[English] 日本語
Yorodumi
- PDB-1ma7: Crystal structure of Cre site-specific recombinase complexed with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ma7
TitleCrystal structure of Cre site-specific recombinase complexed with a mutant DNA substrate, LoxP-A8/T27
Components
  • (LOXP) x 2
  • CRE RECOMBINASE
KeywordsHYDROLASE / LIGASE/DNA / Cre-Lox site-specific recombination / Specificity of protein-DNA interactions / protein-DNA complex / Tyrosine recombinase / LIGASE-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 / Phage integrase family / Core-binding (CB) domain / Core-binding (CB) domain profile. / Integrase, catalytic domain / Tyrosine recombinase domain profile. / Integrase/recombinase, N-terminal ...: / Intergrase catalytic core / Tyrosine recombinase, N-terminal domain / hpI Integrase; Chain A / Phage integrase family / Core-binding (CB) domain / Core-binding (CB) domain profile. / Integrase, catalytic domain / Tyrosine recombinase domain profile. / 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
DNA / DNA (> 10) / Recombinase cre
Similarity search - Component
Biological speciesEnterobacteria phage P1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsMartin, S.S. / Chu, V.C. / Baldwin, E.P.
Citation
Journal: Biochemistry / Year: 2003
Title: Modulation of the active complex assembly and turnover rate by protein-DNA interactions in Cre-LoxP recombination
Authors: Martin, S.S. / Chu, V.C. / Baldwin, E.P.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: The order of strand exchanges in Cre-LoxP recombination and its basis suggested by the crystal structure of a Cre-LoxP Holliday junction complex
Authors: Martin, S.S. / Pulido, E. / Chu, V.C. / Lechner, T.S. / Baldwin, E.P.
#2: Journal: Nature / Year: 1997
Title: Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse
Authors: Guo, F. / Gopaul, D. / van Duyne, G.D.
#3: Journal: Annu.Rev.Biophys.Biomol.Struct. / Year: 2001
Title: A structural view of cre-loxp site-specific recombination
Authors: van Duyne, G.D.
History
DepositionAug 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: LOXP
D: LOXP
A: CRE RECOMBINASE
B: CRE RECOMBINASE


Theoretical massNumber of molelcules
Total (without water)99,7574
Polymers99,7574
Non-polymers00
Water5,098283
1
C: LOXP
D: LOXP
A: CRE RECOMBINASE
B: CRE RECOMBINASE

C: LOXP
D: LOXP
A: CRE RECOMBINASE
B: CRE RECOMBINASE


Theoretical massNumber of molelcules
Total (without water)199,5138
Polymers199,5138
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)107.540, 122.240, 180.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsTHE SECOND HALF OF THE TETRAMERIC BIOLOGICAL ASSEMBLY IS GENERATED BY THE CRYSTALLOGRAPHIC TWO-FOLD AXIS: X, -Y, -Z, AND A TRANSLATION OF 0, 1, 1.

-
Components

#1: DNA chain LOXP


Mass: 10469.798 Da / Num. of mol.: 1 / Fragment: UPPER STRAND / Mutation: C8A,G27T / Source method: obtained synthetically
#2: DNA chain LOXP


Mass: 10438.788 Da / Num. of mol.: 1 / Fragment: LOWER STRAND / Mutation: C8A,G27T / Source method: obtained synthetically
#3: Protein CRE RECOMBINASE / CRE SITE-SPECIFIC RECOMBINASE


Mass: 39424.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P1 (virus) / Genus: P1-like viruses / Plasmid: pET28b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06956
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.24 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.25
Details: 2,4-methylpentanediol, sodium acetate, calcium chloride, pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Components of the solutions
IDNameCrystal-IDSol-ID
12,4-methylpentanediol11
2sodium acetate11
3CaCl211
4CaCl212
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
124-28 %MPD1reservoirpH5.25
225 mM1reservoir
330 mM1reservoirCaCl2
440 mM1reservoirNaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 28, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 54160 / Num. obs: 51997 / % possible obs: 97 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 21
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 3.8 / Num. unique all: 3473 / % possible all: 97.7
Reflection
*PLUS
% possible obs: 96.5 % / Num. measured all: 168540
Reflection shell
*PLUS
% possible obs: 97.7 % / Num. unique obs: 3473

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
TNTrefinement
TNTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1KBU with mutated basepairs, side chains Arg259, Asp262, and Asp266 omitted

1kbu


Resolution: 2.3→5 Å
Isotropic thermal model: No B value correction in scaling Fcalc to Fobs during refinement. Final R calculation with K=1.2137 B=0.44240 (TNT)
σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 2620 -RANDOM
Rwork0.239 ---
all-51364 --
obs-51364 97 %-
Displacement parametersBiso mean: 57 Å2
Refine analyzeLuzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.56 Å
Refinement stepCycle: LAST / Resolution: 2.3→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5069 1347 0 283 6699
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.006
X-RAY DIFFRACTIONt_angle_deg1.174
LS refinement shellResolution: 2.3→2.38 Å /
Num. reflection% reflection
Rfree225 -
obs-92 %
Refinement
*PLUS
Num. reflection obs: 43981 / Num. reflection Rfree: 2383 / Rfactor Rfree: 0.29 / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 1.19
LS refinement shell
*PLUS
Rfactor Rfree: 0.363 / Rfactor Rwork: 0.39

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more