[English] 日本語
Yorodumi
- PDB-6i1g: Crystal structure of TP domain from Chlamydia trachomatis Penicil... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6i1g
TitleCrystal structure of TP domain from Chlamydia trachomatis Penicillin-Binding Protein 3 in complex with piperacillin
ComponentsPenicillin-binding protein,Penicillin-binding protein
KeywordsPEPTIDE BINDING PROTEIN / penicillin-binding protein / peptidoglycan / Transpeptidase
Function / homology
Function and homology information


peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / penicillin binding / membrane => GO:0016020
Similarity search - Function
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
Piperacillin (Open Form) / Penicillin-binding protein
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsBellini, D. / Koekemoer, L. / Newman, H. / Dowson, C.G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)grant.MR/P007503/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of TP domain from Chlamydia trachomatis Penicillin-Binding Protein 3 in complex with piperacillin
Authors: Bellini, D. / Koekemoer, L. / Newman, H. / Dowson, C.G.
History
DepositionOct 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)73,9754
Polymers72,9362
Non-polymers1,0392
Water30617
1
A: Penicillin-binding protein,Penicillin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9872
Polymers36,4681
Non-polymers5201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Penicillin-binding protein,Penicillin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9872
Polymers36,4681
Non-polymers5201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.804, 107.804, 117.735
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Penicillin-binding protein,Penicillin-binding protein


Mass: 36467.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Gene: pbp_2, ERS133248_00492 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0E9FXJ8, peptidoglycan glycosyltransferase
#2: Chemical ChemComp-JPP / Piperacillin (Open Form)


Mass: 519.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H29N5O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 1 M sodium citrate and 0.1 M sodium cacodylate pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.13→93.36 Å / Num. obs: 21761 / % possible obs: 91.8 % / Redundancy: 11.7 % / Rrim(I) all: 0.422 / Net I/σ(I): 9.1
Reflection shellResolution: 2.13→2.42 Å

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
autoPROCdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HZH

6hzh


Resolution: 2.13→93.36 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.839 / SU B: 6.465 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 2.001 / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28357 1118 5.1 %RANDOM
Rwork0.23985 ---
obs0.24207 20640 48.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.032 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å2-0.72 Å20 Å2
2---1.45 Å20 Å2
3---2.17 Å2
Refinement stepCycle: 1 / Resolution: 2.13→93.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5006 0 0 17 5023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.025101
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.521.9746961
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.535660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50824.737190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.08515788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7071524
X-RAY DIFFRACTIONr_chiral_restr0.1050.2818
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213844
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.127→2.182 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 6 -
Rwork0.394 26 -
obs--0.99 %

+
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