SAXSdb — 1dkg

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

NUCLEOTIDE EXCHANGE FACTOR GRPE

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 A； UniProt 1–197 Chain B； UniProt 1–197	Mutation：CHAIN A, B, G122D	MOLECULAR CHAPERONE DNAK × 1 （P04475）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.6；pH 4.6	Resolution 2.80 Å R-free 0.317

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	GRPE_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–197； UniProt 1–197 Author chain B； PDBConstruct 1–197； UniProt 1–197

MOLECULAR CHAPERONE DNAK

Escherichia coli

UniProt P04475

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 D； UniProt 1–382	Fragment：ATPASE DOMAIN RESIDUES 3 - 383 Mutation：CHAIN D, P319L	NUCLEOTIDE EXCHANGE FACTOR GRPE × 2 （P09372）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.6；pH 4.6	Resolution 2.80 Å R-free 0.317

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	DNAK_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 2–383； UniProt 1–382

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	1dkg
Deposition date deposition_date	1997-02-13
Structure title title	CRYSTAL STRUCTURE OF THE NUCLEOTIDE EXCHANGE FACTOR GRPE BOUND TO THE ATPASE DOMAIN OF THE MOLECULAR CHAPERONE DNAK
Keywords keywords	HSP70, GRPE, MOLECULAR CHAPERONE, NUCLEOTIDE EXCHANGE FACTOR, COILED-COIL, COMPLEX (HSP24-HSP70), COMPLEX (HSP24-HSP70) complex; COMPLEX (HSP24/HSP70)
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	31.85 Å
Radius of gyration Rg (electron density) rg_electron	31.31 Å
Forward intensity I(0) i0	87627300.00
Molecular weight molecular_weight	73482.0 kDa
Excluded volume excluded_volume	92059 Å³
Envelope volume envelope_volume	123580 Å³
Hydration-shell volume shell_volume	34712 Å³
Envelope diameter envelope_diameter	123.1 Å
Shell Rg shell_rg	36.06 Å
Envelope Rg envelope_rg	32.06 Å
Shape Rg shape_rg	31.31 Å
Total Rg total_rg	31.75 Å
Total atoms total_atoms	5156
Residues n_residues	685
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	114.7 Å
Rg (real space) rg_real	32.07 Å
Rg uncertainty (real space) rg_real_error	1.38 Å
I(0) (real space) i0_real	8.7630e+07
I(0) uncertainty (real space) i0_real_error	1.6240e+06
Rg (reciprocal space) rg_reciprocal	31.97 Å
I(0) (reciprocal space) i0_reciprocal	87620000.0000
Solution quality estimate total_estimate	0.6265
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	36.7 Å
Skewness Skewness skewness	0.584
Kurtosis Kurtosis kurtosis	0.184
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9441000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.702; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.943; Smooth: 0.904

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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	NUCLEOTIDE EXCHANGE FACTOR GRPE
Molecular weight formula_weight	21882.9 kDa
Mutation mutation	CHAIN A, B, G122D
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	5183

MSSKEQKTPEGQAPEEIIMDQHEEIEAVEPEASAEQVDPRDEKVANLEAQLAEAQTRERDGILRVKAEMENLRRRTELDIEKAHKFALEKFINELLPVIDSLDRALEVADKANPDMSAMVEDIELTLKSMLDVVRKFGVEVIAETNVPLDPNVHQAIAMVESDDVAPGNVLGIMQKGYTLNGRTIRAAMVTVAKAKA

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	MOLECULAR CHAPERONE DNAK
Molecular weight formula_weight	41572.1 kDa
Mutation mutation	CHAIN D, P319L
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MGKIIGIDLGTTNSCVAIMDGTTPRVLENAEGDRTTPSIIAYTQDGETLVGQPAKRQAVTNPQNTLFAIKRLIGRRFQDEEVQRDVSIMPFKIIAADNGDAWVEVKGQKMAPPQISAEVLKKMKKTAEDYLGEPVTEAVITVPAYFNDAQRQATKDAGRIAGLEVKRIINEPTAAALAYGLDKGTGNRTIAVYDLGGGTFDISIIEIDEVDGEKTFEVLATNGDTHLGGEDFDSRLINYLVEEFKKDQGIDLRNDPLAMQRLKEAAEKAKIELSSAQQTDVNLPYITADATGPKHMNIKVTRAKLESLVEDLVNRSIELLKVALQDAGLSVSDIDDVILVGGQTRMPMVQKKVAEFFGKEPRKDVNPDEAVAIGAAVQGGVLT

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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	27

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7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1dkga1
Class class	b — All beta proteins
Fold Fold fold	b.73 — Head domain of nucleotide exchange factor GrpE
Superfamily Superfamily superfamily	b.73.1 — Head domain of nucleotide exchange factor GrpE
Family Family family	b.73.1.1 — Head domain of nucleotide exchange factor GrpE

Domain ID domain_id	d1dkga2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.9 — Coiled-coil domain of nucleotide exchange factor GrpE
Family Family family	h.1.9.1 — Coiled-coil domain of nucleotide exchange factor GrpE

Domain ID domain_id	d1dkgb1
Class class	b — All beta proteins
Fold Fold fold	b.73 — Head domain of nucleotide exchange factor GrpE
Superfamily Superfamily superfamily	b.73.1 — Head domain of nucleotide exchange factor GrpE
Family Family family	b.73.1.1 — Head domain of nucleotide exchange factor GrpE

Domain ID domain_id	d1dkgb2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.9 — Coiled-coil domain of nucleotide exchange factor GrpE
Family Family family	h.1.9.1 — Coiled-coil domain of nucleotide exchange factor GrpE

Domain ID domain_id	d1dkgd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.1 — Actin/HSP70

Domain ID domain_id	d1dkgd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.1 — Actin/HSP70

CATH v4.4 (8 domains)

Domain ID domain_id	1dkgA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily	20 — GrpE nucleotide exchange factor, coiled-coil domain

Domain ID domain_id	1dkgA02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	22 — Nucleotide Exchange Factor Grpe; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Head domain of nucleotide exchange factor GrpE

Domain ID domain_id	1dkgB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily	20 — GrpE nucleotide exchange factor, coiled-coil domain

Domain ID domain_id	1dkgB02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	22 — Nucleotide Exchange Factor Grpe; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Head domain of nucleotide exchange factor GrpE

Domain ID domain_id	1dkgD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	1dkgD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	30 — Defensin A-like
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1dkgD03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	1dkgD04
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	640 — Actin; Chain A, domain 4
Homologous superfamily homologous superfamily	10 — ATPase, substrate binding domain, subdomain 4

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8. Citations (1)

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Unit-cell length a length_a	149.430 Å
Unit-cell length b length_b	149.430 Å
Unit-cell length c length_c	49.030 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 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2230
R_work r_work	0.2230
R_free r_free	0.3170

fit	/app/data/saxs_computation/dk/1dkg/1dkg.fit
pddf	/app/data/pr_computation/dk/1dkg/1dkg.pr.out
profile	/app/data/saxs_computation/dk/1dkg/1dkg.dat

CRYSTAL STRUCTURE OF THE NUCLEOTIDE EXCHANGE FACTOR GRPE BOUND TO THE ATPASE DOMAIN OF THE MOLECULAR CHAPERONE DNAK

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

NUCLEOTIDE EXCHANGE FACTOR GRPE

State in the Current Structure

Other States of the Same Protein in the Database

MOLECULAR CHAPERONE DNAK

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)