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- PDB-1r44: Crystal Structure of VanX -

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Basic information

Entry
Database: PDB / ID: 1r44
TitleCrystal Structure of VanX
ComponentsD-alanyl-D-alanine dipeptidase
KeywordsHYDROLASE / VanX / E.faecium / dipeptidase
Function / homology
Function and homology information


D-Ala-D-Ala dipeptidase / dipeptidase activity / cell wall organization / metallopeptidase activity / response to antibiotic / proteolysis / zinc ion binding
Similarity search - Function
D-alanyl-D-alanine dipeptidase / D-ala-D-ala dipeptidase / Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
D-alanyl-D-alanine dipeptidase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.25 Å
AuthorsPratt, S.D. / Katz, L. / Severin, J.M. / Holzman, T. / Park, C.H.
CitationJournal: Mol.Cell / Year: 1998
Title: The Structure of VanX Reveals a Novel Amino-Dipeptidase Involved in Mediating Transposon-Based Vancomycin Resistance
Authors: Bussiere, D.E. / Pratt, S.D. / Katz, L. / Severin, J.M. / Holzman, T. / Park, C.H.
History
DepositionOct 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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-alanyl-D-alanine dipeptidase
B: D-alanyl-D-alanine dipeptidase
C: D-alanyl-D-alanine dipeptidase
D: D-alanyl-D-alanine dipeptidase
E: D-alanyl-D-alanine dipeptidase
F: D-alanyl-D-alanine dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,84112
Polymers140,4496
Non-polymers3926
Water21612
1
A: D-alanyl-D-alanine dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4742
Polymers23,4081
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D-alanyl-D-alanine dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4742
Polymers23,4081
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: D-alanyl-D-alanine dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4742
Polymers23,4081
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: D-alanyl-D-alanine dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4742
Polymers23,4081
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: D-alanyl-D-alanine dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4742
Polymers23,4081
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: D-alanyl-D-alanine dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4742
Polymers23,4081
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.597, 44.694, 169.428
Angle α, β, γ (deg.)90.00, 103.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
D-alanyl-D-alanine dipeptidase / D-Ala-D-Ala dipeptidase / Vancomycin B-type resistance protein vanX


Mass: 23408.168 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria) / Gene: VANX / Plasmid: pGW1 / Species (production host): Escherichia coli
Production host: Escherichia coli str. K12 substr. W3110 (bacteria)
Strain (production host): w3110
References: UniProt: Q06241, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.16 Å3/Da / Density % sol: 43.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: ammonium sulfate, PEG-monomethyl ester 5000, zinc chloride, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 1, 1997
RadiationMonochromator: Dual Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 56541 / Num. obs: 44765 / % possible obs: 79.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2
Reflection shellResolution: 2.25→2.3 Å / % possible all: 75

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
MLPHAREphasing
CNS0.9refinement
RefinementMethod to determine structure: MIR / Resolution: 2.25→50 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.301 4512 -Random
Rwork0.254 ---
all0.258 56541 --
obs0.258 44756 79.2 %-
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9906 0 6 12 9924
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.72
X-RAY DIFFRACTIONc_bond_d0.015

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