[English] 日本語
Yorodumi
- PDB-2pv1: Crystallographic Structure of SurA first peptidyl-prolyl isomeras... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pv1
TitleCrystallographic Structure of SurA first peptidyl-prolyl isomerase domain complexed with peptide WEYIPNV
Components
  • Chaperone surA
  • Glycosyl transferase, group 1
KeywordsISOMERASE / Survival protein A / Peptidyl-prolyl cis-trans isomerase domain / Complex
Function / homology
Function and homology information


: / maintenance of unfolded protein / Gram-negative-bacterium-type cell outer membrane assembly / glycosyltransferase activity / : / peptide binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / unfolded protein binding / protein folding ...: / maintenance of unfolded protein / Gram-negative-bacterium-type cell outer membrane assembly / glycosyltransferase activity / : / peptide binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / unfolded protein binding / protein folding / outer membrane-bounded periplasmic space / protein stabilization
Similarity search - Function
Peptidyl-prolyl isomerase SurA / SurA N-terminal / SurA N-terminal domain / : / PPIC-type PPIASE domain / Trigger factor/SurA domain superfamily / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. ...Peptidyl-prolyl isomerase SurA / SurA N-terminal / SurA N-terminal domain / : / PPIC-type PPIASE domain / Trigger factor/SurA domain superfamily / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Chaperone SurA / Glycosyl transferase, group 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsXu, X. / McKay, D.B.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: The Periplasmic Bacterial Molecular Chaperone SurA Adapts its Structure to Bind Peptides in Different Conformations to Assert a Sequence Preference for Aromatic Residues.
Authors: Xu, X. / Wang, S. / Hu, Y.X. / McKay, D.B.
#1: Journal: Structure / Year: 2002
Title: Crystallographic structure of SurA, a molecular chaperone that facilitates folding of outer membrane porins
Authors: Bitto, E. / McKay, D.B.
History
DepositionMay 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chaperone surA
B: Glycosyl transferase, group 1


Theoretical massNumber of molelcules
Total (without water)11,8972
Polymers11,8972
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.886, 98.820, 41.053
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

-
Components

#1: Protein Chaperone surA / Peptidyl-prolyl cis-trans isomerase surA / PPIase surA / Rotamase surA / Survival protein A


Mass: 10977.320 Da / Num. of mol.: 1 / Fragment: PpiC 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 EMG2 / Gene: surA / Plasmid: pTYB1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0ABZ6, peptidylprolyl isomerase
#2: Protein/peptide Glycosyl transferase, group 1


Mass: 920.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: Q2RHX9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25~28% polyethylene glycol monomethylether 5000, 0.2 M ammonium sulfate, 0.1 M MES buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.29→50 Å / Num. obs: 26586 / % possible obs: 98.4 % / Redundancy: 4.5 % / Rsym value: 0.034 / Χ2: 2.508 / Net I/σ(I): 39.7
Reflection shellResolution: 1.29→1.34 Å / Redundancy: 3.5 % / Num. unique all: 2504 / Rsym value: 0.126 / Χ2: 2.009 / % possible all: 93.8

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M5Y

1m5y


Resolution: 1.3→41.05 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2552 9.7 %Random
Rwork0.226 ---
obs-25854 97.9 %-
Solvent computationBsol: 44.38 Å2
Displacement parametersBiso mean: 19.142 Å2
Baniso -1Baniso -2Baniso -3
1--0.554 Å20 Å20 Å2
2---0.67 Å20 Å2
3---1.225 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.3→41.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms839 0 0 132 971
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.58
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d1.06
LS refinement shellResolution: 1.3→1.38 Å / Rfactor Rfree error: 0.014
RfactorNum. reflection% reflection
Rfree0.293 419 -
Rwork0.25 --
obs-3770 96.7 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

+
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