[English] 日本語
Yorodumi
- PDB-7rjj: Crystal Structure of the Peptidoglycan Binding Domain of the Oute... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rjj
TitleCrystal Structure of the Peptidoglycan Binding Domain of the Outer Membrane Protein (OmpA) from Klebsiella pneumoniae with bound D-alanine
ComponentsOmpA family protein
KeywordsPEPTIDE BINDING PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Outer Membrane Protein
Function / homologyOuter membrane protein, bacterial / : / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / membrane / D-ALANINE / OmpA family protein
Function and homology information
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.88 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Microbiol Resour Announc / Year: 2023
Title: A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae.
Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / ...Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / Anderson, W.F. / Hauser, A.R. / Joachimiak, A. / Satchell, K.J.F.
History
DepositionJul 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: OmpA family protein
B: OmpA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4666
Polymers28,2172
Non-polymers2494
Water3,189177
1
A: OmpA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2333
Polymers14,1091
Non-polymers1252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: OmpA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2333
Polymers14,1091
Non-polymers1252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.887, 41.887, 267.934
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein OmpA family protein


Mass: 14108.505 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Gene: C4Z38_016670, EJ893_12145, I5002_15200, JMY88_11465 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl-21 Magic / References: UniProt: A0A422WJQ0
#2: Chemical ChemComp-DAL / D-ALANINE


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 9.4 mg/ml, 0.15M Sodium chloride, 0.01M Tris pH 8.3; Screen: PEG's II (C4), 0.2M Magnesium chloride, 0.1M MES pH 6.5, 10% (w/v) PEG4000; Cryo: 0.2M Magnesium chloride, 0.1M MES pH 6.5, 25% (w/v) PEG4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 3, 2021 / Details: Be
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.88→30 Å / Num. obs: 21507 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 11.4 % / Biso Wilson estimate: 17.3 Å2 / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.023 / Rrim(I) all: 0.076 / Rsym value: 0.073 / Χ2: 0.837 / Net I/σ(I): 31.5
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 10.5 % / Rmerge(I) obs: 1.358 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1084 / CC1/2: 0.626 / CC star: 0.878 / Rpim(I) all: 0.439 / Rsym value: 1.358 / Χ2: 0.765 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.88→28.16 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.924 / SU B: 7.379 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2284 932 4.7 %RANDOM
Rwork0.2009 ---
obs0.2022 19054 93.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.21 Å2 / Biso mean: 22.826 Å2 / Biso min: 6.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 1.88→28.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1848 0 14 178 2040
Biso mean--28.27 30.68 -
Num. residues----240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131919
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171859
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.6542602
X-RAY DIFFRACTIONr_angle_other_deg0.3611.594286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4975244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.66320.6100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.14815314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3031520
X-RAY DIFFRACTIONr_chiral_restr0.0590.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0540.022160
X-RAY DIFFRACTIONr_gen_planes_other0.0480.02424
LS refinement shellResolution: 1.882→1.93 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 26 -
Rwork0.274 562 -
all-588 -
obs--37.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9179-0.71090.54964.0068-0.12823.75630.04870.30950.2152-0.6018-0.0071-0.0546-0.2351-0.0345-0.04160.1927-0.00050.02440.06270.0580.0975-3.6928.19-13.835
25.2685-5.1188-1.16349.01342.5471.7181-0.1522-0.1049-0.04080.23420.0570.2839-0.0026-0.22410.09520.12940.03680.0330.07660.03930.1101-7.138.948-1.611
31.776-0.04720.47145.07590.09713.6729-0.02270.07810.086-0.10820.12120.20810.1953-0.4666-0.09840.11180.00170.01150.110.07550.0921-7.8842.585-7.542
43.1624-1.87680.66798.32981.12381.4937-0.1588-0.06560.3305-0.24490.1979-0.3512-0.1697-0.0104-0.03910.15520.03410.04770.02870.03830.1439-2.18313.563-5.835
52.86381.4252-0.85934.0973-0.82283.68570.0704-0.3488-0.29320.5767-0.0211-0.01370.2928-0.119-0.04930.20850.0032-0.02230.06560.05820.1089-4.21-8.55712.53
64.16514.02490.61698.17771.80791.2699-0.07630.0353-0.0204-0.16040.06440.1150.0331-0.18010.01180.1459-0.0404-0.01590.06910.0510.0994-5.621-8.0781.195
71.7280.1886-0.60485.22980.50734.45950.0016-0.099-0.1030.09320.08230.1833-0.1389-0.5156-0.08380.10270.0034-0.01620.11620.0820.1037-8.14-2.9746.049
83.07231.8726-0.56488.99291.10981.4018-0.18350.0965-0.35180.18980.2565-0.39170.1223-0.0129-0.07310.1419-0.0361-0.04220.03910.03850.1418-2.166-13.5574.547
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A428 - 464
2X-RAY DIFFRACTION2A465 - 487
3X-RAY DIFFRACTION3A488 - 518
4X-RAY DIFFRACTION4A519 - 547
5X-RAY DIFFRACTION5B428 - 463
6X-RAY DIFFRACTION6B464 - 486
7X-RAY DIFFRACTION7B487 - 518
8X-RAY DIFFRACTION8B519 - 547

+
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