4n6v

Partial rotational order disorder structure of human stefin B

Method: X-RAY DIFFRACTION D_max: 144.1 Å Quality: GOOD

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

Cystatin-B

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain 2； UniProt 8–98	Fragment：UNP residues 8-98	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234
10	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain 5； UniProt 8–98	Fragment：UNP residues 8-98	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain 1； UniProt 8–98	Fragment：UNP residues 8-98	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain 9； UniProt 8–98	Fragment：UNP residues 8-98	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain 8； UniProt 8–98	Fragment：UNP residues 8-98	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain 7； UniProt 8–98	Fragment：UNP residues 8-98	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain 6； UniProt 8–98	Fragment：UNP residues 8-98	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234
7	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain 4； UniProt 8–98	Fragment：UNP residues 8-98	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234
8	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain 3； UniProt 8–98	Fragment：UNP residues 8-98	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234
9	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain 0； UniProt 8–98	Fragment：UNP residues 8-98	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234

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 4N6V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1STF THE REFINED 2.4 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF RECOMBINANT HUMAN STEFIN B IN COMPLEX WITH THE CYSTEINE PROTEINASE PAPAIN: A NOVEL TYPE OF PROTEINASE INHIBITOR INTERACTION Deposited 1993-04-21	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 1–98（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.37 Å
2OCT Stefin B (Cystatin B) tetramer Deposited 2006-12-21	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 1–98（98 aa） Chain B 1–98（98 aa）	Mutation：C3S, P79S Mutation：C3S, P79S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；30 % MPD, 0.1 M HEPES, 1.4-butanediol as additive, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.40 Å R-free 0.189

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CYTB_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain 0； PDBConstruct 1–91； UniProt 8–98 Author chain 1； PDBConstruct 1–91； UniProt 8–98 Author chain 2； PDBConstruct 1–91； UniProt 8–98 Author chain 3； PDBConstruct 1–91； UniProt 8–98 Author chain 4； PDBConstruct 1–91； UniProt 8–98 Author chain 5； PDBConstruct 1–91； UniProt 8–98 Author chain 6； PDBConstruct 1–91； UniProt 8–98 Author chain 7； PDBConstruct 1–91； UniProt 8–98 Author chain 8； PDBConstruct 1–91； UniProt 8–98 Author chain 9； PDBConstruct 1–91； UniProt 8–98

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4n6v
Deposition date deposition_date	2013-10-14
Structure title title	Partial rotational order disorder structure of human stefin B
Keywords keywords	stefin B, cystatin B, partial rotational order disorder, crystal disorder, HYDROLASE INHIBITOR; HYDROLASE INHIBITOR
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	42.52 Å
Radius of gyration Rg (electron density) rg_electron	42.90 Å
Forward intensity I(0) i0	166816000.00
Molecular weight molecular_weight	105000.0 kDa
Excluded volume excluded_volume	131540 Å³
Envelope volume envelope_volume	198870 Å³
Hydration-shell volume shell_volume	42247 Å³
Envelope diameter envelope_diameter	148.1 Å
Shell Rg shell_rg	42.61 Å
Envelope Rg envelope_rg	42.37 Å
Shape Rg shape_rg	42.89 Å
Total Rg total_rg	42.92 Å
Total atoms total_atoms	7440
Residues n_residues	910
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	144.1 Å
Rg (real space) rg_real	42.92 Å
Rg uncertainty (real space) rg_real_error	1.67 Å
I(0) (real space) i0_real	1.6680e+08
I(0) uncertainty (real space) i0_real_error	3.2380e+06
Rg (reciprocal space) rg_reciprocal	42.53 Å
I(0) (reciprocal space) i0_reciprocal	166700000.0000
Solution quality estimate total_estimate	0.8105
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	42.9 Å
Skewness Skewness skewness	0.541
Kurtosis Kurtosis kurtosis	-0.360
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11870000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.794; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.849; Smooth: 0.300

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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	Cystatin-B
Molecular weight formula_weight	10477.7 kDa
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	2,1,9,8,7,6,4,3,0,5
Atom count atom_count	9934

ATQPATAETQHIADQVRSQLEEKENKKFPVFKAVSFKSQVVAGTNYFIKVHVGDEDFVHLRVFQSLPHENKPLTLSNYQTNKAKHDELTYF

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	SULFATE ION
Molecular weight formula_weight	96.1 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	755

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7. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d4n6v0_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.1 — Cystatin/monellin
Family Family family	d.17.1.2 — Cystatins

Domain ID domain_id	d4n6v1_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.1 — Cystatin/monellin
Family Family family	d.17.1.2 — Cystatins

Domain ID domain_id	d4n6v2_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.1 — Cystatin/monellin
Family Family family	d.17.1.2 — Cystatins

Domain ID domain_id	d4n6v3_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.1 — Cystatin/monellin
Family Family family	d.17.1.2 — Cystatins

Domain ID domain_id	d4n6v4_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.1 — Cystatin/monellin
Family Family family	d.17.1.2 — Cystatins

Domain ID domain_id	d4n6v5_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.1 — Cystatin/monellin
Family Family family	d.17.1.2 — Cystatins

Domain ID domain_id	d4n6v6_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.1 — Cystatin/monellin
Family Family family	d.17.1.2 — Cystatins

Domain ID domain_id	d4n6v7_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.1 — Cystatin/monellin
Family Family family	d.17.1.2 — Cystatins

Domain ID domain_id	d4n6v8_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.1 — Cystatin/monellin
Family Family family	d.17.1.2 — Cystatins

Domain ID domain_id	d4n6v9_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.1 — Cystatin/monellin
Family Family family	d.17.1.2 — Cystatins

CATH v4.4 (10 domains)

Domain ID domain_id	4n6v000
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4n6v100
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4n6v200
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4n6v300
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4n6v400
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4n6v500
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4n6v600
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4n6v700
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4n6v800
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4n6v900
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	95.559 Å
Unit-cell length b length_b	95.559 Å
Unit-cell length c length_c	254.977 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	80

Space group space_group	I 4
Space-group number int_tables_number	79
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	46.370 Å
R factor r_factor	0.1921
R_work r_work	0.1899
R_free r_free	0.2337

fit	/app/data/saxs_computation/n6/4n6v/4n6v.fit
pddf	/app/data/pr_computation/n6/4n6v/4n6v.pr.out
profile	/app/data/saxs_computation/n6/4n6v/4n6v.dat