[English] 日本語
Yorodumi
- PDB-4bjq: Crystal structure of E. coli penicillin binding protein 3, domain... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bjq
TitleCrystal structure of E. coli penicillin binding protein 3, domain V88- S165
ComponentsPENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN
KeywordsTRANSFERASE / TRANSPEPTIDASE
Function / homologyDNA polymerase; domain 1 - #770 / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha / :
Function and homology information
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsSauvage, E. / Joris, M. / Herman, R. / Kerff, F. / Rocaboy, M. / Charlier, P.
CitationJournal: Plos One / Year: 2014
Title: Crystal Structure of Penicillin-Binding Protein 3 (Pbp3) from Escherichia Coli.
Authors: Sauvage, E. / Derouaux, A. / Fraipont, C. / Joris, M. / Herman, R. / Rocaboy, M. / Schloesser, M. / Dumas, J. / Kerff, F. / Nguyen-Disteche, M. / Charlier, P.
History
DepositionApr 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN
B: PENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN
C: PENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN
D: PENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN
E: PENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN
F: PENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN
G: PENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN
H: PENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,51517
Polymers69,6248
Non-polymers8919
Water9,602533
1
A: PENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN
C: PENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6945
Polymers17,4062
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-69.7 kcal/mol
Surface area9430 Å2
MethodPISA
2
B: PENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN
E: PENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7906
Polymers17,4062
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-69.5 kcal/mol
Surface area9180 Å2
MethodPISA
3
F: PENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN

G: PENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN


Theoretical massNumber of molelcules
Total (without water)17,4062
Polymers17,4062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area4570 Å2
ΔGint-43.3 kcal/mol
Surface area9340 Å2
MethodPISA
4
G: PENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN

F: PENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN


Theoretical massNumber of molelcules
Total (without water)17,4062
Polymers17,4062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area4570 Å2
ΔGint-43.3 kcal/mol
Surface area9340 Å2
MethodPISA
5
D: PENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN
H: PENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6244
Polymers17,4062
Non-polymers2182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-42.7 kcal/mol
Surface area9330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.048, 55.959, 82.285
Angle α, β, γ (deg.)89.13, 76.49, 65.99
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
PENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN


Mass: 8703.047 Da / Num. of mol.: 8 / Fragment: RESIDUES 88-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: J2XFH0, peptidoglycan glycosyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 533 / 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: 2.98 Å3/Da / Density % sol: 58.44 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9686
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.1→38 Å / Num. obs: 45669 / % possible obs: 88.5 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.5 / % possible all: 95.4

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.1→35.7 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.908 / SU B: 12.115 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26252 2309 5.1 %RANDOM
Rwork0.20823 ---
obs0.21099 43316 88.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.944 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20.03 Å2
2--0.03 Å2-0.01 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→35.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4886 0 48 533 5467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225029
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.9756809
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2835613
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.15623.929224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.06215885
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5691540
X-RAY DIFFRACTIONr_chiral_restr0.0820.2733
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213764
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_it0.5251.53101
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.01424958
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.61431928
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7144.51851
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: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 194 -
Rwork0.307 3462 -
obs--95.28 %
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)
10.7194-0.3240.00140.9689-0.27850.09970.00240.02120.0478-0.00720.01630.02040.01660.0091-0.01870.0860.01050.01180.0755-0.03020.023256.06640.985100.48
20.7024-0.4791-0.29691.06750.30760.22480.0165-0.00980.01990.01710.01310.05150.03150.0089-0.02960.06370.01670.02140.0979-0.00310.036144.362-18.94151.377
31.2049-0.62080.34720.6367-0.51930.4935-0.0533-0.1311-0.0716-0.06180.03650.03480.0643-0.00770.01670.08580.01060.00920.0575-0.010.050165.98728.888108.657
40.80030.2808-0.10290.47590.09110.3821-0.0850.0296-0.06560.01040.0340.0424-0.04650.00360.05090.062-0.01720.03070.0683-0.01740.039430.75818.23795.982
50.2508-0.0249-0.18551.50490.7240.5802-0.0408-0.0241-0.0217-0.11060.0121-0.0794-0.03410.00160.02880.06010.02230.0250.10010.00460.037651.422-33.30642.945
60.8540.3914-0.40150.3355-0.2780.85650.0539-0.0087-0.02770.0026-0.0446-0.082-0.0032-0.0473-0.00930.043-0.00110.0230.09390.00950.047618.752-4.89355.608
72.47980.7131-0.49050.7053-0.03570.32840.1267-0.0614-0.12090.0641-0.1181-0.0070.025-0.0715-0.00860.0618-0.0321-0.00170.09640.02140.021161.742-10.88165.823
81.08251.1134-0.57382.5549-0.95410.6096-0.17770.1125-0.0729-0.14150.1635-0.24690.0405-0.02910.01420.0656-0.05710.01880.0885-0.01570.050240.81628.57886.009
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A88 - 165
2X-RAY DIFFRACTION2B88 - 165
3X-RAY DIFFRACTION3C88 - 165
4X-RAY DIFFRACTION4D88 - 200
5X-RAY DIFFRACTION5E88 - 164
6X-RAY DIFFRACTION6F88 - 165
7X-RAY DIFFRACTION7G88 - 164
8X-RAY DIFFRACTION8H88 - 164

+
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