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- PDB-4fu0: Crystal Structure of VanG D-Ala:D-Ser Ligase from Enterococcus fa... -

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Basic information

Entry
Database: PDB / ID: 4fu0
TitleCrystal Structure of VanG D-Ala:D-Ser Ligase from Enterococcus faecalis
ComponentsD-alanine--D-alanine ligase 7
KeywordsLIGASE / Vancomycin resistance / Peptidoglycan synthesis / D-Ala:D-Ser ligase / ATP-grasp domain
Function / homology
Function and homology information


D-alanine-D-alanine ligase / D-alanine-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
D-alanine--D-alanine ligase/VANA/B/C, conserved site / D-alanine--D-alanine ligase / D-alanine--D-alanine ligase, C-terminal / D-alanine--D-alanine ligase, N-terminal domain / D-ala D-ala ligase N-terminus / D-ala D-ala ligase C-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / Rossmann fold - #20 / ATP-grasp fold, A domain ...D-alanine--D-alanine ligase/VANA/B/C, conserved site / D-alanine--D-alanine ligase / D-alanine--D-alanine ligase, C-terminal / D-alanine--D-alanine ligase, N-terminal domain / D-ala D-ala ligase N-terminus / D-ala D-ala ligase C-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / D-alanine--D-alanine ligase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMeziane-Cherif, D. / Saul, F.A. / Haouz, A. / Courvalin, P.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural and functional characterization of VanG D-Ala:D-Ser ligase associated with vancomycin resistance in Enterococcus faecalis
Authors: Meziane-Cherif, D. / Saul, F.A. / Haouz, A. / Courvalin, P.
History
DepositionJun 28, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-alanine--D-alanine ligase 7
B: D-alanine--D-alanine ligase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,40413
Polymers79,6852
Non-polymers1,71911
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-144 kcal/mol
Surface area28220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.070, 116.070, 177.228
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein D-alanine--D-alanine ligase 7 / D-Ala-D-Ala ligase 7 / D-alanylalanine synthetase 7


Mass: 39842.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: BM4518 / Gene: ddl7, vanG / Plasmid: pAT911 [pET28a(+) vanG] / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q6WRY5, D-alanine-D-alanine ligase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 4.32 Å3/Da / Density % sol: 71.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.5M ammonium sulfate, 0.9M lithium sulfate, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2009
RadiationMonochromator: Si(111) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.35→33.51 Å / Num. all: 57000 / Num. obs: 57000 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 53.3 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.3
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 1.9 / Num. unique all: 8252 / % possible all: 98.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0072refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E4E

1e4e


Resolution: 2.35→33.5 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.673 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.173 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22412 1747 3.1 %RANDOM
Rwork0.1892 ---
all0.19026 55248 --
obs0.19026 55248 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.033 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å21 Å20 Å2
2--1.99 Å20 Å2
3----2.99 Å2
Refinement stepCycle: LAST / Resolution: 2.35→33.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5342 0 99 300 5741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225543
X-RAY DIFFRACTIONr_bond_other_d0.0010.023699
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.9837507
X-RAY DIFFRACTIONr_angle_other_deg0.85439064
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9825684
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.98224.852237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.39215964
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3351522
X-RAY DIFFRACTIONr_chiral_restr0.0760.2847
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026059
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021097
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_it1.21623397
X-RAY DIFFRACTIONr_mcbond_other0.17721403
X-RAY DIFFRACTIONr_mcangle_it2.25435496
X-RAY DIFFRACTIONr_scbond_it1.91232146
X-RAY DIFFRACTIONr_scangle_it3.15542010
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.38 Å / Total num. of bins used: 40
RfactorNum. reflection% reflection
Rfree0.404 60 -
Rwork0.328 2050 -
obs-2050 98.14 %

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