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- PDB-1crx: CRE RECOMBINASE/DNA COMPLEX REACTION INTERMEDIATE I -

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Basic information

Entry
Database: PDB / ID: 1crx
TitleCRE RECOMBINASE/DNA COMPLEX REACTION INTERMEDIATE I
Components
  • CRE RECOMBINASE
  • DNA (5'-D(*AP*TP*AP*TP*GP*CP*TP*AP*TP*AP*CP*GP*AP*AP*GP*TP*TP*AP*T)-3')
  • DNA (5'-D(*TP*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*G)-3')
  • DNA (5'-D(P*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*GP*C)-3')
KeywordsREPLICATION/DNA / SITE-SPECIFIC RECOMBINASE / PROTEIN:DNA COMPLEX / REACTION INTERMEDIATE / COMPLEX (RECOMBINASE-DNA) / REPLICATION-DNA COMPLEX
Function / homology
Function and homology information


DNA integration / DNA recombination / DNA binding
Similarity search - Function
Intergrase catalytic core / Tyrosine recombinase, N-terminal domain / hpI Integrase; Chain A / Core-binding (CB) domain / Tyrosine recombinase domain profile. / Core-binding (CB) domain profile. / Phage integrase family / Integrase, catalytic domain / Integrase/recombinase, N-terminal / Integrase-like, catalytic domain superfamily ...Intergrase catalytic core / Tyrosine recombinase, N-terminal domain / hpI Integrase; Chain A / Core-binding (CB) domain / Tyrosine recombinase domain profile. / Core-binding (CB) domain profile. / Phage integrase family / Integrase, catalytic domain / Integrase/recombinase, N-terminal / Integrase-like, catalytic domain superfamily / DNA breaking-rejoining enzyme, catalytic core / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / DNA / DNA (> 10) / Recombinase cre
Similarity search - Component
Biological speciesEnterobacteria phage P1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR, MAD / Resolution: 2.4 Å
AuthorsGuo, F. / Gopaul, D.N. / Van Duyne, G.D.
CitationJournal: Nature / Year: 1997
Title: Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse.
Authors: Guo, F. / Gopaul, D.N. / van Duyne, G.D.
History
DepositionJul 2, 1997Deposition site: BNL / Processing site: NDB
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*TP*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*G)-3')
D: DNA (5'-D(*AP*TP*AP*TP*GP*CP*TP*AP*TP*AP*CP*GP*AP*AP*GP*TP*TP*AP*T)-3')
E: DNA (5'-D(P*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*GP*C)-3')
F: DNA (5'-D(*AP*TP*AP*TP*GP*CP*TP*AP*TP*AP*CP*GP*AP*AP*GP*TP*TP*AP*T)-3')
A: CRE RECOMBINASE
B: CRE RECOMBINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,7437
Polymers93,6486
Non-polymers951
Water8,791488
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.700, 121.000, 180.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

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DNA chain , 3 types, 4 molecules CDFE

#1: DNA chain DNA (5'-D(*TP*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*G)-3')


Mass: 4583.009 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*AP*TP*AP*TP*GP*CP*TP*AP*TP*AP*CP*GP*AP*AP*GP*TP*TP*AP*T)-3')


Mass: 5842.821 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(P*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*GP*C)-3')


Mass: 4567.998 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 2 molecules AB

#4: Protein CRE RECOMBINASE


Mass: 36405.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P1 (virus) / Genus: P1-like viruses / Gene: CRE / Plasmid: PET21A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P06956

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Non-polymers , 2 types, 489 molecules

#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 50 %
Crystal growpH: 5 / Details: 100 MM ACETATE, PH 5 24% MPD 20 MM CACL2, pH 5.0
Components of the solutions
IDNameCrystal-IDSol-ID
1ACETATE11
2CACL211
3MPD11
4MPD12
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMsodium acetate1drop
212 %MPD1drop
310 mM1dropCaCl2
40.050 mMCre1drop
50.075 mMloxA1drop
6100 mMacetate1reservoir
724 %MPD1reservoir
820 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1996 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 42896 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Rsym value: 6.9 / Net I/σ(I): 20
Reflection shellResolution: 2.4→2.47 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 10 / Rsym value: 18.9 / % possible all: 87
Reflection
*PLUS
Rmerge(I) obs: 0.069

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Processing

Software
NameVersionClassification
MLPHAREphasing
LOCALmodel building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
LOCALphasing
RefinementMethod to determine structure: MIR, MAD / Resolution: 2.4→50 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.263 4137 10 %RANDOM
Rwork0.201 ---
obs-41368 93 %-
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5100 1386 3 488 6977
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.85
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it31.5
X-RAY DIFFRACTIONx_mcangle_it4.42
X-RAY DIFFRACTIONx_scbond_it4.42
X-RAY DIFFRACTIONx_scangle_it6.12.5
LS refinement shellResolution: 2.4→2.5 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.37 454 10 %
Rwork0.32 4040 -
obs--87 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 42896 / Rfactor all: 0.201 / Rfactor obs: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.85

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