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- PDB-4f78: Crystal Structure of Vancomycin Resistance D,D-dipeptidase VanXYg -

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Basic information

Entry
Database: PDB / ID: 4f78
TitleCrystal Structure of Vancomycin Resistance D,D-dipeptidase VanXYg
ComponentsD,D-dipeptidase/D,D-carboxypeptidase
KeywordsHYDROLASE / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES / NIAID / ALPHA+BETA PROTEIN / METALLOPEPTIDASE / HEDGEHOG/DD-PEPTIDASE FOLD / MEROPS M15B SUBFAMILY / ZN2+-DEPENDENT D / D-DIPEPTIDASE / VANCOMYCIN RESISTANCE / D-ALANINE-D-ALANINE
Function / homology
Function and homology information


carboxypeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Phosphorylase Kinase; domain 1 - #180 / Peptidase M15B / D-alanyl-D-alanine carboxypeptidase / Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
D,D-dipeptidase/D,D-carboxypeptidase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsStogios, P.J. / Wawrzak, Z. / Evdokimova, E. / Minasov, G. / Egorova, O. / Di Leo, R. / Kudritska, M. / Yim, V. / Meziane-Cherif, D. / Courvalin, P. ...Stogios, P.J. / Wawrzak, Z. / Evdokimova, E. / Minasov, G. / Egorova, O. / Di Leo, R. / Kudritska, M. / Yim, V. / Meziane-Cherif, D. / Courvalin, P. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis for the evolution of vancomycin resistance D,D-peptidases.
Authors: Meziane-Cherif, D. / Stogios, P.J. / Evdokimova, E. / Savchenko, A. / Courvalin, P.
History
DepositionMay 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Structure summary
Revision 1.2Oct 16, 2013Group: Structure summary
Revision 1.3Jan 22, 2014Group: Other
Revision 1.4Apr 23, 2014Group: Database references
Revision 1.5May 14, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D,D-dipeptidase/D,D-carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,87017
Polymers29,7761
Non-polymers1,09416
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.912, 43.960, 80.199
Angle α, β, γ (deg.)90.00, 99.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein D,D-dipeptidase/D,D-carboxypeptidase / D / D-peptidase / VanXYG


Mass: 29775.939 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: BM4518 / Gene: vanXYG, vanYG2 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KHL8

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Non-polymers , 6 types, 203 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 0.2 M ammonium sulfate, 0.1 M sodium cacodylate, 30% PEG 8K, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97918 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 9, 2011 / Details: mirrors
RadiationMonochromator: SI {1,1,1} / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.95→79.17 Å / Num. obs: 19747 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 10.6
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 3.6 / Num. unique all: 2850 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→39.584 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1864 949 4.99 %random
Rwork0.1536 ---
obs0.1554 19734 98.35 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.654 Å2 / ksol: 0.399 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.7143 Å20 Å2-4.2779 Å2
2--1.3494 Å2-0 Å2
3---0.3648 Å2
Refinement stepCycle: LAST / Resolution: 1.95→39.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 65 187 2306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162201
X-RAY DIFFRACTIONf_angle_d1.4942966
X-RAY DIFFRACTIONf_dihedral_angle_d14.268840
X-RAY DIFFRACTIONf_chiral_restr0.116310
X-RAY DIFFRACTIONf_plane_restr0.007386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.00270.27751230.21712747X-RAY DIFFRACTION98
2.0027-2.06170.20681460.19472708X-RAY DIFFRACTION98
2.0617-2.12820.21731440.17552768X-RAY DIFFRACTION98
2.1282-2.20430.20521370.15962715X-RAY DIFFRACTION98
2.2043-2.29250.21521460.162811X-RAY DIFFRACTION98
2.2925-2.39680.19721510.15572673X-RAY DIFFRACTION98
2.3968-2.52320.22621510.1582766X-RAY DIFFRACTION98
2.5232-2.68120.19561360.15292757X-RAY DIFFRACTION99
2.6812-2.88820.18821520.15152757X-RAY DIFFRACTION99
2.8882-3.17870.19341530.14972758X-RAY DIFFRACTION99
3.1787-3.63840.17181450.14392772X-RAY DIFFRACTION99
3.6384-4.58290.15641470.12272756X-RAY DIFFRACTION99
4.5829-39.59260.15561440.15962738X-RAY DIFFRACTION98
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)
10.38230.01170.51650.7702-0.08271.4629-0.0166-0.3294-0.26660.17150.04010.10860.1831-0.0589-0.06570.1352-0.01440.01180.12330.03250.1346-13.4764-13.882-18.1936
21.0575-0.424-0.53741.62910.75643.01370.0413-0.02010.0131-0.0517-0.05860.09850.0093-0.13470.00570.0502-0.0142-0.01380.05420.0050.1032-17.2558-5.3482-31.1827
32.6162-0.66-0.06082.2842-0.29192.15230.0153-0.05020.1704-0.06750.05610.0946-0.2049-0.1041-0.02820.0715-0.00350.01970.0411-0.01850.0841-11.87543.1163-23.7725
42.78490.42570.42653.8666-0.50943.098-0.0539-0.6402-0.07150.7326-0.03110.09690.2433-0.06550.01560.17250.0405-0.03850.26560.02230.0305-3.1852-8.8349-5.4101
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 0:50
2X-RAY DIFFRACTION2chain A and resi 51:116
3X-RAY DIFFRACTION3chain A and resi 117:194
4X-RAY DIFFRACTION4chain A and resi 195:250

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