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- PDB-6cau: UDP-N-acetylmuramate--alanine ligase from Acinetobacter baumannii... -

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Basic information

Entry
Database: PDB / ID: 6cau
TitleUDP-N-acetylmuramate--alanine ligase from Acinetobacter baumannii AB5075-UW with AMPPNP
ComponentsUDP-N-acetylmuramate--L-alanine ligase
KeywordsLIGASE / MurC / SSGCID / AMPPNP / Acinetobacter baumannii AB5075-UW / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


UDP-N-acetylmuramate-L-alanine ligase / UDP-N-acetylmuramate-L-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / ATP binding / cytoplasm
Similarity search - Function
UDP-N-acetylmuramate--L-alanine ligase / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain ...UDP-N-acetylmuramate--L-alanine ligase / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / UDP-N-acetylmuramate--L-alanine ligase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHoranyi, P.S. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: UDP-N-acetylmuramate--alanine ligase from Acinetobacter baumannii AB5075-UW with AMPPNP
Authors: Horanyi, P.S. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJan 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6204
Polymers52,0651
Non-polymers5553
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-19 kcal/mol
Surface area13280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.180, 82.180, 154.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein UDP-N-acetylmuramate--L-alanine ligase / UDP-N-acetylmuramoyl-L-alanine synthetase


Mass: 52064.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: murC, ABBFA_000146 / Production host: Escherichia coli (E. coli)
References: UniProt: B7GV74, UDP-N-acetylmuramate-L-alanine ligase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.51 Å3/Da / Density % sol: 51.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.4 uL 20 mg/mL AcbaC.00137.b.B5 PD00479 + 0.4 uL MCSG1 A10 (200 mM magnesium chloride, 100 mM MES/NaOH, pH 6.5, 10% PEG4000, 3 mM AMPPNP, 3 mM UDP, 3 mM magnesium chloride) in XJR trays, ...Details: 0.4 uL 20 mg/mL AcbaC.00137.b.B5 PD00479 + 0.4 uL MCSG1 A10 (200 mM magnesium chloride, 100 mM MES/NaOH, pH 6.5, 10% PEG4000, 3 mM AMPPNP, 3 mM UDP, 3 mM magnesium chloride) in XJR trays, cryoprotectant: 25% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 8, 2017
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 19078 / % possible obs: 100 % / Redundancy: 11.9 % / Net I/σ(I): 31.89
Reflection shellResolution: 2.5→2.56 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→46.482 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.84
RfactorNum. reflection% reflection
Rfree0.1964 1908 10 %
Rwork0.1667 --
obs0.1697 19077 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→46.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2267 0 33 101 2401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072346
X-RAY DIFFRACTIONf_angle_d0.8823196
X-RAY DIFFRACTIONf_dihedral_angle_d5.221865
X-RAY DIFFRACTIONf_chiral_restr0.054376
X-RAY DIFFRACTIONf_plane_restr0.005418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56250.27671330.18951193X-RAY DIFFRACTION100
2.5625-2.63180.28631330.18821202X-RAY DIFFRACTION100
2.6318-2.70920.23211340.18891201X-RAY DIFFRACTION100
2.7092-2.79660.2011320.17861195X-RAY DIFFRACTION100
2.7966-2.89660.22531340.18761195X-RAY DIFFRACTION100
2.8966-3.01250.24841340.19441215X-RAY DIFFRACTION100
3.0125-3.14960.19461340.18241210X-RAY DIFFRACTION100
3.1496-3.31560.22381350.18171207X-RAY DIFFRACTION100
3.3156-3.52330.231360.18781231X-RAY DIFFRACTION100
3.5233-3.79520.20311350.17911210X-RAY DIFFRACTION100
3.7952-4.17690.17191390.13831245X-RAY DIFFRACTION100
4.1769-4.78080.16341360.1341237X-RAY DIFFRACTION100
4.7808-6.02120.16211410.16381266X-RAY DIFFRACTION100
6.0212-46.48950.19421520.16611362X-RAY DIFFRACTION100
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)
15.52860.946-0.28879.5483-1.20611.70390.10190.15980.2308-0.0051-0.0049-0.3955-0.07340.6902-0.04870.44650.0140.0490.5485-0.03340.39953.3816.2977-50.291
23.4152-0.437-0.09614.3195-0.55023.593-0.10840.24540.4227-0.57830.0224-0.7972-0.44620.51460.06670.485-0.05420.0430.4604-0.00580.49924.487323.3974-50.5826
33.16810.61250.7032.630.44982.59760.1282-0.49380.14690.1888-0.1228-0.0450.05030.0654-0.01350.29830.0119-0.02780.5065-0.03010.37740.688618.096-22.1431
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 34 )
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 119 )
3X-RAY DIFFRACTION3chain 'A' and (resid 120 through 328 )

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