SAXSdb — 1nkd

▼

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

ROP

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 1–63	Mutation：INS(A-D31-A)	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.09 Å R-free 0.134

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 1NKD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B6Q ALANINE 31 PROLINE MUTANT OF ROP PROTEIN Deposited 1999-01-16	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–63（63 aa）	Mutation：A31P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.3；pH 4.3	Resolution 1.80 Å R-free 0.240
1F4M P3(2) CRYSTAL STRUCTURE OF ALA2ILE2-6, A VERSION OF ROP WITH A REPACKED HYDROPHOBIC CORE AND A NEW FOLD. Deposited 2000-06-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–63（63 aa） Chain B 1–63（63 aa）	Mutation：M1G,A8I,T19A,L22I,L26A,Q34I,C38A,L41I,L48I,C52A Mutation：M1G,A8I,T19A,L22I,L26A,Q34I,C38A,L41I,L48I,C52A	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；MPD, calcium chloride, sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.25 Å R-free 0.282
1F4M P3(2) CRYSTAL STRUCTURE OF ALA2ILE2-6, A VERSION OF ROP WITH A REPACKED HYDROPHOBIC CORE AND A NEW FOLD. Deposited 2000-06-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–63（63 aa） Chain D 1–63（63 aa）	Mutation：M1G,A8I,T19A,L22I,L26A,Q34I,C38A,L41I,L48I,C52A Mutation：M1G,A8I,T19A,L22I,L26A,Q34I,C38A,L41I,L48I,C52A	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；MPD, calcium chloride, sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.25 Å R-free 0.282
1F4M P3(2) CRYSTAL STRUCTURE OF ALA2ILE2-6, A VERSION OF ROP WITH A REPACKED HYDROPHOBIC CORE AND A NEW FOLD. Deposited 2000-06-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–63（63 aa） Chain F 1–63（63 aa）	Mutation：M1G,A8I,T19A,L22I,L26A,Q34I,C38A,L41I,L48I,C52A Mutation：M1G,A8I,T19A,L22I,L26A,Q34I,C38A,L41I,L48I,C52A	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；MPD, calcium chloride, sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.25 Å R-free 0.282
1F4N C2 CRYSTAL STRUCTURE OF ALA2ILE2-6, A VERSION OF ROP WITH A REPACKED HYDROPHOBIC CORE AND A NEW FOLD. Deposited 2000-06-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–63（63 aa） Chain B 1–63（63 aa）	Mutation：M1G,A8I,T19A,L22I,L26A,Q34I,C38A,L41I,L48I,C52A Mutation：M1G,A8I,T19A,L22I,L26A,Q34I,C38A,L41I,L48I,C52A	CA CALCIUM ION × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；MPD, calcium chloride, sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.90 Å R-free 0.237
1F4N C2 CRYSTAL STRUCTURE OF ALA2ILE2-6, A VERSION OF ROP WITH A REPACKED HYDROPHOBIC CORE AND A NEW FOLD. Deposited 2000-06-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–63（63 aa） Chain B 1–63（63 aa）	Mutation：M1G,A8I,T19A,L22I,L26A,Q34I,C38A,L41I,L48I,C52A Mutation：M1G,A8I,T19A,L22I,L26A,Q34I,C38A,L41I,L48I,C52A	CA CALCIUM ION × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；MPD, calcium chloride, sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.90 Å R-free 0.237
1GMG ALANINE 31 PROLINE MUTANT OF ROP PROTEIN, MONOCLINIC FORM Deposited 2001-09-13	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–63（63 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.8；37% (V/V) ETHANOL, 450 MM NACL, 50 MM CITRATE BUFFER PH4.8, 1MM EDTA, USING THE DIALYSIS METHOD., pH 4.80	Resolution 1.90 Å R-free 0.232
1GMG ALANINE 31 PROLINE MUTANT OF ROP PROTEIN, MONOCLINIC FORM Deposited 2001-09-13	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–63（63 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.8；37% (V/V) ETHANOL, 450 MM NACL, 50 MM CITRATE BUFFER PH4.8, 1MM EDTA, USING THE DIALYSIS METHOD., pH 4.80	Resolution 1.90 Å R-free 0.232
1GTO HIGH RESOLUTION STRUCTURE OF A HYPERSTABLE HELICAL BUNDLE PROTEIN MUTANT Deposited 1996-04-23	Different construct Different mutation/modification Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–62（61 aa）	Mutation：M1G, D30G	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.82 Å R-free 0.280
1GTO HIGH RESOLUTION STRUCTURE OF A HYPERSTABLE HELICAL BUNDLE PROTEIN MUTANT Deposited 1996-04-23	Different construct Different mutation/modification Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 2–62（61 aa） Chain C 2–62（61 aa）	Mutation：M1G, D30G Mutation：M1G, D30G	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.82 Å R-free 0.280
1QX8 Crystal structure of a five-residue deletion mutant of the Rop protein Deposited 2003-09-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–63（63 aa） Chain B 1–63（63 aa）	Mutation：Deletion [30D-34Q] Mutation：Deletion [30D-34Q]	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；NaCl, methanol, Bis-Tris, DTT, EDTA, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.02 Å R-free 0.212
1ROP STRUCTURE OF THE COL*E1 ROP PROTEIN AT 1.7 ANGSTROMS RESOLUTION Deposited 1991-04-02	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–63（63 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å
1RPO RESTORED HEPTAD PATTERN CONTINUITY DOES NOT ALTER THE FOLDING OF A 4-ALPHA-HELICAL BUNDLE Deposited 1994-08-25	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–63（63 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.40 Å
