SAXSdb — 1m3c

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

Proto-oncogene C-crk

Mus musculus

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 A； UniProt 132–191	Fragment：N-TERMINAL SH3 DOMAIN (residues 132-191) Mutation：R191G, added G133, C132	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7.2；307 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure ambient NMR sample composition：1mM SH3 NA, 20mM sodium phosphate, 20 mM DTT-d10, 100 mM NaCl, 0.1% (w/v) NaN3 \| 90% H2O/10% D2O NMR sample composition：1mM SH3 U-15N, 20mM sodium phosphate, 20 mM DTT-d10, 100 mM NaCl, 0.1% (w/v) NaN3 \| 90% H2O/10% D2O	Resolution not provided

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 1M3C	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B07 CRK SH3 DOMAIN COMPLEXED WITH PEPTOID INHIBITOR Deposited 1998-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 134–190（57 aa） Fragment：SH3 DOMAIN	Not recorded	PYJ PHENYLETHANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；29% PEG4000, 0.2 M AMMONIUM ACETATE, PH 6.0, pH 6.00	Resolution 2.50 Å R-free 0.354
1CKA STRUCTURAL BASIS FOR THE SPECIFIC INTERACTION OF LYSINE-CONTAINING PROLINE-RICH PEPTIDES WITH THE N-TERMINAL SH3 DOMAIN OF C-CRK Deposited 1995-01-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 134–190（57 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.50 Å
1CKB STRUCTURAL BASIS FOR THE SPECIFIC INTERACTION OF LYSINE-CONTAINING PROLINE-RICH PEPTIDES WITH THE N-TERMINAL SH3 DOMAIN OF C-CRK Deposited 1995-01-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 134–190（57 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1JU5 Ternary complex of an Crk SH2 domain, Crk-derived phophopeptide, and Abl SH3 domain by NMR spectroscopy Deposited 2001-08-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 217–228（12 aa） Fragment：Crk phosphopeptide	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 50mM sodium phosphate；Pressure ambient NMR sample composition 0.6-1.5mM Crk SH2 domain U-15N, 13C; 50mM sodium phosphate pH6.8, 0.02% sodium azide \| 90% H2O/10% D2O	Resolution not provided
1M30 Solution structure of N-terminal SH3 domain from oncogene protein c-Crk Deposited 2002-06-26	Different construct Different mutation/modification	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 134–191（58 aa） Fragment：N-TERMINAL SH3 DOMAIN (residues 134-191)	Mutation：R191G	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.2；307 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure ambient NMR sample composition 1mM SH3 NA, 20mM sodium phosphate, 20 mM DTT-d10, 100 mM NaCl, 0.1% (w/v) NaN3 \| 90% H2O/10% D2O NMR sample composition 1mM SH3 U-15N, 20mM sodium phosphate, 20 mM DTT-d10, 100 mM NaCl, 0.1% (w/v) NaN3 \| 90% H2O/10% D2O	Resolution not provided
1M3A Solution structure of a circular form of the truncated N-terminal SH3 domain from oncogene protein c-Crk. Deposited 2002-06-27	Different construct Different mutation/modification	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 135–191（57 aa） Fragment：N-TERMINAL SH3 DOMAIN (residues 135-191)	Mutation：R191G, E135C, deleted A134	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.2；307 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure ambient NMR sample composition 1mM SH3 NA, 20mM sodium phosphate, 20 mM DTT-d10, 100 mM NaCl, 0.1% (w/v) NaN3 \| 90% H2O/10% D2O NMR sample composition 1mM SH3 U-15N, 20mM sodium phosphate, 20 mM DTT-d10, 100 mM NaCl, 0.1% (w/v) NaN3 \| 90% H2O/10% D2O	Resolution not provided
1M3B Solution structure of a circular form of the N-terminal SH3 domain (A134C, E135G, R191G mutant) from oncogene protein c-Crk. Deposited 2002-06-27	Different construct Different mutation/modification	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 134–191（58 aa） Fragment：N-TERMINAL SH3 DOMAIN (residues 134-191)	Mutation：R191G, E135G, A134C	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.2；307 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure ambient NMR sample composition 1mM SH3 NA, 20mM sodium phosphate, 20 mM DTT-d10, 100 mM NaCl, 0.1% (w/v) NaN3 \| 90% H2O/10% D2O NMR sample composition 1mM SH3 U-15N, 20mM sodium phosphate, 20 mM DTT-d10, 100 mM NaCl, 0.1% (w/v) NaN3 \| 90% H2O/10% D2O	Resolution not provided
2GGR Solution structure of the C-terminal SH3 domain of c-CrkII Deposited 2006-03-24	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 230–304（75 aa） Fragment：C-terminal Domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 50mM；Pressure ambient NMR sample composition 0.4 mM cSH3 domain U-15N,13C; 10mM phosphate buffer pH7.2; 50mM NaCl; 5mM DTT-d10; 0.1% NaN3; 1mM EDTA; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
5IH2 Structure, thermodynamics, and the role of conformational dynamics in the interactions between the N-terminal SH3 domain of CrkII and proline-rich motifs in cAbl Deposited 2016-02-28	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 × 2 PDB declaration: dimeric	Chain A 134–191（58 aa） Fragment：UNP residues 134-191	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1 NA SODIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K	Resolution 1.80 Å R-free 0.243
5IH2 Structure, thermodynamics, and the role of conformational dynamics in the interactions between the N-terminal SH3 domain of CrkII and proline-rich motifs in cAbl Deposited 2016-02-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 134–191（58 aa） Fragment：UNP residues 134-191	Not recorded	NA SODIUM ION × 1 P4G 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K	Resolution 1.80 Å R-free 0.243
5JN0 CRK-II SH2 domain Deposited 2016-04-29	Different construct Different mutation/modification 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 6–121（116 aa） Fragment：UNP residues 6-121	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；297 K；100 mM MES pH 6.5, 12% PEG 20,000	Resolution 1.68 Å R-free 0.210
5L23 Crystal structure of the complex between the N-terminal SH3 domain of CrkII and a proline-rich ligand Deposited 2016-07-30	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 × 2 PDB declaration: dimeric	Chain A 134–191（58 aa） Fragment：UNP residues 134-191	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；286 K；Lithium sulfate monohydrate, PEG 3350	Resolution 1.77 Å R-free 0.210

