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- PDB-2wjp: CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING... -

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Basic information

Entry
Database: PDB / ID: 2wjp
TitleCRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING RHODANINE INHIBITOR
ComponentsUDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE
KeywordsLIGASE / PEPTIDOGLYCAN SYNTHESIS / CELL WALL BIOGENESIS/DEGRADATION / CELL CYCLE / CELL DIVISION / CELL SHAPE SYNTHESIS
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
AZIDE ION / Chem-D17 / UDP-N-acetylmuramoylalanine--D-glutamate ligase
Similarity search - Component
Biological speciesESCHERICHIA COLI DH5[ALPHA] (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTomasic, T. / Zidar, N. / Sink, R. / Kovac, A. / Rupnik, V. / Turk, S. / Contreras-Martel, C. / Dessen, A. / Blanot, D. / Muller-Premru, M. ...Tomasic, T. / Zidar, N. / Sink, R. / Kovac, A. / Rupnik, V. / Turk, S. / Contreras-Martel, C. / Dessen, A. / Blanot, D. / Muller-Premru, M. / Gobec, S. / Zega, A. / Peterlin-Masic, L. / Kikelj, D.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Discovery of Novel 5-Benzylidenerhodanine and 5-Benzylidenethiazolidine-2,4-Dione Inhibitors of Murd Ligase.
Authors: Zidar, N. / Tomasic, T. / Sink, R. / Rupnik, V. / Kovac, A. / Turk, S. / Patin, D. / Blanot, D. / Contreras Martel, C. / Dessen, A. / Muller Premru, M. / Zega, A. / Gobec, S. / Peterlin Masic, L. / Kikelj, D.
History
DepositionMay 28, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references / Source and taxonomy
Revision 1.2Dec 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,63819
Polymers47,1571
Non-polymers1,48118
Water9,674537
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.917, 65.917, 136.063
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 47157.480 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-438
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI DH5[ALPHA] (bacteria) / Plasmid: PABD16/MURD / Production host: ESCHERICHIA COLI DH5[ALPHA] (bacteria)
References: UniProt: P14900, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase

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Non-polymers , 6 types, 555 molecules

#2: Chemical ChemComp-D17 / N-({3-[({4-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl}amino)methyl]phenyl}carbonyl)-L-glutamic acid


Mass: 499.559 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H21N3O6S2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: N3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 7.5
Details: 1.8 M (NH4)2SO4, 7% PEG 400, 100 MM NACL, 100 MM HEPES, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.6→46.62 Å / Num. obs: 76321 / % possible obs: 92.5 % / Observed criterion σ(I): 3 / Redundancy: 4.5 % / Biso Wilson estimate: 25.99 Å2 / Rsym value: 0.05 / Net I/σ(I): 19.95
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.59 / % possible all: 78.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0089refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UAG

3uag


Resolution: 1.6→46.63 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.284 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.189 3860 5.1 %RANDOM
Rwork0.166 ---
obs0.167 72348 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.2 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.6→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3278 0 84 537 3899
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223517
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.9884788
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5765469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.22324.286154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52415590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5011526
X-RAY DIFFRACTIONr_chiral_restr0.1210.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212667
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0071.52212
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.10223550
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.6231305
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.1954.51220
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: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 266 -
Rwork0.309 5270 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9882-0.14640.34190.8895-0.61820.9263-0.0146-0.0322-0.0067-0.04170.0374-0.0133-0.032-0.111-0.02280.03740.0137-0.00890.02470.00340.0172-2.977960.1834121.5999
20.1203-0.12320.19260.5329-0.29630.3871-0.0146-0.01380.00340.00950.0002-0.06190.02560.00180.01450.05270.00570.00080.03330.00790.03713.481538.0645132.4978
30.99740.72730.0341.96340.14830.5285-0.02060.03460.0085-0.0930.0495-0.03880.0473-0.0276-0.02890.0428-0.0145-0.0090.00750.00940.02933.694524.3109109.8129
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 92
2X-RAY DIFFRACTION2A93 - 295
3X-RAY DIFFRACTION3A296 - 439

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