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- PDB-7ti7: Crystal Structure of UDP-N-acetylmuramoylalanine-D-glutamate liga... -

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Basic information

Entry
Database: PDB / ID: 7ti7
TitleCrystal Structure of UDP-N-acetylmuramoylalanine-D-glutamate ligase from Acinetobacter baumannii AB5075-UW in complex with ADP
ComponentsUDP-N-acetylmuramoylalanine--D-glutamate ligase
KeywordsLIGASE / SSGCID / MurD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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 / cytoplasm
Similarity search - Function
UDP-N-acetylmuramoylalanine-D-glutamate ligase MurD / Mur ligase MurD-like, N-terminal 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
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / UDP-N-acetylmuramoylalanine--D-glutamate ligase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: to be published
Title: Crystal Structure of UDP-N-acetylmuramoylalanine-D-glutamate ligase from Acinetobacter baumannii AB5075-UW in complex with ADP
Authors: Abendroth, J. / DeBouver, N.D. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJan 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)49,7728
Polymers49,0591
Non-polymers7137
Water9,818545
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.490, 91.820, 106.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein UDP-N-acetylmuramoylalanine--D-glutamate ligase / D-glutamic acid-adding enzyme / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase


Mass: 49059.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: AB5075-UW
Gene: murD, Aba9201_12330, ABUW_3630, APC21_11165, C6N18_02095, EA686_02860, EGM95_19310, F2P40_16560, GNY86_17350, NCTC13421_03598, SI89_12870
Plasmid: AcbaC.17938.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0B9W6J3, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase

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Non-polymers , 6 types, 552 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Molecular Dimensions Morpheus screen condition a6: 10% (w/V) PEG 8000, 20% (V/V) ethylene gycol: 30mM magnesium chloride and calcium chloride: 100mM MOPS / HEPES pH 7.5: AcbaC.17938.a.B1. ...Details: Molecular Dimensions Morpheus screen condition a6: 10% (w/V) PEG 8000, 20% (V/V) ethylene gycol: 30mM magnesium chloride and calcium chloride: 100mM MOPS / HEPES pH 7.5: AcbaC.17938.a.B1.PS02380: tray 323738a6: cryo: direct: puck: loi2-1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 9, 2021 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 86055 / % possible obs: 100 % / Redundancy: 8.094 % / Biso Wilson estimate: 27.158 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.066 / Χ2: 0.944 / Net I/σ(I): 19.03
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.548.0830.4444.4962680.9310.474100
1.54-1.588.1140.3535.5761320.9590.377100
1.58-1.638.1270.2856.859430.9710.304100
1.63-1.688.1230.2258.558420.9790.241100
1.68-1.738.1470.17410.7256380.9870.186100
1.73-1.798.1680.14712.6854130.990.157100
1.79-1.868.1660.12215.0152880.9930.13100
1.86-1.948.1730.09817.9350810.9950.105100
1.94-2.028.1680.08321.3548810.9960.089100
2.02-2.128.1730.07424.2346430.9960.079100
2.12-2.248.1510.06726.5144550.9970.072100
2.24-2.378.1410.06328.4542240.9970.068100
2.37-2.548.1220.0629.8339640.9970.064100
2.54-2.748.0970.05731.1137190.9970.061100
2.74-38.0850.05532.7534030.9970.059100
3-3.358.0340.05534.1331170.9970.05999.9
3.35-3.877.9880.05235.127600.9980.055100
3.87-4.747.890.05335.4123540.9970.057100
4.74-6.717.6820.05234.718740.9970.056100
6.71-506.6940.05532.2510560.9940.0697

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20-4438refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo structure, pdb entry 7SIR

7sir


Resolution: 1.5→45.91 Å / SU ML: 0.1468 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.388
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.173 1999 2.32 %0
Rwork0.1497 84053 --
obs0.1502 86052 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.91 Å2
Refinement stepCycle: LAST / Resolution: 1.5→45.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3283 0 42 545 3870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713441
X-RAY DIFFRACTIONf_angle_d0.90734684
X-RAY DIFFRACTIONf_chiral_restr0.0587553
X-RAY DIFFRACTIONf_plane_restr0.0073624
X-RAY DIFFRACTIONf_dihedral_angle_d12.77621294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.2251360.18955909X-RAY DIFFRACTION100
1.54-1.580.1831330.16635943X-RAY DIFFRACTION99.98
1.58-1.630.18681450.15035918X-RAY DIFFRACTION100
1.63-1.680.19211600.13555932X-RAY DIFFRACTION100
1.68-1.740.1951550.13335963X-RAY DIFFRACTION100
1.74-1.810.15181550.13345941X-RAY DIFFRACTION100
1.81-1.890.19761250.15315978X-RAY DIFFRACTION99.98
1.89-1.990.2041280.15075972X-RAY DIFFRACTION100
1.99-2.110.16331490.14545978X-RAY DIFFRACTION100
2.11-2.280.17071430.14566015X-RAY DIFFRACTION100
2.28-2.510.15851360.15326015X-RAY DIFFRACTION100
2.51-2.870.17911440.15986085X-RAY DIFFRACTION100
2.87-3.610.18351320.15236109X-RAY DIFFRACTION99.98
3.61-45.910.1571580.1456295X-RAY DIFFRACTION99.52

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