBAMOYLASE COMPLEXED WITH N-PHOSPHONACETYL-L-ORNITHINE Deposited 1998-10-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 34–354（321 aa）	Not recorded	PAO N-(PHOSPHONOACETYL)-L-ORNITHINE × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；20 MM TRISAC, 2MM EDTA, 20MM KCL, 4MM PALO PH=7.4, pH 7.5	Resolution 1.85 Å R-free 0.201

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	OTC_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–321； UniProt 34–354 Author chain B； PDBConstruct 1–321； UniProt 34–354

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	1fvo
Deposition date deposition_date	2000-09-20
Structure title title	CRYSTAL STRUCTURE OF HUMAN ORNITHINE TRANSCARBAMYLASE COMPLEXED WITH CARBAMOYL PHOSPHATE
Keywords keywords	Two domains, alpha/beta topology, 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	30.73 Å
Radius of gyration Rg (electron density) rg_electron	30.18 Å
Forward intensity I(0) i0	80512000.00
Molecular weight molecular_weight	72405.0 kDa
Excluded volume excluded_volume	91420 Å³
Envelope volume envelope_volume	113040 Å³
Hydration-shell volume shell_volume	32067 Å³
Envelope diameter envelope_diameter	107.2 Å
Shell Rg shell_rg	36.37 Å
Envelope Rg envelope_rg	30.06 Å
Shape Rg shape_rg	30.18 Å
Total Rg total_rg	30.76 Å
Total atoms total_atoms	5090
Residues n_residues	642
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	100.6 Å
Rg (real space) rg_real	30.83 Å
Rg uncertainty (real space) rg_real_error	0.97 Å
I(0) (real space) i0_real	8.0510e+07
I(0) uncertainty (real space) i0_real_error	1.4300e+06
Rg (reciprocal space) rg_reciprocal	30.80 Å
I(0) (reciprocal space) i0_reciprocal	80510000.0000
Solution quality estimate total_estimate	0.8043
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.1 Å
Skewness Skewness skewness	0.365
Kurtosis Kurtosis kurtosis	-0.562
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	46320000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.853; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.893; 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)

Entity 1 Entity 1 polymer

Description description	ORNITHINE TRANSCARBAMYLASE
Molecular weight formula_weight	36106.6 kDa
EC 编号 ec_number	2.1.3.3
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	5133

KVQLKGRDLLTLKNFTGEEIKYMLWLSADLKFRIKQKGEYLPLLQGKSLGMIFEKRSTRTRLSTETGFALLGGHPCFLTTQDIHLGVNESLTDTARVLSSMADAVLARVYKQSDLDTLAKEASIPIINGLSDLYHPIQILADYLTLQEHYSSLKGLTLSWIGDGNNILHSIMMSAAKFGMHLQAATPKGYEPDASVTKLAEQYAKENGTKLLLTNDPLEAAHGGNVLITDTWISMGREEEKKKRLQAFQGYQVTMKTAKVAASDWTFLHCLPRKPEEVDDEVFYSPRSLVFPEAENRKWTIMAVMVSLLTDYSPQLQKPKF

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHORIC ACID MONO(FORMAMIDE)ESTER
Molecular weight formula_weight	141.0 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	43

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1fvoa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.78 — ATC-like
Superfamily Superfamily superfamily	c.78.1 — Aspartate/ornithine carbamoyltransferase
Family Family family	c.78.1.1 — Aspartate/ornithine carbamoyltransferase

Domain ID domain_id	d1fvoa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.78 — ATC-like
Superfamily Superfamily superfamily	c.78.1 — Aspartate/ornithine carbamoyltransferase
Family Family family	c.78.1.1 — Aspartate/ornithine carbamoyltransferase

Domain ID domain_id	d1fvob1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.78 — ATC-like
Superfamily Superfamily superfamily	c.78.1 — Aspartate/ornithine carbamoyltransferase
Family Family family	c.78.1.1 — Aspartate/ornithine carbamoyltransferase

Domain ID domain_id	d1fvob2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.78 — ATC-like
Superfamily Superfamily superfamily	c.78.1 — Aspartate/ornithine carbamoyltransferase
Family Family family	c.78.1.1 — Aspartate/ornithine carbamoyltransferase

CATH v4.4 (4 domains)

Domain ID domain_id	1fvoA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1370 — Aspartate/ornithine carbamoyltransferase

Domain ID domain_id	1fvoA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1370 — Aspartate/ornithine carbamoyltransferase

Domain ID domain_id	1fvoB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1370 — Aspartate/ornithine carbamoyltransferase

Domain ID domain_id	1fvoB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1370 — Aspartate/ornithine carbamoyltransferase

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8. Citations (2)

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Unit-cell length a length_a	203.426 Å
Unit-cell length b length_b	203.426 Å
Unit-cell length c length_c	203.426 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	48

Space group space_group	I 2 3
Space-group number int_tables_number	197
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	29.990 Å
R factor r_factor	0.2020
R_work r_work	0.2020
R_free r_free	0.2360

fit	/app/data/saxs_computation/fv/1fvo/1fvo.fit
pddf	/app/data/pr_computation/fv/1fvo/1fvo.pr.out
profile	/app/data/saxs_computation/fv/1fvo/1fvo.dat

CRYSTAL STRUCTURE OF HUMAN ORNITHINE TRANSCARBAMYLASE COMPLEXED WITH CARBAMOYL PHOSPHATE

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

ORNITHINE TRANSCARBAMYLASE

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