SAXSdb — 2pv3

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

Chaperone surA

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain not uniquely mapped； UniProt —–— Chain A； UniProt 21–281 Chain A； UniProt 391–428 Chain B； UniProt 21–281 Chain B； UniProt 391–428	Fragment：Survivial protein A fragment from which the second peptidyl-prolyl isomerase domain has been deleted	C-peptide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；1.4~1.8M sodium chloride, 0.1M potassium dihydrogen phosphate, 0.1 M sodium dihydrogen phosphate, 0.1M MES buffer, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.39 Å R-free 0.299

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 2PV3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1M5Y Crystallographic Structure of SurA, a Molecular Chaperone that Facilitates Outer Membrane Porin Folding Deposited 2002-07-10	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 21–428（408 aa） Chain B 21–428（408 aa） Chain C 21–428（408 aa） Chain D 21–428（408 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；303 K；0.75M ammonium sulphate, 100mM sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP at 303K, VAPOR DIFFUSION, HANGING DROP, temperature 303.0K	Resolution 3.00 Å R-free 0.283
2PV1 Crystallographic Structure of SurA first peptidyl-prolyl isomerase domain complexed with peptide WEYIPNV Deposited 2007-05-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 172–274（103 aa） Fragment：PpiC 1	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；25~28% polyethylene glycol monomethylether 5000, 0.2 M ammonium sulfate, 0.1 M MES buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.30 Å R-free 0.243
2PV2 Crystallographic Structure of SurA first peptidyl-prolyl isomerase domain complexed with peptide NFTLKFWDIFRK Deposited 2007-05-09	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 172–274（103 aa） Fragment：PPIC 1 Chain B 172–274（103 aa） Fragment：PPIC 1	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；24% ployethylene glycol 8000, 0.1 M imdidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.30 Å R-free 0.227
2PV2 Crystallographic Structure of SurA first peptidyl-prolyl isomerase domain complexed with peptide NFTLKFWDIFRK Deposited 2007-05-09	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 172–274（103 aa） Fragment：PPIC 1 Chain D 172–274（103 aa） Fragment：PPIC 1	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；24% ployethylene glycol 8000, 0.1 M imdidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.30 Å R-free 0.227
8PZ1 Wait Complex: Lateral open BAM bound Compact SurA Deposited 2023-07-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 20–428（409 aa）	Mutation：K27C	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
8PZ2 Wait Complex: Lateral open BAM bound Extended SurA Deposited 2023-07-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 21–428（408 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
8PZU Wait Complex: BAM bound Darobactin-B and Compact SurA Deposited 2023-07-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain F 21–428（408 aa）	Mutation：K27C	MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8Q0G Release Complex: BAM bound EspP and Compact SurA Deposited 2023-07-28	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain F 21–428（408 aa）	Mutation：K27C	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
8QP5 Release Complex: BAM bound EspP (SurA released) Deposited 2023-09-29	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain P 21–428（408 aa）	Mutation：S1299C	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
8QPU Release Complex: BAM bound EspP and Extended SurA Deposited 2023-10-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain F 21–428（408 aa）	Mutation：K27C	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.20 Å
8QPV Handover Complex: BAM bound OmpX and extended SurA Deposited 2023-10-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: heptameric	Chain F 21–428（408 aa）	Mutation：K27C,R170C	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
8QPW Arrival Complex: Lateral open BAM bound extended SurA plus OmpX Deposited 2023-10-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain F 21–428（408 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.30 Å
9HG5 BAM-SurA complex in the swing-in state with full length BamC resolved Deposited 2024-11-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 21–428（408 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20mM Tris-HCl, 150mM NaCl, 0.05% DDM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.82 Å
9HG6 BAM-SurA complex in the swing-in state Deposited 2024-11-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 21–428（408 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20mM Tris-HCl, 150mM NaCl, 0.05% DDM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.73 Å
9HG7 BAM-SurA complex in the swing-out state Deposited 2024-11-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 21–428（408 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20mM Tris-HCl, 150mM NaCl, 0.05% DDM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.83 Å
9HG8 BAM-SurA complex in the swing-out state with BamC resolved Deposited 2024-11-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 21–428（408 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20mM Tris-HCl, 150mM NaCl, 0.05% DDM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9HG9 BAM-SurA-darobactin complex in the swing-in state Deposited 2024-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain F 21–428（408 aa）	Not recorded	MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20mM Tris-HCl, 150mM NaCl, 0.05% DDM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.88 Å
9HGA BAM-SurA-darobactin complex in the swing-out state Deposited 2024-11-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain F 21–428（408 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20mM Tris-HCl, 150mM NaCl, 0.05% DDM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.62 Å

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

View Construct and Data Evidence

UniProt name	SURA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–261； UniProt 21–281 Author chain A； PDBConstruct 262–299； UniProt 391–428 Author chain B； PDBConstruct 1–261； UniProt 21–281 Author chain B； PDBConstruct 262–299； UniProt 391–428

