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- PDB-1wvi: Crystal structure of putative phosphatase from Streptococcus muta... -

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Basic information

Entry
Database: PDB / ID: 1wvi
TitleCrystal structure of putative phosphatase from Streptococcus mutans UA159
Componentsputative phosphatases involved in N-acetyl-glucosamine catabolism
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / protein structure initiative / PSI / New York SGX Research Center for Structural Genomics / NYSGXRC / target T1939 / putative phosphatase
Function / homology
Function and homology information


HAD-superfamily hydrolase, subfamily IIA, hypothetical 1 / HAD-superfamily hydrolase, subfamily IIA / Haloacid dehalogenase-like hydrolase / HAD-hyrolase-like / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphatases involved in N-acetyl-glucosamine catabolism
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of putative phosphatase from Streptococcus mutans UA159
Authors: Fedorov, A.A. / Fedorov, E.V. / Almo, S.C.
History
DepositionDec 15, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 3, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative phosphatases involved in N-acetyl-glucosamine catabolism
B: putative phosphatases involved in N-acetyl-glucosamine catabolism
C: putative phosphatases involved in N-acetyl-glucosamine catabolism
D: putative phosphatases involved in N-acetyl-glucosamine catabolism


Theoretical massNumber of molelcules
Total (without water)113,6714
Polymers113,6714
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8450 Å2
ΔGint-39 kcal/mol
Surface area39940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.644, 107.418, 81.940
Angle α, β, γ (deg.)90.00, 97.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
putative phosphatases involved in N-acetyl-glucosamine catabolism


Mass: 28417.766 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DTD6

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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: 2.44 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: PEG2000, Thiocyanate, pH 7.0, VAPOR DIFFUSION, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.97934, 0.97911, 0.97166
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 16, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979341
20.979111
30.971661
ReflectionResolution: 2.3→25 Å / Num. all: 47794 / Num. obs: 47794 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.38 Å / % possible all: 96.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.3→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2394 -RANDOM
Rwork0.248 ---
all0.249 47794 --
obs0.248 47794 98.4 %-
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7840 0 0 0 7840
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.38

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