[English] 日本語
Yorodumi
- PDB-3gkr: Crystal Structure of Weissella viridescens FemX:UDP-MurNAc-hexape... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gkr
TitleCrystal Structure of Weissella viridescens FemX:UDP-MurNAc-hexapeptide complex
Components
  • FemXLipid II:glycine glycyltransferase
  • UDP-MurNAc-peptide
KeywordsTransferase/Transferase Product / FEMX / PEPTIDOGLYCAN / HEXAPEPTIDE / transferase / Transferase-Transferase Product complex
Function / homology
Function and homology information


UDP-N-acetylmuramoylpentapeptide-lysine N6-alanyltransferase / UDP-N-acetylmuramoylpentapeptide-lysine N6-alanyltransferase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape
Similarity search - Function
FemABX peptidyl transferase / FemAB family / FemABX peptidyl transferase family profile. / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ALANINE / UDP-N-acetylmuramoylpentapeptide-lysine N(6)-alanyltransferase
Similarity search - Component
Biological speciesLactobacillus viridescens (bacteria)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDelfosse, V. / Piton, J. / Villet, R. / Lecerf, M. / Arthur, M. / Mayer, C.
CitationJournal: To be Published
Title: Structure of Weissella viridescens FemX with the UDP-MurNAc-hexapeptide product of the alanine transfer reaction
Authors: Delfosse, V. / Piton, J. / Villet, R. / Lecerf, M. / Arthur, M. / Mayer, C.
History
DepositionMar 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Version format compliance
Revision 1.2Aug 1, 2012Group: Structure summary
Revision 1.3Sep 5, 2012Group: Derived calculations
Revision 1.4Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_validate_polymer_linkage / struct_conn / struct_site
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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 400 COMPOUND GROUP: 1 NAME: UDP-MURNAC-HEXAPEPTIDE PRODUCT CHAIN: A, B COMPONENT_1: UDP-MURNAC-PEPTIDE ... COMPOUND GROUP: 1 NAME: UDP-MURNAC-HEXAPEPTIDE PRODUCT CHAIN: A, B COMPONENT_1: UDP-MURNAC-PEPTIDE COMPONENT_2: ALANINE DESCRIPTION: UDP-MURNAC-HEXAPEPTIDE PRODUCT OF THE ALANINE TRANSFER REACTION. ALANINE IS TRANSFERRED BY FEMX TO THE NZ OF LYSINE RESIDUE OF UDP-MURNAC-PEPTIDE

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FemX
B: UDP-MurNAc-peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7327
Polymers39,4782
Non-polymers2545
Water9,260514
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-34 kcal/mol
Surface area15430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.324, 101.836, 46.847
Angle α, β, γ (deg.)90.00, 102.85, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein FemX / Lipid II:glycine glycyltransferase


Mass: 38326.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus viridescens (bacteria) / Gene: femX / Plasmid: PTYB2 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
References: UniProt: Q9EY50, UDP-N-acetylmuramoylpentapeptide-lysine N6-alanyltransferase
#2: Protein/peptide UDP-MurNAc-peptide


Mass: 1150.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria)

-
Non-polymers , 4 types, 519 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ALA / ALANINE / Alanine


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 514 / 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: 2.57 Å3/Da / Density % sol: 52.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG6000, 0.3M chlorure de sodium, 0.01M chlorure de magnesium, 0.07M sulfate d'ammonium, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97985 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 11, 2006 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97985 Å / Relative weight: 1
ReflectionResolution: 1.6→27.2 Å / Num. all: 51014 / Num. obs: 50198 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.033 / Rsym value: 0.033 / Net I/σ(I): 18.4
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 5.6 / Num. unique all: 8475 / Rsym value: 0.139 / % possible all: 96.2

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0066refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NE9

1ne9


Resolution: 1.6→27.2 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.531 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.087 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21561 2533 5 %RANDOM
Rwork0.17301 ---
all0.17513 50653 --
obs0.17513 48120 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.912 Å2
Baniso -1Baniso -2Baniso -3
1-0.4242 Å20 Å20.0943 Å2
2--0.4196 Å20 Å2
3---0.4351 Å2
Refine analyzeLuzzati coordinate error obs: 0.153 Å / Luzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 1.6→27.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2764 0 14 514 3292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0222833
X-RAY DIFFRACTIONr_angle_refined_deg2.3491.9893840
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0715334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96524.42138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08315464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.351517
X-RAY DIFFRACTIONr_chiral_restr0.1880.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212157
X-RAY DIFFRACTIONr_mcbond_it1.4661.51675
X-RAY DIFFRACTIONr_mcangle_it2.30722705
X-RAY DIFFRACTIONr_scbond_it3.55331158
X-RAY DIFFRACTIONr_scangle_it5.2174.51135
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 185 -
Rwork0.236 3510 -
obs-3700 96.2 %

+
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