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	2pv3
Deposition date deposition_date	2007-05-09
Structure title title	Crystallographic Structure of SurA fragment lacking the second peptidyl-prolyl isomerase domain complexed with peptide NFTLKFWDIFRK
Keywords keywords	Survival protein A, Peptidyl-prolyl cis-trans isomerase domain, Isomerase; ISOMERASE
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	29.23 Å
Radius of gyration Rg (electron density) rg_electron	28.35 Å
Forward intensity I(0) i0	74378500.00
Molecular weight molecular_weight	64624.0 kDa
Excluded volume excluded_volume	80029 Å³
Envelope volume envelope_volume	111730 Å³
Hydration-shell volume shell_volume	32553 Å³
Envelope diameter envelope_diameter	95.2 Å
Shell Rg shell_rg	36.14 Å
Envelope Rg envelope_rg	27.67 Å
Shape Rg shape_rg	28.34 Å
Total Rg total_rg	29.19 Å
Total atoms total_atoms	4529
Residues n_residues	578
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	87.0 Å
Rg (real space) rg_real	29.05 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	7.4380e+07
I(0) uncertainty (real space) i0_real_error	9.7200e+05
Rg (reciprocal space) rg_reciprocal	29.13 Å
I(0) (reciprocal space) i0_reciprocal	74380000.0000
Solution quality estimate total_estimate	0.9144
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	40.3 Å
Skewness Skewness skewness	0.005
Kurtosis Kurtosis kurtosis	-0.692
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8855000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.970; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.977

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Chaperone surA
Molecular weight formula_weight	33221.6 kDa
EC 编号 ec_number	5.2.1.8
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	4529

APQVVDKVAAVVNNGVVLESDVDGLMQSVKLNAAQARQQLPDDATLRHQIMERLIMDQIILQMGQKMGVKISDEQLDQAIANIAKQNNMTLDQMRSRLAYDGLNYNTYRNQIRKEMIISEVRNNEVRRRITILPQEVESLAQQVGNQNDASTELNLSHILIPLPENPTSDQVNEAESQARAIVDQARNGADFGKLAIAHSADQQALNGGQMGWGRIQELPGIFAQALSTAKKGDIVGPIRSGVGFHILKVNDLRGESKNISAAQKDRAYRMLMNRKFSEEAASWMQEQRASAYVKILSN

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 polymer

Description description	C-peptide
Molecular weight formula_weight	1617.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

NFTLKFWDIFRK

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2pv3a1
Class class	a — All alpha proteins
Fold Fold fold	a.223 — Triger factor/SurA peptide-binding domain-like
Superfamily Superfamily superfamily	a.223.1 — Triger factor/SurA peptide-binding domain-like
Family Family family	a.223.1.2 — Porin chaperone SurA, peptide-binding domain

Domain ID domain_id	d2pv3a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.26 — FKBP-like
Superfamily Superfamily superfamily	d.26.1 — FKBP-like
Family Family family	d.26.1.1 — FKBP immunophilin/proline isomerase

Domain ID domain_id	d2pv3b1
Class class	a — All alpha proteins
Fold Fold fold	a.223 — Triger factor/SurA peptide-binding domain-like
Superfamily Superfamily superfamily	a.223.1 — Triger factor/SurA peptide-binding domain-like
Family Family family	a.223.1.2 — Porin chaperone SurA, peptide-binding domain

Domain ID domain_id	d2pv3b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.26 — FKBP-like
Superfamily Superfamily superfamily	d.26.1 — FKBP-like
Family Family family	d.26.1.1 — FKBP immunophilin/proline isomerase

CATH v4.4 (4 domains)

Domain ID domain_id	2pv3A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4030 — Triger factor/SurA peptide-binding fold
Homologous superfamily homologous superfamily	10 — Porin chaperone SurA, peptide-binding domain

Domain ID domain_id	2pv3A02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	2pv3B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4030 — Triger factor/SurA peptide-binding fold
Homologous superfamily homologous superfamily	10 — Porin chaperone SurA, peptide-binding domain

Domain ID domain_id	2pv3B02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily	40 —

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8. Citations (2)

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Unit-cell length a length_a	148.330 Å
Unit-cell length b length_b	148.330 Å
Unit-cell length c length_c	188.680 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	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	3.390 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2840
R_work r_work	0.2840
R_free r_free	0.2990

fit	/app/data/saxs_computation/pv/2pv3/2pv3.fit
pddf	/app/data/pr_computation/pv/2pv3/2pv3.pr.out
profile	/app/data/saxs_computation/pv/2pv3/2pv3.dat

Crystallographic Structure of SurA fragment lacking the second peptidyl-prolyl isomerase domain complexed with peptide NFTLKFWDIFRK

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

Chaperone surA

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 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)