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- PDB-3mgv: Cre recombinase-DNA transition state -

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Basic information

Entry
Database: PDB / ID: 3mgv
TitleCre recombinase-DNA transition state
Components
  • DNA (5'-D(*CP*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')
  • Recombinase cre
KeywordsISOMERASE/DNA / CRE-LOXP / TRANSITION STATE / ISOMERASE-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
VANADATE ION / DNA / DNA (> 10) / Recombinase cre
Similarity search - Component
Biological speciesEnterobacteria phage P1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsGibb, B.P. / Gupta, K. / Ghosh, K. / Sharp, R. / Chen, J. / Van Duyne, G.D.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Requirements for catalysis in the Cre recombinase active site.
Authors: Gibb, B. / Gupta, K. / Ghosh, K. / Sharp, R. / Chen, J. / Van Duyne, G.D.
History
DepositionApr 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Recombinase cre
B: Recombinase cre
C: Recombinase cre
D: Recombinase cre
E: DNA (5'-D(*TP*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*G)-3')
F: DNA (5'-D(*CP*AP*TP*AP*TP*GP*CP*TP*AP*TP*AP*CP*GP*AP*AP*GP*TP*TP*AP*T)-3')
G: DNA (5'-D(*TP*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*G)-3')
H: DNA (5'-D(*CP*AP*TP*AP*TP*GP*CP*TP*AP*TP*AP*CP*GP*AP*AP*GP*TP*TP*AP*T)-3')
I: DNA (5'-D(*TP*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*G)-3')
K: DNA (5'-D(*CP*AP*TP*AP*TP*GP*CP*TP*AP*TP*AP*CP*GP*AP*AP*GP*TP*TP*AP*T)-3')
L: DNA (5'-D(*TP*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*G)-3')
M: DNA (5'-D(*CP*AP*TP*AP*TP*GP*CP*TP*AP*TP*AP*CP*GP*AP*AP*GP*TP*TP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,47114
Polymers197,24112
Non-polymers2302
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45500 Å2
ΔGint-165 kcal/mol
Surface area63490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.046, 136.046, 218.431
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Recombinase cre


Mass: 38595.164 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P1 (virus) / Gene: cre / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06956
#2: 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.: 4 / Fragment: Upstream cleaved strand / Source method: obtained synthetically
#3: DNA chain
DNA (5'-D(*CP*AP*TP*AP*TP*GP*CP*TP*AP*TP*AP*CP*GP*AP*AP*GP*TP*TP*AP*T)-3')


Mass: 6132.003 Da / Num. of mol.: 4 / Fragment: Downstream cleaved strand / Source method: obtained synthetically
#4: Chemical ChemComp-VO4 / VANADATE ION / Vanadate


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.96 Å3/Da / Density % sol: 58.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.02M calcium chloride, 0.02M sodium acetate, MPD, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Components of the solutions
IDNameCrystal-IDSol-ID
1calcium chloride11
2sodium acetate11
3MPD11
4calcium chloride12
5sodium acetate12
6MPD12

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2007
RadiationMonochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 102079 / % possible obs: 97.2 % / Observed criterion σ(F): 16.17 / Observed criterion σ(I): 4.15 / Redundancy: 7.1 % / Rsym value: 0.103
Reflection shellResolution: 2.29→2.38 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 4.15 / Num. unique all: 9855 / Rsym value: 0.462 / % possible all: 95.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HOI

2hoi


Resolution: 2.29→49.57 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.133 / SU ML: 0.127 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.253 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22218 5105 5 %RANDOM
Rwork0.19277 ---
obs0.19426 96905 97.11 %-
all-105050 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.648 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.195 Å0.253 Å
Refinement stepCycle: LAST / Resolution: 2.29→49.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10200 2844 6 343 13393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02113556
X-RAY DIFFRACTIONr_angle_refined_deg1.6192.2218882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.15251284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.81622.222504
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.619151876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.35215140
X-RAY DIFFRACTIONr_chiral_restr0.0920.22096
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029312
X-RAY DIFFRACTIONr_mcbond_it0.7261.56384
X-RAY DIFFRACTIONr_mcangle_it1.446210216
X-RAY DIFFRACTIONr_scbond_it2.22937172
X-RAY DIFFRACTIONr_scangle_it3.5284.58666
LS refinement shellResolution: 2.29→2.353 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 369 -
Rwork0.238 6850 -
obs--94.03 %

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