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- PDB-4qf5: Crystal structure I of MurF from Acinetobacter baumannii -

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Basic information

Entry
Database: PDB / ID: 4qf5
TitleCrystal structure I of MurF from Acinetobacter baumannii
ComponentsUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
KeywordsLIGASE / UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-ananine ligase / MurF
Function / homology
Function and homology information


UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate-D-alanyl-D-alanine ligase activity / UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase / UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / MurE/MurF, N-terminal domain / MurE/MurF, N-terminal / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain ...UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / MurE/MurF, N-terminal domain / MurE/MurF, N-terminal / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Mur ligase, C-terminal 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 / Protein-Tyrosine Phosphatase; Chain A / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / :
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsAn, Y.J. / Jeong, C.S. / Cha, S.S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: ATP-binding mode including a carbamoylated lysine and two Mg(2+) ions, and substrate-binding mode in Acinetobacter baumannii MurF
Authors: Cha, S.S. / An, Y.J. / Jeong, C.S. / Yu, J.H. / Chung, K.M.
History
DepositionMay 19, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
B: UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6178
Polymers103,5052
Non-polymers1,1126
Water0
1
A: UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3084
Polymers51,7531
Non-polymers5563
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3084
Polymers51,7531
Non-polymers5563
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.559, 89.716, 126.896
Angle α, β, γ (deg.)90.00, 93.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase


Mass: 51752.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: AB307-0294 / Gene: ABBFA_000315 / Plasmid: pRSET-A / Production host: Escherichia coli (E. coli)
References: UniProt: B7GVN5, UniProt: A0A0J9X1Z8*PLUS, UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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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: 2.45 Å3/Da / Density % sol: 49.72 %
Crystal growTemperature: 295 K / Method: micro-batch crystallization method / pH: 8.5
Details: 0.16M Magnesium Chloride, 0.08M Tris-HCl pH 8.5, 24%(w/v) polyethylene glycol(PEG) 4,000, 20%(w/v) glycerol, micro-batch crystallization method, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 9, 2013
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 24942 / % possible obs: 99.7 %
Reflection shellResolution: 2.8→2.85 Å / % possible all: 92.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CCP4model building
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→37.439 Å / SU ML: 0.36 / σ(F): 1.54 / Phase error: 24.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 1236 5.14 %
Rwork0.1919 --
obs0.1949 24046 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→37.439 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6913 0 66 0 6979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017107
X-RAY DIFFRACTIONf_angle_d1.2469651
X-RAY DIFFRACTIONf_dihedral_angle_d13.672573
X-RAY DIFFRACTIONf_chiral_restr0.0321100
X-RAY DIFFRACTIONf_plane_restr0.0041264
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8-2.91210.31491180.2446240194
2.9121-3.04450.32091270.2425246395
3.0445-3.2050.2731360.2317252697
3.205-3.40570.2881350.2059252898
3.4057-3.66840.25271460.1921254198
3.6684-4.03720.22731490.1782256399
4.0372-4.62050.23291360.1655256299
4.6205-5.81780.21381450.1744259499
5.8178-37.44250.22821440.1749263298

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