[English] 日本語
Yorodumi
- PDB-7b6p: Crystal structure of E.coli MurE - C269S C340S C450S in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7b6p
TitleCrystal structure of E.coli MurE - C269S C340S C450S in complex with Ellman's reagent
ComponentsUDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase
KeywordsBIOSYNTHETIC PROTEIN / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2 / 6-diaminopimelate ligase cell wall biosynthesis ligase drug target / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase / UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase / MurE/MurF, N-terminal / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain
Similarity search - Domain/homology
N-phenyl-2-selanylbenzamide / CITRIC ACID / ISOPROPYL ALCOHOL / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsKoekemoer, L. / Steindel, M. / Fairhead, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F. / Krojer, T. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of MurE from E.coli
Authors: Koekemoer, L. / Steindel, M. / Fairhead, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F. / Krojer, T.
History
DepositionDec 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Derived calculations / Structure summary
Category: atom_type / chem_comp ...atom_type / chem_comp / database_2 / entity / pdbx_entity_nonpoly
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Feb 7, 2024Group: 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: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase
B: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,07010
Polymers106,8912
Non-polymers1,1798
Water6,071337
1
A: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0345
Polymers53,4451
Non-polymers5894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA and gel filtration
2
B: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0365
Polymers53,4451
Non-polymers5904
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA and gel filtration
Unit cell
Length a, b, c (Å)58.590, 58.940, 74.380
Angle α, β, γ (deg.)96.720, 91.480, 104.470
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase / Meso-A2pm-adding enzyme / Meso-diaminopimelate-adding enzyme / UDP-MurNAc-L-Ala-D-Glu:meso- ...Meso-A2pm-adding enzyme / Meso-diaminopimelate-adding enzyme / UDP-MurNAc-L-Ala-D-Glu:meso-diaminopimelate ligase / UDP-MurNAc-tripeptide synthetase / UDP-N-acetylmuramyl-tripeptide synthetase


Mass: 53445.320 Da / Num. of mol.: 2 / Mutation: C269S C340S C450S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: murE, b0085, JW0083 / Plasmid: pNIC28-Bsa4
Details (production host): N-terminal His6-tag -Twin-Strep-tag II -TEV-cleavage site
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): -R3-Rosetta
References: UniProt: P22188, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase

-
Non-polymers , 5 types, 345 molecules

#2: Chemical ChemComp-9JT / N-phenyl-2-selanylbenzamide / ~{N}-phenyl-2-selanyl-benzamide / Ebselen, bound form


Mass: 276.193 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11NOSe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M citrate pH 5.5 13% PEG4K 19.5% 2-propanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97622 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.68→56.6 Å / Num. obs: 105615 / % possible obs: 97 % / Redundancy: 3.6 % / CC1/2: 0.999 / Net I/σ(I): 12.1
Reflection shellResolution: 1.68→1.72 Å / Num. unique obs: 7696 / CC1/2: 0.384

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7B53

7b53


Resolution: 1.68→56.6 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.486 / SU ML: 0.105 / Cross valid method: FREE R-VALUE / ESU R: 0.113 / ESU R Free: 0.114
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2392 5286 5.005 %
Rwork0.197 100321 -
all0.199 --
obs-105607 96.981 %
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: 37.212 Å2
Baniso -1Baniso -2Baniso -3
1--0.626 Å20.715 Å20.036 Å2
2--0.226 Å21.149 Å2
3----0.341 Å2
Refinement stepCycle: LAST / Resolution: 1.68→56.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7217 0 74 337 7628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0137499
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177140
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.6310193
X-RAY DIFFRACTIONr_angle_other_deg1.3751.57916368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7025969
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52721.921380
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.886151202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5211555
X-RAY DIFFRACTIONr_chiral_restr0.0710.2965
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028676
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021686
X-RAY DIFFRACTIONr_nbd_refined0.2080.21346
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.26456
X-RAY DIFFRACTIONr_nbtor_refined0.1560.23624
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.23732
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1410.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1420.213
X-RAY DIFFRACTIONr_nbd_other0.1530.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2280.217
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1130.21
X-RAY DIFFRACTIONr_mcbond_it2.9313.6663869
X-RAY DIFFRACTIONr_mcbond_other2.9283.6653868
X-RAY DIFFRACTIONr_mcangle_it4.0125.4854841
X-RAY DIFFRACTIONr_mcangle_other4.0135.4854842
X-RAY DIFFRACTIONr_scbond_it3.9884.2263630
X-RAY DIFFRACTIONr_scbond_other3.9884.2273631
X-RAY DIFFRACTIONr_scangle_it6.0116.1455350
X-RAY DIFFRACTIONr_scangle_other6.016.1465351
X-RAY DIFFRACTIONr_lrange_it7.24443.7897960
X-RAY DIFFRACTIONr_lrange_other7.22843.77918
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.68-1.7240.3724140.37472730.37480780.4790.4995.15970.376
1.724-1.7710.3664090.32670550.32978000.6060.61695.69230.318
1.771-1.8220.3273770.3169800.31176490.7030.71696.18250.296
1.822-1.8780.3313370.28267730.28473780.7740.78996.36760.265
1.878-1.940.3193200.27565640.27772040.7910.81795.5580.253
1.94-2.0080.2883000.23263900.23469310.8660.88296.52290.208
2.008-2.0830.2913070.23961840.24267280.8650.8896.47740.216
2.083-2.1680.272870.2160030.21264730.8990.91597.17290.191
2.168-2.2650.2553090.256900.20262110.9110.93596.58670.182
2.265-2.3750.2353250.19154250.19458860.9240.93597.68940.176
2.375-2.5030.252870.18851760.19155900.9270.94297.72810.176
2.503-2.6550.2372650.18750030.18953770.9340.94697.97280.177
2.655-2.8370.222700.18845900.1949710.9340.94397.76710.182
2.837-3.0640.2282130.20443520.20546520.9310.9498.12980.203
3.064-3.3560.2292050.19840220.19942890.9380.94598.55440.202
3.356-3.750.2381770.19436310.19638690.9320.94998.42340.201
3.75-4.3270.211500.16532230.16734140.9540.95998.79910.186
4.327-5.2920.1941480.15527430.15729220.9610.96998.93910.18
5.292-7.4510.2711140.18820980.19222290.9420.96299.23730.216
7.451-56.6040.173720.15711460.15812410.9690.9798.14670.189

+
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