1RPR THE STRUCTURE OF COLE1 ROP IN SOLUTION Deposited 1991-10-09	Different construct Different mutation/modification Different experimental method Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–63（63 aa） Chain B 1–63（63 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1YO7 Re-engineering topology of the homodimeric ROP protein into a single-chain 4-helix bundle Deposited 2005-01-26	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 1–56（56 aa） Chain A 32–56（25 aa） Chain A 3–29（27 aa）	Mutation：R55S Mutation：R55S Mutation：R55S	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；293 K；10% PEG 2000, 50mM Tris-HCl pH6.6, 40mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.310
1YO7 Re-engineering topology of the homodimeric ROP protein into a single-chain 4-helix bundle Deposited 2005-01-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–56（56 aa） Chain B 32–56（25 aa） Chain B 3–29（27 aa）	Mutation：R55S Mutation：R55S Mutation：R55S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；293 K；10% PEG 2000, 50mM Tris-HCl pH6.6, 40mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.310
2GHY Novel Crystal Form of the ColE1 Rom Protein Deposited 2006-03-28	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–63（63 aa） Chain B 1–63（63 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；295 K；30% PEG MME 2000, 0.1M sodium acetate, pH4.6, and 0.2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.263
2IJH Crystal structure analysis of ColE1 ROM mutant F14W Deposited 2006-09-29	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–63（63 aa） Chain B 1–63（63 aa）	Mutation：M1G, F14W Mutation：M1G, F14W	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；273 K；Well solution: 20% glycerol, 0.1 M sodium acetate pH 5.5, 0.1 M sodium chloride. Protein solution: protein 5 mg/ml, 0.01 M Tris pH 6.8, 0.05 M sodium chloride. Drops: equal volumes of well and protein solutions., VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 1.80 Å R-free 0.230
2IJH Crystal structure analysis of ColE1 ROM mutant F14W Deposited 2006-09-29	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–63（63 aa）	Mutation：M1G, F14W	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；273 K；Well solution: 20% glycerol, 0.1 M sodium acetate pH 5.5, 0.1 M sodium chloride. Protein solution: protein 5 mg/ml, 0.01 M Tris pH 6.8, 0.05 M sodium chloride. Drops: equal volumes of well and protein solutions., VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 1.80 Å R-free 0.230
2IJI Structure of F14H mutant of ColE1 Rom protein Deposited 2006-09-29	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–63（63 aa）	Mutation：M1G, F14H	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；1uL protein solution (0.5-1 mM) was mixed with 1 uL well buffer (0.1M sodium acetate pH 5.5, 0.1M sodium chloride, 37 40% ethanol, and 20% glycerol), VAPOR DIFFUSION, HANGING DROP	Resolution 2.30 Å R-free 0.292
2IJJ Crystal structure analysis of ColE1 ROM mutant F14Y Deposited 2006-09-29	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–63（63 aa） Chain B 1–63（63 aa）	Mutation：M1G, F14Y Mutation：M1G, F14Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；273 K；Well solution: 22% MPD, 0.1 M sodium acetate pH 5.5, 0.1 M sodium chloride. Protein solution: protein 2.5 mg/ml, 0.01 M Tris pH 6.5, 0.05 M sodium chloride. Drops: equal volumes of well and protein solutions., VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 1.90 Å R-free 0.263
2IJJ Crystal structure analysis of ColE1 ROM mutant F14Y Deposited 2006-09-29	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–63（63 aa）	Mutation：M1G, F14Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；273 K；Well solution: 22% MPD, 0.1 M sodium acetate pH 5.5, 0.1 M sodium chloride. Protein solution: protein 2.5 mg/ml, 0.01 M Tris pH 6.5, 0.05 M sodium chloride. Drops: equal volumes of well and protein solutions., VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 1.90 Å R-free 0.263
2IJK Structure of a Rom protein dimer at 1.55 angstrom resolution Deposited 2006-09-29	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–63（63 aa） Chain B 1–63（63 aa）	Mutation：M1G Mutation：M1G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；Hanging drop contained 1 uL protein/RNA mixture (0.3 0.4 mM complex) and 1 uL well buffer (50 mM sodium cacodylate pH 6.0, 0.1 M potassium chloride, 25 mM magnesium chloride, and 15% isopropanol)., VAPOR DIFFUSION, HANGING DROP	Resolution 1.55 Å R-free 0.216
3K79 C38A, C52V Cysteine-Free Variant of Rop (Rom) Deposited 2009-10-12	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–63（62 aa）	Mutation：C38A, C52V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；25-30% methanol, 100 mM MES, 300 mM NaCl, 10% glycerol, pH 5.7-5.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.96 Å R-free 0.250
4DO2 Crystal Structure of the Rop protein mutant D30P/A31G at resolution 1.4 resolution. Deposited 2012-02-09	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–63（63 aa） Chain B 1–63（63 aa）	Mutation：D30P, A31G Mutation：D30P, A31G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；45%(v/v) methanol, 50 mM HEPES pH 6.4 and 100 mM Li2SO4, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.40 Å R-free 0.188
7KAE Rop protein variant with a buried tryptophan Deposited 2020-09-30	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–57（56 aa） Fragment：engineered variant Chain B 2–57（56 aa） Fragment：engineered variant	Mutation：R16Q, S17N, L20Q, C38A, C52A, F56W Mutation：R16Q, S17N, L20Q, C38A, C52A, F56W	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；295 K；28% (w/v) PEG 400, 300 mM NaCl, 100 mM NaHEPES	Resolution 1.60 Å R-free 0.224

