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- PDB-5a5f: CRYSTAL STRUCTURE OF MURD LIGASE FROM ESCHERICHIA COLI IN COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 5a5f
TitleCRYSTAL STRUCTURE OF MURD LIGASE FROM ESCHERICHIA COLI IN COMPLEX WITH UMA AND ADP
ComponentsUDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE
KeywordsLIGASE / PEPTIDOGLYCAN SYNTHESIS / ADP-FORMING ENZYME / CELL WALL / CELL SHAPE / CELL CYCLE / NUCLEOTIDE-BINDING / ATP- BINDING / CELL DIVISION / LIGAND / CONFORMATION
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
ADENOSINE-5'-DIPHOSPHATE / MALONATE ION / URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE / UDP-N-acetylmuramoylalanine--D-glutamate ligase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSink, R. / Kotnik, M. / Zega, A. / Barreteau, H. / Gobec, S. / Blanot, D. / Dessen, A. / Contreras-Martel, C.
CitationJournal: PLoS ONE / Year: 2016
Title: Crystallographic Study of Peptidoglycan Biosynthesis Enzyme MurD: Domain Movement Revisited.
Authors: Sink, R. / Kotnik, M. / Zega, A. / Barreteau, H. / Gobec, S. / Blanot, D. / Dessen, A. / Contreras-Martel, C.
History
DepositionJun 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.2Jan 10, 2024Group: 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)48,3585
Polymers46,9761
Non-polymers1,3824
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.440, 89.840, 108.540
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-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE / D-GLUTAMIC ACID-ADDING ENZYME / UDP-N-ACETYLMURAMOYL-L-ALANY L-D-GLUTAMATE SYNTHETASE / MURD LIGASE


Mass: 46976.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Production host: Escherichia coli DH5[alpha] (bacteria)
References: UniProt: P14900, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase
#2: Chemical ChemComp-UMA / URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE


Type: L-peptide linking / Mass: 750.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H36N4O20P2
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.37 Å3/Da / Density % sol: 63.55 % / Description: NONE
Crystal growpH: 7.4
Details: 4 MG/ML PROTEIN, 1 MM UMA, 5 MM AMP-PNP, 1 MM NAN3, 1 MM DTT, 20 MM HEPES, PH 7.4, 1.8 M NA-MALONATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97623
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.9→46.46 Å / Num. obs: 51890 / % possible obs: 98.2 % / Observed criterion σ(I): 3 / Redundancy: 5.4 % / Biso Wilson estimate: 37.009 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.75
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.22 / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UAG

3uag


Resolution: 1.9→46.47 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.549 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23227 2561 5 %RANDOM
Rwork0.19809 ---
obs0.19982 48594 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.207 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å20 Å20 Å2
2--0.47 Å20 Å2
3---0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3254 0 90 269 3613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193439
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4922.0014686
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0275444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.13324.545143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90615560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1151521
X-RAY DIFFRACTIONr_chiral_restr0.1210.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212576
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_it1.971.8331744
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.6222.7342179
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0872.1471695
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.463 174 -
Rwork0.411 3479 -
obs--97.21 %
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)
14.34630.3906-1.16743.3946-1.21572.46790.06780.66540.2185-0.42390.04470.22560.0538-0.3296-0.11250.12240.0238-0.01970.27070.08220.08358.329475.8096-22.2046
22.00930.222-0.44161.4647-0.82163.4677-0.01620.0614-0.0693-0.01490.02780.12390.1157-0.1351-0.01160.0095-0.00820.00850.00940.00050.08671.516163.90834.4001
33.1661-0.1887-0.0194.0611.59123.1722-0.033-0.16990.1640.11410.0356-0.0625-0.0618-0.0264-0.00270.1017-0.03060.0040.0517-0.05240.09527.399786.210219.998
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 92
2X-RAY DIFFRACTION2A94 - 295
3X-RAY DIFFRACTION3A304 - 439

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