[English] 日本語
Yorodumi
- PDB-6tix: Crystal structure of penicillin-binding protein 2 from Yersinia p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tix
TitleCrystal structure of penicillin-binding protein 2 from Yersinia pestis in complex with mecillinam
ComponentsPeptidoglycan D,D-transpeptidase MrdA
KeywordsMEMBRANE PROTEIN / Class B PBP / Yersinia pestis / HMM transpeptidase / periplasmic protein / peptidoglycan crosslinking / mecillinam
Function / homology
Function and homology information


serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis / plasma membrane
Similarity search - Function
Penicillin-binding protein 2 / 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-DH4 / Peptidoglycan D,D-transpeptidase MrdA / Peptidoglycan D,D-transpeptidase MrdA
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPankov, G. / Hunter, W.N. / Dawson, A.
CitationJournal: To Be Published
Title: The structure of penicillin-binding protein 2 from Yersinia pestis in complex with mecillinam
Authors: Pankov, G.
History
DepositionNov 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Peptidoglycan D,D-transpeptidase MrdA
BBB: Peptidoglycan D,D-transpeptidase MrdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,7614
Polymers131,1062
Non-polymers6552
Water1,874104
1
AAA: Peptidoglycan D,D-transpeptidase MrdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8802
Polymers65,5531
Non-polymers3271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Peptidoglycan D,D-transpeptidase MrdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8802
Polymers65,5531
Non-polymers3271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.172, 84.035, 87.099
Angle α, β, γ (deg.)112.917, 95.306, 104.566
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB)

-
Components

#1: Protein Peptidoglycan D,D-transpeptidase MrdA / Penicillin-binding protein 2 / PBP-2


Mass: 65552.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: mrdA, YPO2604 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A384KFW3, UniProt: A0A5P8YJF3*PLUS, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-DH4 / 2-[(1R)-1-{[(E)-azepan-1-ylmethylidene]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / Mecillinam, bound form


Mass: 327.442 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H25N3O3S / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.6 % / Description: Branched rectangular prisms
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: Crystals were grown in a condition containing 1 uL of 0.8 mg/mL YpPBP2 (in 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM mecillinam) and 1 uL of reservoir solution (0.45 M Na+/K+ tartrate, 0.1 M ...Details: Crystals were grown in a condition containing 1 uL of 0.8 mg/mL YpPBP2 (in 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM mecillinam) and 1 uL of reservoir solution (0.45 M Na+/K+ tartrate, 0.1 M HEPES-NaOH pH 7.5, 7.2% PEG 4000). The size of these crystals was optimised by three rounds of macroseeding into condition containing (0.45 M Na+/K+ tartrate, 0.1 M HEPES-NaOH pH 7.5, 7.2% PEG 4000 and 2 mM mecillinam)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Apr 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.8→45.693 Å / Num. obs: 27215 / % possible obs: 92.9 % / Redundancy: 2.1 % / CC1/2: 0.991 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.097 / Net I/σ(I): 4.1
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4118 / CC1/2: 0.677 / Rpim(I) all: 0.452 / Rrim(I) all: 0.64 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LP4

5lp4


Resolution: 2.8→45.693 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.891 / WRfactor Rfree: 0.274 / WRfactor Rwork: 0.214 / SU B: 29.964 / SU ML: 0.529 / Average fsc free: 0.7294 / Average fsc work: 0.772 / Cross valid method: FREE R-VALUE / ESU R Free: 0.48
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2902 1308 4.831 %
Rwork0.228 25768 -
all0.231 --
obs-27076 92.432 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 66.303 Å2
Baniso -1Baniso -2Baniso -3
1--4.63 Å2-8.426 Å2-6.118 Å2
2--1.424 Å24.642 Å2
3---3.222 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.693 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8166 0 0 104 8270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0138355
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177816
X-RAY DIFFRACTIONr_angle_refined_deg1.2991.65411341
X-RAY DIFFRACTIONr_angle_other_deg1.0911.57818119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7851020
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13621.59434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.661151394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0941560
X-RAY DIFFRACTIONr_chiral_restr0.0460.21091
X-RAY DIFFRACTIONr_chiral_restr_other0.0350.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029267
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021757
X-RAY DIFFRACTIONr_nbd_refined0.1950.22136
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.28798
X-RAY DIFFRACTIONr_nbtor_refined0.1620.24009
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.23930
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1210.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2170.239
X-RAY DIFFRACTIONr_nbd_other0.2370.2150
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2470.28
X-RAY DIFFRACTIONr_mcbond_it3.2026.9834113
X-RAY DIFFRACTIONr_mcbond_other3.2026.9834112
X-RAY DIFFRACTIONr_mcangle_it5.3310.4635122
X-RAY DIFFRACTIONr_mcangle_other5.32910.4645123
X-RAY DIFFRACTIONr_scbond_it2.7117.3394242
X-RAY DIFFRACTIONr_scbond_other2.7117.3394243
X-RAY DIFFRACTIONr_scangle_it4.72810.8696219
X-RAY DIFFRACTIONr_scangle_other4.72710.8696220
X-RAY DIFFRACTIONr_lrange_it8.63282.4379706
X-RAY DIFFRACTIONr_lrange_other8.63182.4429705
X-RAY DIFFRACTIONr_ncsr_local_group_10.0950.0516393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.872-2.9510.38950.341878X-RAY DIFFRACTION95.3601
2.951-3.0360.3711080.3181884X-RAY DIFFRACTION96.3716
3.036-3.1290.397990.2961774X-RAY DIFFRACTION95.7077
3.129-3.2310.422880.2811789X-RAY DIFFRACTION95.4245
3.231-3.3440.306770.2631693X-RAY DIFFRACTION96.8801
3.344-3.4690.308840.2571656X-RAY DIFFRACTION95.4995
3.469-3.610.271640.2281546X-RAY DIFFRACTION94.6502
3.61-3.770.287730.2241521X-RAY DIFFRACTION94.3195
3.77-3.9520.298810.2071414X-RAY DIFFRACTION93.3208
3.952-4.1640.269530.1841286X-RAY DIFFRACTION89.7453
4.164-4.4150.274680.1711214X-RAY DIFFRACTION88.7812
4.415-4.7160.198570.1721062X-RAY DIFFRACTION84.1353
4.716-5.090.261540.1871009X-RAY DIFFRACTION84.4321
5.09-5.5680.355510.214964X-RAY DIFFRACTION87.8028
5.568-6.2140.279420.191903X-RAY DIFFRACTION90
6.214-7.1540.197360.179804X-RAY DIFFRACTION91.5033
7.154-8.7080.257300.2661X-RAY DIFFRACTION88.7035

+
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