SAXSdb — 1ddz

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

CARBONIC ANHYDRASE

Porphyridium purpureum

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 76–571 Chain B； UniProt 76–571	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.75；293 K；PEG4000, AMMONIUM SULFATE, SODIUM CACODYLATE, pH 6.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.274

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	Q43060_9RHOD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–496； UniProt 76–571 Author chain B； PDBConstruct 1–496； UniProt 76–571

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	1ddz
Deposition date deposition_date	1999-11-12
Structure title title	X-RAY STRUCTURE OF A BETA-CARBONIC ANHYDRASE FROM THE RED ALGA, PORPHYRIDIUM PURPUREUM R-1
Keywords keywords	ALPHA-BETA-ALPHA, LYASE; LYASE
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	28.52 Å
Radius of gyration Rg (electron density) rg_electron	27.48 Å
Forward intensity I(0) i0	191278000.00
Molecular weight molecular_weight	106800.0 kDa
Excluded volume excluded_volume	132470 Å³
Envelope volume envelope_volume	154540 Å³
Hydration-shell volume shell_volume	44156 Å³
Envelope diameter envelope_diameter	98.5 Å
Shell Rg shell_rg	36.90 Å
Envelope Rg envelope_rg	27.80 Å
Shape Rg shape_rg	27.48 Å
Total Rg total_rg	28.28 Å
Total atoms total_atoms	7488
Residues n_residues	962
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	92.7 Å
Rg (real space) rg_real	28.39 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	1.9130e+08
I(0) uncertainty (real space) i0_real_error	2.7070e+06
Rg (reciprocal space) rg_reciprocal	28.45 Å
I(0) (reciprocal space) i0_reciprocal	191300000.0000
Solution quality estimate total_estimate	0.8815
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	36.4 Å
Skewness Skewness skewness	0.212
Kurtosis Kurtosis kurtosis	-0.349
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	74000000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.960

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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	CARBONIC ANHYDRASE
Molecular weight formula_weight	54993.5 kDa
EC 编号 ec_number	4.2.1.1
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	8100

VKLAAGMGVMSDLEKKFIELEAKLVAQPAGQAMPGKSNIFANNEAWRQEMLKQDPEFFNRLANGQSPEYLWIGCADSRVPANQLLDLPAGEVFVHRNIANQCIHSDISFLSVLQYAVQYLKVKHILVCGHYGCGGAKAALGDSRLGLIDNWLRHIRDVRRMNAKYLDKCKDGDEELNRLIELNVLEQVHNVCATSIVQDAWDAGQELTVQGVVYGVGDGKLRDLGVVVNSSDDISKFYRTKSDSGALKAGNPNAPLVQVTKGGESELDSTMEKLTAELVQQTPGKLKEGANRVFVNNENWRQKMLKQDPQFFSNLAHTQTPEILWIGCADSRVPANQIINLPAGEVFVHRNIANQCIHSDMSFLSVLQYAVQYLKVKRVVVCGHYACGGCAAALGDSRLGLIDNWLRHIRDVRRHNQAELSRITDPKDSLNRLIEINVLEQMHNVCATSIVQDAWDAGQELEVQGVVYGVGDGKLRDMGVVAKANDDIGQIFRTKQ

来源 Source

来源生物 organism	Porphyridium purpureum
NCBI Class编号 ncbi_taxonomy_id	35688
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	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	612

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1ddza1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.53 — Resolvase-like
Superfamily Superfamily superfamily	c.53.2 — beta-carbonic anhydrase, cab
Family Family family	c.53.2.1 — beta-carbonic anhydrase, cab

Domain ID domain_id	d1ddza2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.53 — Resolvase-like
Superfamily Superfamily superfamily	c.53.2 — beta-carbonic anhydrase, cab
Family Family family	c.53.2.1 — beta-carbonic anhydrase, cab

Domain ID domain_id	d1ddzb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.53 — Resolvase-like
Superfamily Superfamily superfamily	c.53.2 — beta-carbonic anhydrase, cab
Family Family family	c.53.2.1 — beta-carbonic anhydrase, cab

Domain ID domain_id	d1ddzb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.53 — Resolvase-like
Superfamily Superfamily superfamily	c.53.2 — beta-carbonic anhydrase, cab
Family Family family	c.53.2.1 — beta-carbonic anhydrase, cab

CATH v4.4 (4 domains)

Domain ID domain_id	1ddzA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1050 — Beta-carbonic Anhydrase; Chain A
Homologous superfamily homologous superfamily	10 — Carbonic anhydrase

Domain ID domain_id	1ddzA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1050 — Beta-carbonic Anhydrase; Chain A
Homologous superfamily homologous superfamily	10 — Carbonic anhydrase

Domain ID domain_id	1ddzB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1050 — Beta-carbonic Anhydrase; Chain A
Homologous superfamily homologous superfamily	10 — Carbonic anhydrase

Domain ID domain_id	1ddzB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1050 — Beta-carbonic Anhydrase; Chain A
Homologous superfamily homologous superfamily	10 — Carbonic anhydrase

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8. Citations (1)

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Unit-cell length a length_a	63.500 Å
Unit-cell length b length_b	112.800 Å
Unit-cell length c length_c	73.200 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.60 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2080
R_work r_work	0.2080
R_free r_free	0.2740

fit	/app/data/saxs_computation/dd/1ddz/1ddz.fit
pddf	/app/data/pr_computation/dd/1ddz/1ddz.pr.out
profile	/app/data/saxs_computation/dd/1ddz/1ddz.dat

X-RAY STRUCTURE OF A BETA-CARBONIC ANHYDRASE FROM THE RED ALGA, PORPHYRIDIUM PURPUREUM R-1

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

CARBONIC ANHYDRASE

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