[English] 日本語
Yorodumi
- PDB-7q6p: Crystal Structure of bacterial Prolyl Peptidyl Isomerase with 5,5... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7q6p
TitleCrystal Structure of bacterial Prolyl Peptidyl Isomerase with 5,5'-difluoroleucines
ComponentsPeptidyl-prolyl cis-trans isomerase B
KeywordsISOMERASE / prolyl peptidyl isomerase / difluoroleucine
Function / homology
Function and homology information


: / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cytosol
Similarity search - Function
Cyclophilin-type peptidyl-prolyl cis-trans isomerase, E. coli cyclophilin A-like / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsTars, K. / Jaudzems, K. / Recacha, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal Structure of bacterial Prolyl Peptidyl Isomerase with 5,5'-difluoroleucines
Authors: Tars, K. / Jaudzems, K. / Recacha, R.
History
DepositionNov 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase B
B: Peptidyl-prolyl cis-trans isomerase B
C: Peptidyl-prolyl cis-trans isomerase B
D: Peptidyl-prolyl cis-trans isomerase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0217
Polymers76,7334
Non-polymers2883
Water8,809489
1
A: Peptidyl-prolyl cis-trans isomerase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2792
Polymers19,1831
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-prolyl cis-trans isomerase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2792
Polymers19,1831
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Peptidyl-prolyl cis-trans isomerase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2792
Polymers19,1831
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Peptidyl-prolyl cis-trans isomerase B


Theoretical massNumber of molelcules
Total (without water)19,1831
Polymers19,1831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.061, 83.460, 122.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Peptidyl-prolyl cis-trans isomerase B / PPIase B / Rotamase B


Mass: 19183.238 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ppiB, b0525, JW0514 / Production host: Escherichia coli (E. coli) / References: UniProt: P23869, peptidylprolyl isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris (pH 8.5), 0.2 M sodium acetate, 30% (w/v) polyethylene glycol 3400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→61 Å / Num. obs: 72608 / % possible obs: 98.8 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 5.8
Reflection shellResolution: 1.82→1.92 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 26704 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NUL

2nul


Resolution: 1.82→57.4 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2786 3596 4.96 %
Rwork0.2393 68943 -
obs0.2413 72539 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.77 Å2 / Biso mean: 25.7983 Å2 / Biso min: 9.21 Å2
Refinement stepCycle: final / Resolution: 1.82→57.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5040 0 15 489 5544
Biso mean--36.24 28.26 -
Num. residues----641
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.82-1.840.41761150.36592426254191
1.84-1.870.38951590.34372473263294
1.87-1.890.34481460.33492521266795
1.89-1.920.39461220.3092615273797
1.92-1.950.32111300.285926542784100
1.95-1.990.30891290.278626802809100
1.99-2.020.32451370.281626392776100
2.02-2.060.33381370.271926862823100
2.06-2.10.34321470.250526372784100
2.1-2.140.28461310.248726642795100
2.14-2.190.26991410.242226712812100
2.19-2.240.26871240.239126662790100
2.24-2.290.27731010.230827022803100
2.29-2.350.3091520.237726722824100
2.35-2.420.31251490.2426442793100
2.42-2.50.31021210.23562701282299
2.5-2.590.26671460.239526672813100
2.59-2.690.28211480.24162665281399
2.69-2.820.30271570.242426752832100
2.82-2.970.28271090.24442703281299
2.97-3.150.28141510.24242679283099
3.15-3.390.27051630.22932654281799
3.39-3.740.2351680.21022661282999
3.74-4.280.23491340.2052702283698
4.28-5.390.24041480.19512694284297
5.39-57.40.22981310.23832792292395
Refinement TLS params.Method: refined / Origin x: 17.956 Å / Origin y: 38.664 Å / Origin z: 15.2629 Å
111213212223313233
T0.1289 Å2-0.0334 Å2-0.0009 Å2-0.1333 Å2-0.0082 Å2--0.0775 Å2
L0.4284 °2-0.0085 °2-0.0097 °2-0.7829 °2-0.1676 °2--0.2806 °2
S-0.0027 Å °-0.0649 Å °0.0257 Å °0.0703 Å °0.0238 Å °-0.0722 Å °-0.0603 Å °0.0186 Å °-0.0221 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 169
2X-RAY DIFFRACTION1allB1 - 168
3X-RAY DIFFRACTION1allC1 - 170
4X-RAY DIFFRACTION1allD1 - 162
5X-RAY DIFFRACTION1allG1 - 3
6X-RAY DIFFRACTION1allS1 - 610

+
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