SAXSdb — 1cku

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

PROTEIN (HIPIP)

Allochromatium vinosum

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 38–122 Chain B； UniProt 38–122	Not recorded	SF4 IRON/SULFUR CLUSTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.3；1.3 M AMMONIUM SULPHATE, 40 MM TRIS 180 MM KCL, pH 5.3	Resolution 1.20 Å R-free 0.178

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 1CKU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B0Y MUTANT H42Q OF HIPIP FROM CHROMATIUM VINOSUM AT 0.93A Deposited 1998-11-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 38–122（85 aa）	Mutation：H42Q	SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.3；2M AMMONIUM SULPHATE, 40 MM TRI 180 MM KCL, pH 5.3	Resolution 0.93 Å R-free 0.205
1HIP TWO-ANGSTROM CRYSTAL STRUCTURE OF OXIDIZED CHROMATIUM HIGH POTENTIAL IRON PROTEIN Deposited 1975-04-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–86（85 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1HRQ THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE REDUCED HIGH-POTENTIAL IRON-SULFUR PROTEIN FROM CHROMATIUM VINOSUM THROUGH NMR Deposited 1995-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 38–122（85 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1HRR THE THREE DIMENSIONAL STRUCTURE OF THE REDUCED HIGH POTENTIAL IRON-SULFUR PROTEIN FROM CHROMATIUM VINOSUM THROUGH NMR Deposited 1995-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 38–122（85 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1JS2 Crystal structure of C77S HiPIP: a serine ligated [4Fe-4S] cluster Deposited 2001-08-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 38–122（85 aa） Fragment：residues 38-122 of P00260 Chain B 38–122（85 aa） Fragment：residues 38-122 of P00260 Chain C 38–122（85 aa） Fragment：residues 38-122 of P00260 Chain D 38–122（85 aa） Fragment：residues 38-122 of P00260	Mutation：C77S Mutation：C77S Mutation：C77S Mutation：C77S	SF4 IRON/SULFUR CLUSTER × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION, HANGING DROP at pH 8.0, 293K	Resolution 1.90 Å R-free 0.234
1NEH HIGH POTENTIAL IRON-SULFUR PROTEIN Deposited 1995-12-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 38–122（85 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1NOE NMR STUDY OF REDUCED HIGH POTENTIAL IRON SULFUR PROTEIN Deposited 1996-01-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 37–122（86 aa）	Mutation：C77S	SF4 IRON/SULFUR CLUSTER × 1	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HIP_CHRVI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–85； UniProt 38–122 Author chain B； PDBConstruct 1–85； UniProt 38–122

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	1cku
Deposition date deposition_date	1999-04-24
Structure title title	AB INITIO SOLUTION AND REFINEMENT OF TWO HIGH POTENTIAL IRON PROTEIN STRUCTURES AT ATOMIC RESOLUTION
Keywords keywords	ELECTRON TRANSFER PROTEIN, ATOMIC RESOLUTION, DIRECT METHODS, IRON-SULPHUR CLUSTER, METALLOPROTEIN; ELECTRON TRANSFER PROTEIN
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	16.48 Å
Radius of gyration Rg (electron density) rg_electron	15.77 Å
Forward intensity I(0) i0	7754080.00
Molecular weight molecular_weight	18509.0 kDa
Excluded volume excluded_volume	22261 Å³
Envelope volume envelope_volume	25709 Å³
Hydration-shell volume shell_volume	13838 Å³
Envelope diameter envelope_diameter	57.4 Å
Shell Rg shell_rg	21.42 Å
Envelope Rg envelope_rg	16.20 Å
Shape Rg shape_rg	15.91 Å
Total Rg total_rg	16.35 Å
Total atoms total_atoms	1264
Residues n_residues	170
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	55.2 Å
Rg (real space) rg_real	16.45 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	7.7540e+06
I(0) uncertainty (real space) i0_real_error	9.5040e+04
Rg (reciprocal space) rg_reciprocal	16.45 Å
I(0) (reciprocal space) i0_reciprocal	7754000.0000
Solution quality estimate total_estimate	0.8012
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	4
Primary peak position r_peak_primary	17.0 Å
Skewness Skewness skewness	0.270
Kurtosis Kurtosis kurtosis	-0.396
Angular range angular_range	— – 0.4850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2823000.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.812; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; 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	PROTEIN (HIPIP)
Molecular weight formula_weight	8912.9 kDa
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	1599

SAPANAVAADDATAIALKYNQDATKSERVAAARPGLPPEEQHCANCQFMQADAAGATDEWKGCQLFPGKLINVNGWCASWTLKAG

来源 Source

来源生物 organism	Allochromatium vinosum
NCBI Class编号 ncbi_taxonomy_id	1049
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 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	334

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ckua_
Class class	g — Small proteins
Fold Fold fold	g.35 — HIPIP (high potential iron protein)
Superfamily Superfamily superfamily	g.35.1 — HIPIP (high potential iron protein)
Family Family family	g.35.1.1 — HIPIP (high potential iron protein)

Domain ID domain_id	d1ckub_
Class class	g — Small proteins
Fold Fold fold	g.35 — HIPIP (high potential iron protein)
Superfamily Superfamily superfamily	g.35.1 — HIPIP (high potential iron protein)
Family Family family	g.35.1.1 — HIPIP (high potential iron protein)

CATH v4.4 (2 domains)

Domain ID domain_id	1ckuA00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	490 — High-Potential Iron-Sulfur Protein; Chain A
Homologous superfamily homologous superfamily	10 — High potential iron-sulphur protein

Domain ID domain_id	1ckuB00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	490 — High-Potential Iron-Sulfur Protein; Chain A
Homologous superfamily homologous superfamily	10 — High potential iron-sulphur protein

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8. Citations (2)

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Unit-cell length a length_a	35.067 Å
Unit-cell length b length_b	51.389 Å
Unit-cell length c length_c	92.390 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	8

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

Resolution resolution	1.200 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1315
R_work r_work	—
R_free r_free	0.1780

fit	/app/data/saxs_computation/ck/1cku/1cku.fit
pddf	/app/data/pr_computation/ck/1cku/1cku.pr.out
profile	/app/data/saxs_computation/ck/1cku/1cku.dat

AB INITIO SOLUTION AND REFINEMENT OF TWO HIGH POTENTIAL IRON PROTEIN STRUCTURES AT ATOMIC RESOLUTION

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

PROTEIN (HIPIP)

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