[English] 日本語
Yorodumi
- PDB-5w2z: Crystal structure of mutant CJ YCEI protein (CJ-N48C) with 5-merc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5w2z
TitleCrystal structure of mutant CJ YCEI protein (CJ-N48C) with 5-mercapto-2-nitrobenzoic acid guest structure
ComponentsPutative periplasmic protein
KeywordsUNKNOWN FUNCTION / nanotechnology nanoporous
Function / homology
Function and homology information


Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like superfamily / YceI-like domain / YceI-like domain / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
5-MERCAPTO-2-NITRO-BENZOIC ACID / Unknown ligand / Periplasmic protein
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHuber, T.R. / Snow, C.D.
CitationJournal: Bioconjug. Chem. / Year: 2018
Title: Installing Guest Molecules at Specific Sites within Scaffold Protein Crystals.
Authors: Huber, T.R. / McPherson, E.C. / Keating, C.E. / Snow, C.D.
History
DepositionJun 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 4, 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8635
Polymers20,1891
Non-polymers6744
Water37821
1
A: Putative periplasmic protein
hetero molecules

A: Putative periplasmic protein
hetero molecules

A: Putative periplasmic protein
hetero molecules

A: Putative periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,45120
Polymers80,7554
Non-polymers2,69516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
crystal symmetry operation9_556-x,-x+y,-z+11
crystal symmetry operation12_546x,x-y-1,-z+11
Buried area23150 Å2
ΔGint-207 kcal/mol
Surface area32420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.858, 179.858, 50.623
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-415-

HOH

-
Components

#1: Protein Putative periplasmic protein


Mass: 20188.832 Da / Num. of mol.: 1 / Mutation: N48C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (Campylobacter)
Strain: ATCC 700819 / NCTC 11168 / Gene: Cj0420 / Plasmid: pSB3 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q0PB90
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Mass: 282.547 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MNB / 5-MERCAPTO-2-NITRO-BENZOIC ACID


Mass: 199.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5NO4S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalMosaicity: 0.24 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 3.2 M Ammonium Sulfate, 0.1 M Bis-Tris

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Apr 4, 2016
RadiationMonochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→38.384 Å / Num. all: 12372 / Num. obs: 12372 / % possible obs: 99.9 % / Redundancy: 20.6 % / Rpim(I) all: 0.049 / Rrim(I) all: 0.221 / Rsym value: 0.216 / Net I/av σ(I): 2.9 / Net I/σ(I): 11.2 / Num. measured all: 255445
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
2.8-2.9520.94.7210.11.054.8384.72199.8
2.95-3.1321.42.160.30.4742.2122.1699.9
3.13-3.3521.60.7760.90.170.7940.776100
3.35-3.6121.20.41.70.0880.410.4100
3.61-3.9621.10.24330.0540.2490.243100
3.96-4.4320.40.164.30.0360.1640.16100
4.43-5.1119.70.1265.20.0290.1290.126100
5.11-6.2619.90.1155.60.0270.1180.115100
6.26-8.8519.60.0926.80.0210.0950.092100
8.85-38.38416.80.0658.60.0160.0670.06598.8

-
Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDS20161101data reduction
REFMAC5.8.0158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W2X

5w2x


Resolution: 2.8→38.38 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 11.26 / SU ML: 0.198 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.23 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 616 5 %RANDOM
Rwork0.2032 ---
obs0.2048 11730 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 171.31 Å2 / Biso mean: 78.318 Å2 / Biso min: 48.76 Å2
Baniso -1Baniso -2Baniso -3
1-2.25 Å21.13 Å20 Å2
2--2.25 Å2-0 Å2
3----7.31 Å2
Refinement stepCycle: final / Resolution: 2.8→38.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1315 0 40 21 1376
Biso mean--111.62 73.96 -
Num. residues----171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191371
X-RAY DIFFRACTIONr_angle_refined_deg1.8841.9831835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1875170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.31426.31657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.52715253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.291152
X-RAY DIFFRACTIONr_chiral_restr0.1120.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02987
LS refinement shellResolution: 2.8→2.872 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 40 -
Rwork0.344 836 -
all-876 -
obs--99.77 %

+
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