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- PDB-1gqy: MURC - CRYSTAL STRUCTURE OF THE ENZYME FROM HAEMOPHILUS INFLUENZA... -

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Basic information

Entry
Database: PDB / ID: 1gqy
TitleMURC - CRYSTAL STRUCTURE OF THE ENZYME FROM HAEMOPHILUS INFLUENZAE COMPLEXED WITH AMPPCP
ComponentsUDP-N-ACETYLMURAMATE-L-ALANINE LIGASE
KeywordsCELL WALL BIOSYNTHESIS / PEPTIDOGLYCAN / MUREIN / LIGASE / ATP BINDING
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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / UDP-N-acetylmuramate--L-alanine ligase
Similarity search - Component
Biological speciesHAEMOPHILUS INFLUENZAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 6, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 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 1.5Dec 13, 2023Group: Data collection / Database references ...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 / struct_conn
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.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.pdbx_dist_value / _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_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

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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)105,1736
Polymers104,1142
Non-polymers1,0594
Water16,664925
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)71.600, 93.200, 86.800
Angle α, β, γ (deg.)90.00, 101.40, 90.00
Int Tables number4
Space group name H-MP1211

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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
Source: (gene. exp.) HAEMOPHILUS INFLUENZAE (bacteria) / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P45066, UDP-N-acetylmuramate-L-alanine ligase
#2: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 925 / Source method: isolated from a natural source / Formula: H2O

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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: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growpH: 6.8
Details: THE AMPPCP COMPLEX WAS FORMED BY ADDING 10MM AMPPCP AND 10MM MGCL2 TO THE CONCENTRATED PROTEIN SOLUTION AT 12MG/ML. CRYSTALS WERE GROWN USING WELL SOLUTION MADE OF 20%PEG 3350 AND 200MM SODIUM FORMATE, PH 6.8.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 7, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 93715 / % possible obs: 89.5 % / Redundancy: 2 % / Rmerge(I) obs: 0.069
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.453 / % possible all: 47.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
ARP/wARPphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AN EARLY VERSION OF PDB ENTRY 1GQQ

1gqq


Resolution: 1.8→20 Å / SU B: 3.26087 / SU ML: 0.09953 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12872 / ESU R Free: 0.12945
Details: DISORDERED SIDE CHAINS WERE MODELLED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23273 4678 5 %RANDOM
Rwork0.18383 ---
obs0.18624 88743 89.5 %-
Displacement parametersBiso mean: 30.035 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20.64 Å2
2--1.1 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7197 0 64 925 8186

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