SAXSdb — 1af2

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

CYTIDINE DEAMINASE

Escherichia coli

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 1–294	Not recorded	ZN ZINC ION × 2 U5P URIDINE-5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.2；pH 6.2	Resolution 2.30 Å

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 1AF2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ALN CRYSTAL STRUCTURE OF CYTIDINE DEAMINASE COMPLEXED WITH 3-DEAZACYTIDINE Deposited 1997-06-02	Different ligand/ion	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–294（294 aa）	Not recorded	ZN ZINC ION × 2 CTD 3-DEAZACYTIDINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；pH 6.2	Resolution 2.30 Å
1CTT TRANSITION-STATE SELECTIVITY FOR A SINGLE OH GROUP DURING CATALYSIS BY CYTIDINE DEAMINASE Deposited 1995-02-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–294（294 aa）	Not recorded	ZN ZINC ION × 2 DHZ 3,4-DIHYDRO-1H-PYRIMIDIN-2-ONE NUCLEOSIDE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1CTU TRANSITION-STATE SELECTIVITY FOR A SINGLE OH GROUP DURING CATALYSIS BY CYTIDINE DEAMINASE Deposited 1995-02-11	Different ligand/ion Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–294（294 aa）	Not recorded	ZN ZINC ION × 2 ZEB 4-HYDROXY-3,4-DIHYDRO-ZEBULARINE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CDD_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–294； UniProt 1–294

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	1af2
Deposition date deposition_date	1997-03-20
Structure title title	CRYSTAL STRUCTURE OF CYTIDINE DEAMINASE COMPLEXED WITH URIDINE
Keywords keywords	DEAMINASE, PROTON TRANSFER, STRAIN, PRODUCT RELEASE, HYDROLASE; HYDROLASE
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	19.60 Å
Radius of gyration Rg (electron density) rg_electron	18.57 Å
Forward intensity I(0) i0	17840100.00
Molecular weight molecular_weight	31839.0 kDa
Excluded volume excluded_volume	39728 Å³
Envelope volume envelope_volume	44663 Å³
Hydration-shell volume shell_volume	19881 Å³
Envelope diameter envelope_diameter	65.2 Å
Shell Rg shell_rg	25.05 Å
Envelope Rg envelope_rg	18.81 Å
Shape Rg shape_rg	18.58 Å
Total Rg total_rg	19.41 Å
Total atoms total_atoms	2238
Residues n_residues	294
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	19.48 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	1.7840e+07
I(0) uncertainty (real space) i0_real_error	2.0380e+05
Rg (reciprocal space) rg_reciprocal	19.50 Å
I(0) (reciprocal space) i0_reciprocal	17840000.0000
Solution quality estimate total_estimate	0.8044
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.7 Å
Skewness Skewness skewness	0.200
Kurtosis Kurtosis kurtosis	-0.393
Angular range angular_range	— – 0.4050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3988000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.818; Stabil: 1.000; 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 (4)

Entity 1 Entity 1 polymer

Description description	CYTIDINE DEAMINASE
Molecular weight formula_weight	31569.8 kDa
EC 编号 ec_number	3.5.4.5
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	2287

MHPRFQTAFAQLADNLQSALEPILADKYFPALLTGEQVSSLKSATGLDEDALAFALLPLAAACARTPLSNFNVGAIARGVSGTWYFGANMEFIGATMQQTVHAEQSAISHAWLSGEKALAAITVNYTPCGHCRQFMNELNSGLDLRIHLPGREAHALRDYLPDAFGPKDLEIKTLLMDEQDHGYALTGDALSQAAIAAANRSHMPYSKSPSGVALECKDGRIFSGSYAENAAFNPTLPPLQGALILLNLKGYDYPDIQRAVLAEKADAPLIQWDATSATLKALGCHSIDRVLLA

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	URIDINE-5'-MONOPHOSPHATE
Molecular weight formula_weight	324.2 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	49

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1af2a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.97 — Cytidine deaminase-like
Superfamily Superfamily superfamily	c.97.1 — Cytidine deaminase-like
Family Family family	c.97.1.1 — Cytidine deaminase

Domain ID domain_id	d1af2a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.97 — Cytidine deaminase-like
Superfamily Superfamily superfamily	c.97.1 — Cytidine deaminase-like
Family Family family	c.97.1.1 — Cytidine deaminase

CATH v4.4 (2 domains)

Domain ID domain_id	1af2A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

Domain ID domain_id	1af2A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

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8. Citations (1)

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Unit-cell length a length_a	120.300 Å
Unit-cell length b length_b	120.300 Å
Unit-cell length c length_c	78.400 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	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	7.000 Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/af/1af2/1af2.fit
pddf	/app/data/pr_computation/af/1af2/1af2.pr.out
profile	/app/data/saxs_computation/af/1af2/1af2.dat

CRYSTAL STRUCTURE OF CYTIDINE DEAMINASE COMPLEXED WITH URIDINE

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

CYTIDINE DEAMINASE

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