[English] 日本語
Yorodumi
- PDB-8vbw: Structure of the monofunctional Staphylococcus aureus PBP1 in its... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vbw
TitleStructure of the monofunctional Staphylococcus aureus PBP1 in its beta-lactam (Ertapenem) inhibited form
ComponentsPenicillin-binding protein 1
KeywordsHYDROLASE/INHIBITOR / ANTIBIOTIC / Penicillin Binding Protein 1 / Peptidoglycan Transpeptidase domain / Pedestal domain / MEMBRANE PROTEIN / HYDROLASE-INHIBITOR / ANTIBIOTIC complex
Function / homology
Function and homology information


penicillin binding / cell wall organization / membrane
Similarity search - Function
PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-1RG / Penicillin-binding protein 1
Similarity search - Component
Biological speciesStaphylococcaceae bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBon, C.G. / Lee, J. / Caveney, N.A. / Strynadka, N.C.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: J.Struct.Biol. / Year: 2024
Title: Structural and kinetic analysis of the monofunctional Staphylococcus aureus PBP1.
Authors: Bon, C.G. / Grigg, J.C. / Lee, J. / Robb, C.S. / Caveney, N.A. / Eltis, L.D. / Strynadka, N.C.J.
History
DepositionDec 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Penicillin-binding protein 1
B: Penicillin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,2444
Polymers133,2892
Non-polymers9552
Water5,657314
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)183.399, 72.717, 90.111
Angle α, β, γ (deg.)90.00, 103.47, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1052-

HOH

-
Components

#1: Protein Penicillin-binding protein 1


Mass: 66644.258 Da / Num. of mol.: 2 / Fragment: residues 39-608
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcaceae bacterium (bacteria) / Gene: SAOUHSC_01145 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q2FZ94
#2: Chemical ChemComp-1RG / (4R,5S)-3-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid / ERTAPENEM, bound form PRE-ISOMERIZED / Ertapenem


Mass: 477.531 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H27N3O7S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antibiotic*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.19 Å3/Da / Density % sol: 43.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.18M ammonium citrate, 22% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.5211 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5211 Å / Relative weight: 1
ReflectionResolution: 2.3→46.03 Å / Num. obs: 51028 / % possible obs: 99.1 % / Redundancy: 4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.062 / Net I/σ(I): 11.7
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 4.1 % / Rmerge(I) obs: 2.687 / Num. unique obs: 4391 / CC1/2: 0.429 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→46.03 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2325 2449 4.84 %
Rwork0.1925 --
obs0.1945 50582 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→46.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7746 0 66 314 8126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087984
X-RAY DIFFRACTIONf_angle_d0.90910796
X-RAY DIFFRACTIONf_dihedral_angle_d7.511127
X-RAY DIFFRACTIONf_chiral_restr0.0531150
X-RAY DIFFRACTIONf_plane_restr0.0071422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.71341280.76882407X-RAY DIFFRACTION84
2.35-2.40.43591360.44822839X-RAY DIFFRACTION99
2.4-2.450.35571480.31852828X-RAY DIFFRACTION99
2.45-2.520.35671610.26492845X-RAY DIFFRACTION99
2.52-2.580.29991400.23222805X-RAY DIFFRACTION99
2.58-2.660.24741410.22852828X-RAY DIFFRACTION99
2.66-2.740.26511430.22732823X-RAY DIFFRACTION98
2.75-2.840.28671380.23672834X-RAY DIFFRACTION100
2.84-2.960.30111500.26142878X-RAY DIFFRACTION100
2.96-3.090.29661250.23082901X-RAY DIFFRACTION100
3.09-3.250.24831570.19742841X-RAY DIFFRACTION100
3.25-3.460.26211520.1932847X-RAY DIFFRACTION99
3.46-3.730.22021300.18312851X-RAY DIFFRACTION98
3.73-4.10.19561450.15142852X-RAY DIFFRACTION98
4.1-4.690.16571430.12392883X-RAY DIFFRACTION100
4.69-5.910.14771580.13722903X-RAY DIFFRACTION100
5.91-46.030.18821540.16132968X-RAY DIFFRACTION99
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)
11.8449-0.8358-0.53090.7920.84841.21620.05690.03070.1262-0.42920.4688-0.6425-0.21120.6735-0.42070.3923-0.10250.14690.6158-0.1820.706441.1144-29.3-10.8493
20.8201-0.1688-0.31440.7320.19671.5817-0.0586-0.11190.04640.14980.0055-0.0566-0.0322-0.06840.05080.3339-0.0024-0.06580.27420.00190.294310.4238-19.830720.1421
31.5099-0.3202-0.42941.1530.02092.554-0.0065-0.17870.02710.32870.0569-0.0219-0.1520.2038-0.01890.3781-0.0077-0.12640.332-0.02790.374719.6956-12.398726.9915
41.74080.82711.43491.0281.39412.6662-0.1346-0.182-0.08330.25570.3087-0.1988-0.05020.6274-0.17710.48430.0228-0.09060.60590.00130.377732.7599-43.175827.4336
50.51720.38490.76630.64561.1162.1077-0.0103-0.1788-0.03910.2630.1408-0.34730.05350.3061-0.15120.53250.051-0.12550.52070.02560.462831.7249-44.658324.1826
61.2371.36460.92423.58820.65971.47090.0961-0.248-0.00540.3503-0.15540.2020.1885-0.13620.04410.33890.02350.00770.3650.01550.373915.4446-45.293211.4098
71.67580.43590.10241.20090.20161.673-0.19820.3499-0.1812-0.32580.1328-0.183-0.00910.0370.05230.3806-0.04070.09890.3308-0.04690.353620.9959-51.891-20.8488
81.41360.051-0.57960.78020.33981.9275-0.1630.1845-0.2697-0.13630.0696-0.19930.10350.08670.0840.3301-0.02820.06370.3071-0.04550.404417.4616-59.2629-14.8912
92.98741.2605-0.98352.4055-1.03232.97-0.19230.064-0.5684-0.38020.0667-0.58320.51180.44780.08970.36840.04090.08340.3707-0.10940.580230.5872-61.8857-12.2641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 61 through 177 )
2X-RAY DIFFRACTION2chain 'A' and (resid 178 through 494 )
3X-RAY DIFFRACTION3chain 'A' and (resid 495 through 590 )
4X-RAY DIFFRACTION4chain 'B' and (resid 61 through 129 )
5X-RAY DIFFRACTION5chain 'B' and (resid 130 through 182 )
6X-RAY DIFFRACTION6chain 'B' and (resid 183 through 245 )
7X-RAY DIFFRACTION7chain 'B' and (resid 246 through 430 )
8X-RAY DIFFRACTION8chain 'B' and (resid 431 through 548 )
9X-RAY DIFFRACTION9chain 'B' and (resid 549 through 590 )

+
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