[English] 日本語
Yorodumi
- PDB-7rcz: Crystal structure of C. difficile SpoVD in complex with ampicillin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rcz
TitleCrystal structure of C. difficile SpoVD in complex with ampicillin
ComponentsStage V sporulation protein D (Sporulation specific penicillin-binding protein)
KeywordsPEPTIDE BINDING PROTEIN / Peptidoglycan / PBP / PBP2 / cell wall / transpeptidase / b-lactam / gram-positive / spore / sporulation
Function / homologyDI(HYDROXYETHYL)ETHER / N-PROPANOL / Chem-ZZ7 / :
Function and homology information
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSacco, M. / Chen, Y.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI161762
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133617 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128624 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM008804 United States
CitationJournal: Nat Commun / Year: 2022
Title: A unique class of Zn 2+ -binding serine-based PBPs underlies cephalosporin resistance and sporogenesis in Clostridioides difficile.
Authors: Sacco, M.D. / Wang, S. / Adapa, S.R. / Zhang, X. / Lewandowski, E.M. / Gongora, M.V. / Keramisanou, D. / Atlas, Z.D. / Townsend, J.A. / Gatdula, J.R. / Morgan, R.T. / Hammond, L.R. / Marty, ...Authors: Sacco, M.D. / Wang, S. / Adapa, S.R. / Zhang, X. / Lewandowski, E.M. / Gongora, M.V. / Keramisanou, D. / Atlas, Z.D. / Townsend, J.A. / Gatdula, J.R. / Morgan, R.T. / Hammond, L.R. / Marty, M.T. / Wang, J. / Eswara, P.J. / Gelis, I. / Jiang, R.H.Y. / Sun, X. / Chen, Y.
History
DepositionJul 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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
Revision 1.2Oct 18, 2023Group: 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: Stage V sporulation protein D (Sporulation specific penicillin-binding protein)
B: Stage V sporulation protein D (Sporulation specific penicillin-binding protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,67320
Polymers121,2042
Non-polymers2,46918
Water5,729318
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-104 kcal/mol
Surface area43180 Å2
Unit cell
Length a, b, c (Å)76.640, 95.620, 176.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Stage V sporulation protein D (Sporulation specific penicillin-binding protein)


Mass: 60601.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (strain R20291) (bacteria)
Strain: R20291 / Gene: spoVD, CDR20291_2544
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: C9YPN0

-
Non-polymers , 7 types, 336 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL / Propan-1-ol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-ZZ7 / (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / AMPICILLIN (open form)


Mass: 367.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H21N3O5S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 15 % PEG 3350, 0.2 M AmSO4, 10 % PropOH, 0.1 M Na Citrate pH 5.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.2→49.58 Å / Num. obs: 62415 / % possible obs: 94.6 % / Redundancy: 3.5 % / CC1/2: 0.985 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.063 / Rrim(I) all: 0.123 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.253.40.51511944720.8590.2990.5862.596.8
10.08-49.533.70.08222886230.9590.0490.09714.281.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UN1

6un1


Resolution: 2.2→49.58 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.018 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.247 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2252 3192 5.1 %RANDOM
Rwork0.1871 ---
obs0.1891 59183 93.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 142.75 Å2 / Biso mean: 41.966 Å2 / Biso min: 14.08 Å2
Baniso -1Baniso -2Baniso -3
1--3.23 Å20 Å2-0 Å2
2--1.2 Å20 Å2
3---2.03 Å2
Refinement stepCycle: final / Resolution: 2.2→49.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7855 0 141 319 8315
Biso mean--75.28 37.8 -
Num. residues----1014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138278
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177783
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.66211201
X-RAY DIFFRACTIONr_angle_other_deg1.2161.59618174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.12351021
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.91823.883358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.096151470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.131530
X-RAY DIFFRACTIONr_chiral_restr0.0670.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028992
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021546
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 266 -
Rwork0.246 4421 -
all-4687 -
obs--96.22 %

+
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