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- PDB-1gqq: MURC - Crystal structure of the apo-enzyme from Haemophilus influenzae -

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Basic information

Entry
Database: PDB / ID: 1gqq
TitleMURC - Crystal structure of the apo-enzyme from Haemophilus influenzae
ComponentsUDP-N-ACETYLMURAMATE-L-ALANINE LIGASE
KeywordsCELL WALL BIOSYNTHESIS / PEPTIDOGLYCAN / MUREIN / LIGASE
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 ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central ...UDP-N-acetylmuramate--L-alanine ligase / : / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Mur ligase, C-terminal 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 / Protein-Tyrosine Phosphatase; Chain A / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
UDP-N-acetylmuramate--L-alanine ligase
Similarity search - Component
Biological speciesHAEMOPHILUS INFLUENZAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.1 Å
AuthorsSkarzynski, T. / Cleasby, A. / Domenici, E. / Gevi, M. / Shaw, J.
CitationJournal: To be Published
Title: Crystal Structures of Udp-N-Acetylmuramate-L-Alanine Ligase (Murc) from Haemophilus Influenzae
Authors: Skarzynski, T. / Cleasby, A. / Domenici, E. / Gevi, M. / Shaw, J.
History
DepositionDec 3, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-N-ACETYLMURAMATE-L-ALANINE LIGASE
B: UDP-N-ACETYLMURAMATE-L-ALANINE LIGASE


Theoretical massNumber of molelcules
Total (without water)104,1142
Polymers104,1142
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)65.508, 99.485, 180.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UDP-N-ACETYLMURAMATE-L-ALANINE LIGASE


Mass: 52057.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: APO-ENZYME / Source: (gene. exp.) HAEMOPHILUS INFLUENZAE (bacteria) / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P45066, UDP-N-acetylmuramate-L-alanine ligase

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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: 2.83 Å3/Da / Density % sol: 56.48 %
Crystal growpH: 8.6
Details: PROTEIN SOLUTION 12MG/ML CONTAINING 10% GLYCEROL MIXED WITH WELL SOLUTION CONTAINING 2.4M AMMONIUM SULPHATE, 100MM BICINE BUFFER AND 3%ETHANOL., pH 8.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 20892 / % possible obs: 99.9 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.051
Reflection shellResolution: 3.1→3.2 Å / Rmerge(I) obs: 0.396 / % possible all: 99.8

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 3.1→19.88 Å / SU B: 20.187 / SU ML: 0.37361 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.50665
Details: DISORDERED SIDE CHAINS WERE MODELED STEREOCHEMICALLY, 6 TLS GROUPS WERE USED IN REFINEMENT. THE TLS PARAMETERS ARE GIVEN BELOW AND NOT IN THE MAIN TLS SECTION AS THEY ARE NOT IN A STANDARD FORMAT.
RfactorNum. reflection% reflectionSelection details
Rfree0.28624 1119 5.1 %RANDOM
Rwork0.23895 ---
obs0.24134 20892 100 %-
Displacement parametersBiso mean: 37.58 Å2
Baniso -1Baniso -2Baniso -3
1-2.6 Å20 Å20 Å2
2--2.99 Å20 Å2
3----5.58 Å2
Refinement stepCycle: LAST / Resolution: 3.1→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6578 0 0 0 6578

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