11 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CRK_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–60； UniProt 132–191

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	1m3c
Deposition date deposition_date	2002-06-27
Structure title title	Solution structure of a circular form of the N-terminal SH3 domain (E132C, E133G, R191G mutant) from oncogene protein c-Crk
Keywords keywords	SH3, SH3 DOMAIN, CIRCULAR PROTEIN, CYCLIZED PROTEIN, ADAPTOR PROTEIN, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	10.93 Å
Radius of gyration Rg (electron density) rg_electron	10.59 Å
Forward intensity I(0) i0	286313000.00
Molecular weight molecular_weight	140020.0 kDa
Excluded volume excluded_volume	173450 Å³
Envelope volume envelope_volume	15217 Å³
Hydration-shell volume shell_volume	10512 Å³
Envelope diameter envelope_diameter	40.8 Å
Shell Rg shell_rg	18.09 Å
Envelope Rg envelope_rg	12.57 Å
Shape Rg shape_rg	10.54 Å
Total Rg total_rg	10.96 Å
Total atoms total_atoms	19140
Residues n_residues	1200
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	37.0 Å
Rg (real space) rg_real	10.85 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	2.8630e+08
I(0) uncertainty (real space) i0_real_error	2.9390e+06
Rg (reciprocal space) rg_reciprocal	10.85 Å
I(0) (reciprocal space) i0_reciprocal	286300000.0000
Solution quality estimate total_estimate	0.6814
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.0 Å
Skewness Skewness skewness	0.073
Kurtosis Kurtosis kurtosis	-0.225
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	88100.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.701; Stabil: 1.000; Sysdev: 0.256; Positv: 1.000; Valcen: 1.000; Smooth: 0.982

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1m3ca_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.2 — SH3-domain
Family Family family	b.34.2.1 — SH3-domain

CATH v4.4 (1 domains)

Domain ID domain_id	1m3cA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

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8. Citations (2)

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Description description	Proto-oncogene C-crk
Molecular weight formula_weight	7031.8 kDa
Mutation mutation	R191G, added G133, C132
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	19140

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/m3/1m3c/1m3c.fit
pddf	/app/data/pr_computation/m3/1m3c/1m3c.pr.out
profile	/app/data/saxs_computation/m3/1m3c/1m3c.dat

Solution structure of a circular form of the N-terminal SH3 domain (E132C, E133G, R191G mutant) from oncogene protein c-Crk

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

Proto-oncogene C-crk

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)