18 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ROP_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–65； UniProt 1–63

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1nkd
Deposition date deposition_date	1997-09-23
Structure title title	ATOMIC RESOLUTION (1.07 ANGSTROMS) STRUCTURE OF THE ROP MUTANT <2AA>
Keywords keywords	ROP (COLE1 REPRESSOR OF PRIMER), ATOMIC RESOLUTION STRUCTURE, 4-ALPHA-HELIX BUNDLE, TRANSCRIPTION REGULATION; TRANSCRIPTION REGULATION
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	14.48 Å
Radius of gyration Rg (electron density) rg_electron	13.88 Å
Forward intensity I(0) i0	1137080.00
Molecular weight molecular_weight	6706.0 kDa
Excluded volume excluded_volume	8238 Å³
Envelope volume envelope_volume	9971 Å³
Hydration-shell volume shell_volume	7119 Å³
Envelope diameter envelope_diameter	53.0 Å
Shell Rg shell_rg	17.49 Å
Envelope Rg envelope_rg	14.37 Å
Shape Rg shape_rg	13.85 Å
Total Rg total_rg	14.83 Å
Total atoms total_atoms	893
Residues n_residues	59
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	55.8 Å
Rg (real space) rg_real	14.69 Å
Rg uncertainty (real space) rg_real_error	0.73 Å
I(0) (real space) i0_real	1.1370e+06
I(0) uncertainty (real space) i0_real_error	1.6450e+04
Rg (reciprocal space) rg_reciprocal	14.67 Å
I(0) (reciprocal space) i0_reciprocal	1137000.0000
Solution quality estimate total_estimate	0.7521
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	12.7 Å
Skewness Skewness skewness	0.615
Kurtosis Kurtosis kurtosis	-0.121
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	151400.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.526; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.203; Smooth: 0.992

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1nkda_
Class class	a — All alpha proteins
Fold Fold fold	a.30 — ROP-like
Superfamily Superfamily superfamily	a.30.1 — ROP protein
Family Family family	a.30.1.1 — ROP protein

CATH v4.4 (1 domains)

Domain ID domain_id	1nkdA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	230 —

▶

8. Citations (4)

▶

Unit-cell length a length_a	47.060 Å
Unit-cell length b length_b	37.880 Å
Unit-cell length c length_c	31.650 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.80 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.090 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1040
R_work r_work	—
R_free r_free	0.1340

Description description	ROP
Molecular weight formula_weight	7379.2 kDa
Mutation mutation	INS(A-D31-A)
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1063

ATOMIC RESOLUTION (1.07 ANGSTROMS) STRUCTURE OF THE ROP MUTANT <2AA>

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

ROP

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (4)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	114

fit	/app/data/saxs_computation/nk/1nkd/1nkd.fit
pddf	/app/data/pr_computation/nk/1nkd/1nkd.pr.out
profile	/app/data/saxs_computation/nk/1nkd/1nkd.dat