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- PDB-7d27: Structure of UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diam... -

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Basic information

Entry
Database: PDB / ID: 7d27
TitleStructure of UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase
ComponentsUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase
KeywordsLIGASE / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2 / 6-diaminopimelate ligase / murE / Acinetobacter baumannii / antibiotics
Function / homology
Function and homology information


UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase / UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase activity / cell cycle / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase / MurE/MurF, N-terminal / 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
Similarity search - Domain/homology
UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsPark, H.H. / Jeong, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Febs Lett. / Year: 2021
Title: Wide-open conformation of UDP-MurNc-tripeptide ligase revealed by the substrate-free structure of MurE from Acinetobacter baumannii.
Authors: Jung, K.H. / Kim, Y.G. / Kim, C.M. / Ha, H.J. / Lee, C.S. / Lee, J.H. / Park, H.H.
History
DepositionSep 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase


Theoretical massNumber of molelcules
Total (without water)55,1191
Polymers55,1191
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22710 Å2
Unit cell
Length a, b, c (Å)119.960, 119.960, 116.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase / Meso-A2pm-adding enzyme / Meso-diaminopimelate-adding enzyme / UDP-MurNAc-L-Ala-D-Glu:meso- ...Meso-A2pm-adding enzyme / Meso-diaminopimelate-adding enzyme / UDP-MurNAc-L-Ala-D-Glu:meso-diaminopimelate ligase / UDP-MurNAc-tripeptide synthetase / UDP-N-acetylmuramyl-tripeptide synthetase


Mass: 55118.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: murE, EA667_001595, EA685_00960, EA746_009110 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A429M5V5, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 4 Å3/Da / Density % sol: 69.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 21%(v/v) 2-propanl, 30% (v/v) Glyceol 0.07M sodium cacodylate trihydrate pH 6.5, 0.14M Sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 104.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.48→29.18 Å / Num. obs: 30793 / % possible obs: 100 % / Redundancy: 17.7 % / Rpim(I) all: 0.023 / Net I/σ(I): 20.4
Reflection shellResolution: 2.48→2.57 Å / Num. unique obs: 3022 / Rpim(I) all: 0.424

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
MxDCdata collection
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BUB

4bub


Resolution: 2.48→20.001 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.883 / Cross valid method: THROUGHOUT / ESU R: 0.318 / ESU R Free: 0.244
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2598 1983 6.453 %
Rwork0.2281 28746 -
all0.23 --
obs-30729 99.727 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.554 Å2
Baniso -1Baniso -2Baniso -3
1--0.002 Å20 Å20 Å2
2---0.002 Å20 Å2
3---0.005 Å2
Refinement stepCycle: LAST / Resolution: 2.48→20.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3796 0 0 136 3932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0133869
X-RAY DIFFRACTIONr_bond_other_d0.0360.0173537
X-RAY DIFFRACTIONr_angle_refined_deg1.7761.6355250
X-RAY DIFFRACTIONr_angle_other_deg2.3251.5728194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.255483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.06122.936218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.06815637
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7921525
X-RAY DIFFRACTIONr_chiral_restr0.1010.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024394
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02801
X-RAY DIFFRACTIONr_nbd_refined0.230.2797
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2360.23338
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21897
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21951
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2157
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1140.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2840.216
X-RAY DIFFRACTIONr_nbd_other0.2670.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1840.26
X-RAY DIFFRACTIONr_mcbond_it3.0433.0531944
X-RAY DIFFRACTIONr_mcbond_other3.0413.0511943
X-RAY DIFFRACTIONr_mcangle_it4.1354.5462423
X-RAY DIFFRACTIONr_mcangle_other4.1354.5482424
X-RAY DIFFRACTIONr_scbond_it4.4783.2781925
X-RAY DIFFRACTIONr_scbond_other4.4773.2791926
X-RAY DIFFRACTIONr_scangle_it6.0384.8042827
X-RAY DIFFRACTIONr_scangle_other6.0374.8062828
X-RAY DIFFRACTIONr_lrange_it6.48136.1084266
X-RAY DIFFRACTIONr_lrange_other6.4836.0354241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.5440.3221430.2782108X-RAY DIFFRACTION100
2.544-2.6140.3171380.2522035X-RAY DIFFRACTION99.954
2.614-2.690.271400.2511962X-RAY DIFFRACTION100
2.69-2.7720.2851320.2391927X-RAY DIFFRACTION100
2.772-2.8630.31280.2281869X-RAY DIFFRACTION100
2.863-2.9640.3071230.2211827X-RAY DIFFRACTION100
2.964-3.0750.2131250.21763X-RAY DIFFRACTION100
3.075-3.2010.2351170.2091679X-RAY DIFFRACTION100
3.201-3.3430.241130.2091626X-RAY DIFFRACTION100
3.343-3.5060.2651080.2191555X-RAY DIFFRACTION100
3.506-3.6950.2341010.2151482X-RAY DIFFRACTION100
3.695-3.9190.234950.2051406X-RAY DIFFRACTION100
3.919-4.1890.249910.2061342X-RAY DIFFRACTION100
4.189-4.5230.225850.1961253X-RAY DIFFRACTION100
4.523-4.9540.257810.2031145X-RAY DIFFRACTION100
4.954-5.5360.321730.2641052X-RAY DIFFRACTION100
5.536-6.3880.275660.256939X-RAY DIFFRACTION100
6.388-7.8120.274570.255805X-RAY DIFFRACTION100
7.812-9.0020.29450.25646X-RAY DIFFRACTION100
8-100.349220.33325X-RAY DIFFRACTION80.6977

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