[English] 日本語
Yorodumi
- PDB-1pvp: BASIS FOR A SWITCH IN SUBSTRATE SPECIFICITY: CRYSTAL STRUCTURE OF... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pvp
TitleBASIS FOR A SWITCH IN SUBSTRATE SPECIFICITY: CRYSTAL STRUCTURE OF SELECTED VARIANT OF CRE SITE-SPECIFIC RECOMBINASE, ALSHG BOUND TO THE ENGINEERED RECOGNITION SITE LOXM7
Components
  • (34-MER) x 2
  • Recombinase cre
KeywordsRECOMBINATION/DNA / Cre / recombinase / DNA / CRE-LOXP RECOMBINATION / RECOMBINATION-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 speciesEscherichia phage P1 (virus)
Escherichia virus P1
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.35 Å
AuthorsBaldwin, E.P. / Martin, S.S. / Abel, J. / Gelato, K.A. / Kim, H. / Schultz, P.G. / Santoro, S.W.
Citation
Journal: Chem.Biol. / Year: 2003
Title: A specificity switch in selected cre recombinase variants is mediated by macromolecular plasticity and water.
Authors: Baldwin, E.P. / Martin, S.S. / Abel, J. / Gelato, K.A. / Kim, H. / Schultz, P.G. / Santoro, S.W.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Directed evolution of the site specificity of Cre recombinase.
Authors: Santoro, S.W. / Schultz, P.G.
#2: 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.
#3: 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.
History
DepositionJun 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2012Group: Other
Revision 2.0Apr 7, 2021Group: Advisory / Database references ...Advisory / Database references / Non-polymer description / Source and taxonomy / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_src_gen / pdbx_entity_src_syn / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.entity_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.mon_id / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_ref_seq_dif.pdbx_pdb_strand_id / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_name / _struct_ref_seq_dif.pdbx_seq_db_seq_num / _struct_ref_seq_dif.seq_num
Revision 2.1Aug 16, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: 34-MER
D: 34-MER
A: Recombinase cre
B: Recombinase cre


Theoretical massNumber of molelcules
Total (without water)99,4304
Polymers99,4304
Non-polymers00
Water4,612256
1
C: 34-MER
D: 34-MER
A: Recombinase cre
B: Recombinase cre

C: 34-MER
D: 34-MER
A: Recombinase cre
B: Recombinase cre


Theoretical massNumber of molelcules
Total (without water)198,8618
Polymers198,8618
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)107.780, 121.470, 180.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe second part of the tetrameric biological assembly is generated by the two fold axis: x, -y+1, -z+1.

-
Components

#1: DNA chain 34-MER


Mass: 10469.798 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: TOP STRAND OF LOXM7 ENGINEERED DNA SUBSTRATE (LOXP(C7/G28,T8/A27,A9/T26)
Source: (synth.) Escherichia virus P1 / References: GenBank: M10145
#2: DNA chain 34-MER


Mass: 10438.787 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: BOTTOM STRAND OF LOXM7 ENGINEERED DNA SUBSTRATE (LOXP(C7/G28,T8/A27,A9/T26)
Source: (synth.) Escherichia virus P1 / References: GenBank: M10494
#3: Protein Recombinase cre


Mass: 39260.875 Da / Num. of mol.: 2 / Mutation: I174A,T258L,R259S,E262H,E266G
Source method: isolated from a genetically manipulated source
Details: Cre site-specific recombinase mutant (I174A, T258L, R259S, E262H, E266G)
Source: (gene. exp.) Escherichia phage P1 (virus) / Genus: P1-like viruses / Gene: cre / 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.: 256 / 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: 58.36 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.75
Details: Sodium Acetate, Calcium Chloride, 2,4-methylpentanediol, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Components of the solutions
IDNameCrystal-IDSol-ID
1Sodium Acetate11
2Calcium Chloride11
32,4-methylpentanediol11
4H2O11
5Sodium Acetate12
6Calcium Chloride12
72,4-methylpentanediol12
8H2O12
Crystal grow
*PLUS
Temperature: 21-25 ℃ / Method: vapor diffusion / Details: Martin, S.S., (2002) J.Mol.Biol., 319, 107. / PH range low: 5.5 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
135-45 mg/mlprotein1drop
225 mMsodium acetate1reservoir
340 mM1reservoirNaCl
420 mM1reservoirCaCl2
522.5 %ALSHG/LoxM71reservoirpH5.75
61
71
81

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 13, 2002
RadiationMonochromator: DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.35→81 Å / Num. obs: 46927 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 22.7
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 4 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 3.7 / Num. unique all: 4289 / % possible all: 88
Reflection
*PLUS
% possible obs: 95 %
Reflection shell
*PLUS
% possible obs: 88 %

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
TNTrefinement
TNTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1KBU

1kbu


Resolution: 2.35→5 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1916 -RANDOM
Rwork0.232 ---
obs0.232 40013 95 %-
all-44309 --
Refine analyzeLuzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.42 Å
Refinement stepCycle: LAST / Resolution: 2.35→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5053 1348 0 256 6657
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.006
X-RAY DIFFRACTIONt_angle_deg1.2
Refinement
*PLUS
Lowest resolution: 5 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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