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- PDB-7bvb: Crystal structure of UDP-N-acetylmuramic Acid L-alanine ligase (M... -

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Basic information

Entry
Database: PDB / ID: 7bvb
TitleCrystal structure of UDP-N-acetylmuramic Acid L-alanine ligase (MurC) from Mycobacterium bovis in complex with UDP-N-acetylglucosamine
ComponentsUDP-N-acetylmuramate--L-alanine ligase
KeywordsLIGASE / MurC / Peptidoglycan / UDP-GlcNAc
Function / homology
Function and homology information


UDP-N-acetylmuramate-L-alanine ligase / UDP-N-acetylmuramate-L-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / ATP binding / cytoplasm
Similarity search - Function
UDP-N-acetylmuramate--L-alanine ligase / : / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central / Mur-like, catalytic domain superfamily ...UDP-N-acetylmuramate--L-alanine ligase / : / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / UDP-N-acetylmuramate--L-alanine ligase
Similarity search - Component
Biological speciesMycobacterium bovis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.191 Å
AuthorsSeo, P.W. / Kim, J.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2019R1I1A3A01061866 Korea, Republic Of
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Crystal structures of UDP-N-acetylmuramic acid L-alanine ligase (MurC) from Mycobacterium bovis with and without UDP-N-acetylglucosamine.
Authors: Seo, P.W. / Park, S.Y. / Hofmann, A. / Kim, J.S.
History
DepositionApr 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 19, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 29, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylmuramate--L-alanine ligase
B: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,1516
Polymers108,8052
Non-polymers1,3464
Water1,36976
1
A: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0763
Polymers54,4031
Non-polymers6732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-43 kcal/mol
Surface area19610 Å2
MethodPISA
2
B: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0763
Polymers54,4031
Non-polymers6732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-38 kcal/mol
Surface area18780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.285, 75.762, 104.679
Angle α, β, γ (deg.)90.000, 105.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UDP-N-acetylmuramate--L-alanine ligase / UDP-N-acetylmuramoyl-L-alanine synthetase


Mass: 54402.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97) (bacteria)
Gene: murC, BQ2027_MB2176C / Production host: Escherichia coli (E. coli)
References: UniProt: P65473, UDP-N-acetylmuramate-L-alanine ligase
#2: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES pH 7.5, 0.2M NaCl, 30% (w/v) PEG 1500, 5% (v/v) MPD, 2mM UNAG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.19→50 Å / Num. obs: 16184 / % possible obs: 98.7 % / Redundancy: 7.3 % / Biso Wilson estimate: 58.33 Å2 / Rsym value: 0.144 / Net I/σ(I): 31.4
Reflection shellResolution: 3.19→3.36 Å / Rmerge(I) obs: 0.417 / Num. unique obs: 811

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HV4

4hv4


Resolution: 3.191→39.251 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.64
RfactorNum. reflection% reflection
Rfree0.2469 971 6.01 %
Rwork0.1946 --
obs0.1978 16161 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.34 Å2 / Biso mean: 53.0862 Å2 / Biso min: 31.04 Å2
Refinement stepCycle: final / Resolution: 3.191→39.251 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6825 0 80 76 6981
Biso mean--64.48 51.01 -
Num. residues----938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037020
X-RAY DIFFRACTIONf_angle_d0.5499552
X-RAY DIFFRACTIONf_chiral_restr0.0441132
X-RAY DIFFRACTIONf_plane_restr0.0041251
X-RAY DIFFRACTIONf_dihedral_angle_d14.1944149
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.191-3.3590.28561270.2472201290
3.359-3.56940.27031380.2145214998
3.5694-3.84470.2551410.2071219999
3.8447-4.23120.26331350.1895216499
4.2312-4.84260.22791450.1771218899
4.8426-6.09740.27641420.2048220899
6.0974-39.2510.20421430.1713227099

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