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- PDB-2uup: Crystal structure of MurD ligase in complex with D-Glu containing... -

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Basic information

Entry
Database: PDB / ID: 2uup
TitleCrystal structure of MurD ligase in complex with D-Glu containing sulfonamide inhibitor
ComponentsUDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE
KeywordsLIGASE / MURD-INHIBITOR COMPLEX / PEPTIDOGLYCAN SYNTHESIS / CELL WALL / CELL SHAPE / CELL CYCLE / NUCLEOTIDE-BINDING / SULFONAMIDE INHIBITOR / MURD LIGASE / ATP-BINDING / CELL DIVISION
Function / homology
Function and homology information


UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase / UDP-N-acetylmuramoylalanine-D-glutamate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
UDP-N-acetylmuramoylalanine-D-glutamate ligase MurD / Mur ligase MurD-like, N-terminal 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-acetylmuramoylalanine-D-glutamate ligase MurD / Mur ligase MurD-like, N-terminal 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
Chem-LK4 / UDP-N-acetylmuramoylalanine--D-glutamate ligase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsHumljan, J. / Kotnik, M. / Contreras-Martel, C. / Blanot, D. / Urleb, U. / Dessen, A. / Solmajer, T. / Gobec, S.
CitationJournal: J. Med. Chem. / Year: 2008
Title: Novel naphthalene-N-sulfonyl-D-glutamic acid derivatives as inhibitors of MurD, a key peptidoglycan biosynthesis enzyme.
Authors: Humljan, J. / Kotnik, M. / Contreras-Martel, C. / Blanot, D. / Urleb, U. / Dessen, A. / Solmajer, T. / Gobec, S.
History
DepositionMar 6, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _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 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7365
Polymers47,9791
Non-polymers7574
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)65.517, 65.517, 136.174
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE / UDP-N- ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE SYNTHETASE / D-GLUTAMIC ACID- ADDING ENZYME / UDP-N- ...UDP-N- ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE SYNTHETASE / D-GLUTAMIC ACID- ADDING ENZYME / UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE LIGASE


Mass: 47979.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: INHIBITOR N-(6-(4-CYANO-BENZYLOXY)-NAPHTHALENE-2-SULFONYL)-D-GLUTAMIC ACID BOUND
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PABD16 / Production host: Escherichia coli DH5[alpha] (bacteria)
References: UniProt: P14900, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase
#2: Chemical ChemComp-LK4 / N-({6-[(4-CYANOBENZYL)OXY]NAPHTHALEN-2-YL}SULFONYL)-D-GLUTAMIC ACID


Mass: 468.479 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H20N2O7S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsC-TERMINAL HIS-TAG (SHHHHHH)

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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: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 1.7 M (NH4)2SO4, 7% PEG 400, 100 MM HEPES, PH 7.5; THEN SOAKED IN 1 MM INHIBITOR SOLUTION.

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 45633 / % possible obs: 98.1 % / Observed criterion σ(I): 3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.6
Reflection shellResolution: 1.88→1.99 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 6.1 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UAG

3uag


Resolution: 1.88→65.51 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.914 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2303 5 %RANDOM
Rwork0.183 ---
obs0.184 43882 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.88→65.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3305 0 48 418 3771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223416
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.9854643
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9865442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.80924.558147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09615557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9431522
X-RAY DIFFRACTIONr_chiral_restr0.1020.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022586
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.21588
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22302
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2340
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8551.52184
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50323485
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2731232
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6044.51156
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.93 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.291 178
Rwork0.208 3165

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