SAXSdb — 1c9y

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

ORNITHINE CARBAMOYLTRANSFERASE

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	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

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 1C9Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EP9 HUMAN ORNITHINE TRANSCARBAMYLASE: CRYSTALLOGRAPHIC INSIGHTS INTO SUBSTRATE RECOGNITION AND CONFORMATIONAL CHANGE Deposited 2000-03-28	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	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
1FVO CRYSTAL STRUCTURE OF HUMAN ORNITHINE TRANSCARBAMYLASE COMPLEXED WITH CARBAMOYL PHOSPHATE Deposited 2000-09-20	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	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
1FVO CRYSTAL STRUCTURE OF HUMAN ORNITHINE TRANSCARBAMYLASE COMPLEXED WITH CARBAMOYL PHOSPHATE Deposited 2000-09-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain B 34–354（321 aa）	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
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 5 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

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	1c9y
Deposition date deposition_date	1999-08-03
Structure title title	HUMAN ORNITHINE TRANSCARBAMYLASE: CRYSTALLOGRAPHIC INSIGHTS INTO SUBSTRATE RECOGNITION AND CATALYTIC MECHANISM
Keywords keywords	ORNITHINE TRANSCARBAMYLASE, SUBSTRATE RECOGNITION, CATALYTIC MECHANISM, 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	20.34 Å
Radius of gyration Rg (electron density) rg_electron	19.21 Å
Forward intensity I(0) i0	21624100.00
Molecular weight molecular_weight	36261.0 kDa
Excluded volume excluded_volume	45772 Å³
Envelope volume envelope_volume	51206 Å³
Hydration-shell volume shell_volume	21761 Å³
Envelope diameter envelope_diameter	65.8 Å
Shell Rg shell_rg	26.17 Å
Envelope Rg envelope_rg	19.62 Å
Shape Rg shape_rg	19.21 Å
Total Rg total_rg	20.15 Å
Total atoms total_atoms	2549
Residues n_residues	321
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	65.0 Å
Rg (real space) rg_real	20.23 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	2.1620e+07
I(0) uncertainty (real space) i0_real_error	2.3230e+05
Rg (reciprocal space) rg_reciprocal	20.25 Å
I(0) (reciprocal space) i0_reciprocal	21620000.0000
Solution quality estimate total_estimate	0.8935
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.1 Å
Skewness Skewness skewness	0.198
Kurtosis Kurtosis kurtosis	-0.437
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5539000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	ORNITHINE CARBAMOYLTRANSFERASE
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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2772

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	NORVALINE
Molecular weight formula_weight	117.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 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	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	223

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1c9ya1
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	d1c9ya2
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 (2 domains)

Domain ID domain_id	1c9yA01
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	1c9yA02
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 (1)

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Unit-cell length a length_a	125.410 Å
Unit-cell length b length_b	125.410 Å
Unit-cell length c length_c	125.410 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	12

Space group space_group	P 21 3
Space-group number int_tables_number	198
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1870
R_work r_work	0.1870
R_free r_free	0.2080

fit	/app/data/saxs_computation/c9/1c9y/1c9y.fit
pddf	/app/data/pr_computation/c9/1c9y/1c9y.pr.out
profile	/app/data/saxs_computation/c9/1c9y/1c9y.dat

HUMAN ORNITHINE TRANSCARBAMYLASE: CRYSTALLOGRAPHIC INSIGHTS INTO SUBSTRATE RECOGNITION AND CATALYTIC MECHANISM

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

ORNITHINE CARBAMOYLTRANSFERASE

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