[English] 日本語
Yorodumi
- PDB-6dz8: Crystal structure of S. aureus penicillin binding protein 4 (PBP4... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dz8
TitleCrystal structure of S. aureus penicillin binding protein 4 (PBP4) mutant (S75C)
ComponentsPenicillin-binding protein 4
KeywordsHYDROLASE / Penicillin binding protein
Function / homology
Function and homology information


serine-type D-Ala-D-Ala carboxypeptidase activity / beta-lactam antibiotic catabolic process / peptidoglycan biosynthetic process / cell wall organization / beta-lactamase activity / regulation of cell shape / response to antibiotic / proteolysis / membrane
Similarity search - Function
Penicillin-binding protein 4, C-terminal domain / Penicillin-binding protein 4, C-terminal domain / Penicillin-binding protein 4, C-terminal domain superfamily / Domain of unknown function (DUF1958) / Penicillin-binding protein, C-terminal domain superfamily / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A / D-alanyl-D-alanine carboxypeptidase / Spermidine Synthase; Chain: A, domain 2 / Beta-lactamase, class-A ...Penicillin-binding protein 4, C-terminal domain / Penicillin-binding protein 4, C-terminal domain / Penicillin-binding protein 4, C-terminal domain superfamily / Domain of unknown function (DUF1958) / Penicillin-binding protein, C-terminal domain superfamily / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A / D-alanyl-D-alanine carboxypeptidase / Spermidine Synthase; Chain: A, domain 2 / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Roll / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Penicillin-binding protein 4
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsAlexander, J.A.N. / Strynadka, N.C.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Front Microbiol / Year: 2018
Title: Recognition of Peptidoglycan Fragments by the Transpeptidase PBP4 FromStaphylococcus aureus.
Authors: Maya-Martinez, R. / Alexander, J.A.N. / Otten, C.F. / Ayala, I. / Vollmer, D. / Gray, J. / Bougault, C.M. / Burt, A. / Laguri, C. / Fonvielle, M. / Arthur, M. / Strynadka, N.C.J. / Vollmer, W. / Simorre, J.P.
History
DepositionJul 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Penicillin-binding protein 4
B: Penicillin-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7976
Polymers80,5352
Non-polymers2624
Water5,459303
1
A: Penicillin-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3983
Polymers40,2671
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Penicillin-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3983
Polymers40,2671
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.511, 89.730, 77.489
Angle α, β, γ (deg.)90.000, 98.090, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-504-

HOH

21B-638-

HOH

31B-662-

HOH

-
Components

#1: Protein Penicillin-binding protein 4


Mass: 40267.480 Da / Num. of mol.: 2 / Mutation: S75C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain COL) (bacteria)
Strain: COL / Gene: pbp4, SACOL0699 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2WY27
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 8 mM zinc chloride, 80 mM sodium acetate pH 5, 100 mM sodium fluoride, and 16% polyethylene glycol 6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2017
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→29.16 Å / Num. obs: 59159 / % possible obs: 99.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 23.18 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.066 / Rrim(I) all: 0.124 / Net I/σ(I): 7.6 / Num. measured all: 200133 / Scaling rejects: 1
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
1.86-1.93.31.0861232437860.5020.711.3011.299.6
8.92-29.163.40.0318825470.9990.0190.03623.596.8

-
Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TXI

5txi


Resolution: 1.86→29.155 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 2925 4.95 %
Rwork0.1746 56180 -
obs0.1767 59105 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.02 Å2 / Biso mean: 36.6556 Å2 / Biso min: 13.72 Å2
Refinement stepCycle: final / Resolution: 1.86→29.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5654 0 4 303 5961
Biso mean--50.56 37.58 -
Num. residues----718
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8601-1.89050.34021450.32452633277899
1.8905-1.92310.28631450.30012678282399
1.9231-1.95810.30051500.26312654280499
1.9581-1.99570.33221260.246626652791100
1.9957-2.03650.25721250.22926992824100
2.0365-2.08070.26281400.20872667280799
2.0807-2.12910.22591310.194126592790100
2.1291-2.18240.26831390.192226792818100
2.1824-2.24130.23441490.19142637278699
2.2413-2.30730.24431290.176626822811100
2.3073-2.38170.21741500.168126792829100
2.3817-2.46680.21421290.157327042833100
2.4668-2.56550.21271410.154726632804100
2.5655-2.68220.20831370.159526932830100
2.6822-2.82350.22831300.157526812811100
2.8235-3.00020.20641440.16222687283199
3.0002-3.23160.20021380.15632663280199
3.2316-3.55630.21861330.15562694282799
3.5563-4.06970.16111510.13972679283099
4.0697-5.12290.17171510.14332645279699
5.1229-29.15880.22851420.19462739288199
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)
11.3678-0.6853-0.75611.87770.5111.9359-0.027-0.1624-0.00040.29670.02050.05040.0918-0.05360.00460.2724-0.014-0.02380.20140.00370.1513-25.9691-1.442239.8512
23.49373.1361-1.86625.7182-2.67113.62940.0689-0.1824-0.0223-0.13960.01060.06940.3616-0.1708-0.02980.3853-0.00290.01430.22940.00570.2196-23.3825-24.989821.4626
30.5225-0.344-0.16252.20090.72710.9945-0.0645-0.071-0.09170.24720.0151-0.04790.2642-0.01420.04320.2828-0.00620.00140.19990.00880.1584-23.5165-11.671731.3751
44.16812.4591-0.81343.4241-0.65251.3796-0.0520.13690.4445-0.0810.0860.0689-0.15840.0774-0.02450.2678-0.0076-0.03860.2279-0.0260.1805-17.405417.32232.7879
51.5053-0.7368-1.07211.91240.85391.7193-0.02880.0329-0.0260.0628-0.010.11740.0695-0.070.04380.2-0.011-0.02410.16960.00710.1514-20.585-3.3431.3641
62.06381.4082-0.76045.9712-0.6642.34130.0033-0.0308-0.1474-0.078-0.02830.07540.119-0.060.04280.2293-0.0176-0.02130.1924-0.00630.1501-17.6383-25.156-16.5784
72.30781.36781.01796.2521.22483.21970.0638-0.0905-0.1510.28040.0303-0.19270.2694-0.0305-0.0970.20990.0178-0.00440.15160.01050.1641-9.9389-21.0919-2.9548
80.95350.13970.63241.28010.91641.9110.01490.0717-0.0534-0.13110.01870.17960.1017-0.0996-0.03430.2922-0.0096-0.01460.19110.01930.2066-22.3897-8.776-10.7911
92.48120.8552-0.2322.52880.15881.01050.05570.14190.3216-0.187-0.0301-0.0119-0.12810.0718-0.01190.28050.02140.0110.18710.01790.172-15.180210.4754-4.7548
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 90 )A25 - 90
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 124 )A91 - 124
3X-RAY DIFFRACTION3chain 'A' and (resid 125 through 296 )A125 - 296
4X-RAY DIFFRACTION4chain 'A' and (resid 297 through 383 )A297 - 383
5X-RAY DIFFRACTION5chain 'B' and (resid 25 through 90 )B25 - 90
6X-RAY DIFFRACTION6chain 'B' and (resid 91 through 137 )B91 - 137
7X-RAY DIFFRACTION7chain 'B' and (resid 138 through 204 )B138 - 204
8X-RAY DIFFRACTION8chain 'B' and (resid 205 through 266 )B205 - 266
9X-RAY DIFFRACTION9chain 'B' and (resid 267 through 383 )B267 - 383

+
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