[English] 日本語
Yorodumi
- PDB-3hun: Crystal structure of Penicillin binding protein 4 from Staphyloco... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hun
TitleCrystal structure of Penicillin binding protein 4 from Staphylococcus aureus COL in complex with Ampicillin
ComponentsPenicillin-binding protein 4
KeywordsHYDROLASE/Antibiotics / Penicillin binding protein 4 / Ampicillin / beta-lactamase / Serine type D-Ala / D-Ala-carboxypeptidase / Antibiotics / HYDROLASE-Antibiotics complex
Function / homology
Function and homology information


serine-type D-Ala-D-Ala carboxypeptidase activity / beta-lactam antibiotic catabolic process / membrane => GO:0016020 / peptidoglycan biosynthetic process / cell wall organization / beta-lactamase activity / regulation of cell shape / response to antibiotic / proteolysis / metal ion binding / 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
Chem-ZZ7 / Penicillin-binding protein 4 / Penicillin-binding protein 4
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNavratna, V. / Gopal, B.
CitationJournal: J.Bacteriol. / Year: 2009
Title: Molecular basis for the role of Staphylococcus aureus Penicillin Binding Protein 4 in antimicrobial resistance
Authors: Navratna, V. / Nadig, S. / Sood, V. / Prasad, K. / Arakere, G. / Gopal, B.
History
DepositionJun 15, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Nov 10, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 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: Penicillin-binding protein 4
B: Penicillin-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,0934
Polymers101,3582
Non-polymers7352
Water5,368298
1
A: Penicillin-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0462
Polymers50,6791
Non-polymers3671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Penicillin-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0462
Polymers50,6791
Non-polymers3671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.810, 98.480, 99.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Penicillin-binding protein 4


Mass: 50678.930 Da / Num. of mol.: 2 / Mutation: T189S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: COL / Gene: pbp4 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3
References: UniProt: Q5HI26, UniProt: A0A0H2WY27*PLUS, serine-type D-Ala-D-Ala carboxypeptidase
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE ARE CONFLICT BETWEEN SEQRES (SER A,B 189) AND SEQUENCE DATABASE (THR 189 ). THE AUTHOR ...THERE ARE CONFLICT BETWEEN SEQRES (SER A,B 189) AND SEQUENCE DATABASE (THR 189 ). THE AUTHOR BELIEVE THAT THE SEQRES IS CORRECT AND IS THE TRUE IDENTITY OF THESE RESIDUES AND IS NATURAL MUTANT.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 24% PEG3350, 240mM Ammonium Sulphate, 100mM Bis-tris, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.2818 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2818 Å / Relative weight: 1
ReflectionResolution: 2→34.99 Å / Num. obs: 60831 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 16.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 7 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 4.1 / Num. unique all: 8756 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TVF

1tvf


Resolution: 2→33.53 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.908 / SU B: 3.756 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25079 3079 5.1 %RANDOM
Rwork0.20373 ---
obs0.20612 57683 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.27 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å20 Å20 Å2
2---0.87 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 2→33.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5652 0 48 298 5998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0225746
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9621.9647804
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8545716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17625.415253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30515965
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.931518
X-RAY DIFFRACTIONr_chiral_restr0.1320.2889
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214326
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0321.53571
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.65825771
X-RAY DIFFRACTIONr_scbond_it2.94932175
X-RAY DIFFRACTIONr_scangle_it4.4264.52033
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 238 -
Rwork0.218 4176 -
obs--99.5 %

+
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