SAXSdb — 1crx

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

Cre recombinase

Punavirus P1

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–DNA Homooligomer Protein × 2 DNA 4 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain A； UniProt 20–341 Chain B； UniProt 20–341	Non-standard monomer：Yes (specific site not provided by mmCIF)	;DNA (5'-D(TPAPTPAPAPCPTPTPCPGPTPAPTPAPG)-3') ; × 1 ;DNA (5'-D(APTPAPTPGPCPTPAPTPAPCPGPAPAPGPTPTPAPT)-3') ; × 2 ;DNA (5'-D(PAPTPAPAPCPTPTPCPGPTPAPTPAPGP*C)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5；100 MM ACETATE, PH 5 24% MPD 20 MM CACL2, pH 5.0	Resolution 2.40 Å R-free 0.263

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	Q71TG5_9CAUD
Isoform	—
PDB entities	4, 5
Chains and sequence ranges	Author chain A； PDBConstruct 1–322； UniProt 20–341 Author chain B； PDBConstruct 1–322； UniProt 20–341

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	1crx
Deposition date deposition_date	1997-07-02
Structure title title	CRE RECOMBINASE/DNA COMPLEX REACTION INTERMEDIATE I
Keywords keywords	SITE-SPECIFIC RECOMBINASE, PROTEIN:DNA COMPLEX, REACTION INTERMEDIATE, COMPLEX (RECOMBINASE-DNA), REPLICATION-DNA COMPLEX; REPLICATION/DNA
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	31.43 Å
Radius of gyration Rg (electron density) rg_electron	30.70 Å
Forward intensity I(0) i0	189070000.00
Molecular weight molecular_weight	93651.0 kDa
Excluded volume excluded_volume	110570 Å³
Envelope volume envelope_volume	144740 Å³
Hydration-shell volume shell_volume	39250 Å³
Envelope diameter envelope_diameter	105.0 Å
Shell Rg shell_rg	37.77 Å
Envelope Rg envelope_rg	30.51 Å
Shape Rg shape_rg	30.68 Å
Total Rg total_rg	31.29 Å
Total atoms total_atoms	6489
Residues n_residues	711
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	100.5 Å
Rg (real space) rg_real	31.41 Å
Rg uncertainty (real space) rg_real_error	0.71 Å
I(0) (real space) i0_real	1.8910e+08
I(0) uncertainty (real space) i0_real_error	2.6270e+06
Rg (reciprocal space) rg_reciprocal	31.42 Å
I(0) (reciprocal space) i0_reciprocal	189100000.0000
Solution quality estimate total_estimate	0.8979
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.2 Å
Skewness Skewness skewness	0.300
Kurtosis Kurtosis kurtosis	-0.485
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	36520000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.885

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(TPAPTPAPAPCPTPTPCPGPTPAPTPAP*G)-3') ;
Molecular weight formula_weight	4583.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C
Atom count atom_count	6977

TATAACTTCGTATAG

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(APTPAPTPGPCPTPAPTPAPCPGPAPAPGPTPTPAP*T)-3') ;
Molecular weight formula_weight	5842.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,F

ATATGCTATACGAAGTTAT

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(PAPTPAPAPCPTPTPCPGPTPAPTPAPGP*C)-3') ;
Molecular weight formula_weight	4568.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

ATAACTTCGTATAGC

Entity 4 Entity 4 polymer

Description description	Cre recombinase
Molecular weight formula_weight	36405.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

SDEVRKNLMDMFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNRKWFPAEPEDVRDYLLYLQARGLAVKTIQQHLGQLNMLHRRSGLPRPSDSNAVSLVMRRIRKENVDAGERAKQALAFERTDFDQVRSLMENSDRCQDIRNLAFLGIAYNTLLRIAEIARIRVKDISRTDGGRMLIHIGRTKTLVSTAGVEKALSLGVTKLVERWISVSGVADDPNNYLFCRVRKNGVAAPSATSQLSTRALEGIFEATHRLIYGAKDDSGQRYLAWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVMNYIRNLDSETGAMVRLLED

来源 Source

来源生物 organism	Punavirus P1
NCBI Class编号 ncbi_taxonomy_id	10678
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	Cre recombinase
Molecular weight formula_weight	36485.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SDEVRKNLMDMFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNRKWFPAEPEDVRDYLLYLQARGLAVKTIQQHLGQLNMLHRRSGLPRPSDSNAVSLVMRRIRKENVDAGERAKQALAFERTDFDQVRSLMENSDRCQDIRNLAFLGIAYNTLLRIAEIARIRVKDISRTDGGRMLIHIGRTKTLVSTAGVEKALSLGVTKLVERWISVSGVADDPNNYLFCRVRKNGVAAPSATSQLSTRALEGIFEATHRLIYGAKDDSGQRYLAWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVMNYIRNLDSETGAMVRLLED

来源 Source

来源生物 organism	Punavirus P1
NCBI Class编号 ncbi_taxonomy_id	10678
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	488

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1crxa1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.9 — lambda integrase-like, N-terminal domain
Family Family family	a.60.9.1 — lambda integrase-like, N-terminal domain

Domain ID domain_id	d1crxa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.163 — DNA breaking-rejoining enzymes
Superfamily Superfamily superfamily	d.163.1 — DNA breaking-rejoining enzymes
Family Family family	d.163.1.1 — Lambda integrase-like, catalytic core

Domain ID domain_id	d1crxb1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.9 — lambda integrase-like, N-terminal domain
Family Family family	a.60.9.1 — lambda integrase-like, N-terminal domain

Domain ID domain_id	d1crxb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.163 — DNA breaking-rejoining enzymes
Superfamily Superfamily superfamily	d.163.1 — DNA breaking-rejoining enzymes
Family Family family	d.163.1.1 — Lambda integrase-like, catalytic core

CATH v4.4 (4 domains)

Domain ID domain_id	1crxA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	443 — hpI Integrase; Chain A
Homologous superfamily homologous superfamily	10 — Intergrase catalytic core

Domain ID domain_id	1crxA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	130 — Tyrosine recombinase, N-terminal domain

Domain ID domain_id	1crxB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	443 — hpI Integrase; Chain A
Homologous superfamily homologous superfamily	10 — Intergrase catalytic core

Domain ID domain_id	1crxB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	130 — Tyrosine recombinase, N-terminal domain

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8. Citations (1)

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Unit-cell length a length_a	107.700 Å
Unit-cell length b length_b	121.000 Å
Unit-cell length c length_c	180.400 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2010
R_free r_free	0.2630

fit	/app/data/saxs_computation/cr/1crx/1crx.fit
pddf	/app/data/pr_computation/cr/1crx/1crx.pr.out
profile	/app/data/saxs_computation/cr/1crx/1crx.dat

CRE RECOMBINASE/DNA COMPLEX REACTION INTERMEDIATE I

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

Cre recombinase

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)