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- PDB-2nyv: X-ray crystal structure of a phosphoglycolate phosphatase from Aq... -

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Basic information

Entry
Database: PDB / ID: 2nyv
TitleX-ray crystal structure of a phosphoglycolate phosphatase from Aquifex aeolicus
ComponentsPhosphoglycolate phosphatase
KeywordsHYDROLASE / phosphatase / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


phosphoglycolate phosphatase / phosphoglycolate phosphatase activity / glycolate biosynthetic process / dephosphorylation / carbohydrate metabolic process / DNA repair / metal ion binding / cytosol
Similarity search - Function
Phosphoglycolate phosphatase, prokaryotic / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 ...Phosphoglycolate phosphatase, prokaryotic / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Phosphoglycolate phosphatase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.103 Å
AuthorsCiatto, C. / Min, T. / Gorman, J. / Burley, S.K. / Shapiro, L. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: X-ray crystal structure of a phosphoglycolate phosphatase from Aquifex aeolicus
Authors: Ciatto, C. / Min, T. / Gorman, J. / Burley, S.K. / Shapiro, L.
History
DepositionNov 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE Residue MSE 1 A is an initiating methionine and a modified residue

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoglycolate phosphatase


Theoretical massNumber of molelcules
Total (without water)25,0981
Polymers25,0981
Non-polymers00
Water4,252236
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.084, 121.698, 74.474
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-228-

HOH

21A-249-

HOH

31A-264-

HOH

41A-277-

HOH

51A-443-

HOH

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Components

#1: Protein Phosphoglycolate phosphatase / / PGPase / PGP


Mass: 25097.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: gph / Plasmid: BC pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O67359, phosphoglycolate phosphatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.85 Å3/Da / Density % sol: 56.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 15 % PEG 3350, 0.1 M Na acetate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 16996 / % possible obs: 100 % / Rmerge(I) obs: 0.107 / Χ2: 1.011 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
2.1-2.170.30516590.942100
2.17-2.260.26216771.067100
2.26-2.360.22916811.03100
2.36-2.490.16916721.025100
2.49-2.640.14716891.023100
2.64-2.850.12216841.013100
2.85-3.130.10316981.006100
3.13-3.590.08517081.001100
3.59-4.510.06917171100
4.51-200.07418110.999100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.103→19.963 Å / Stereochemistry target values: ml
RfactorNum. reflection% reflection
Rfree0.269 861 5.07 %
Rwork0.204 --
obs-16974 -
Displacement parametersBiso mean: 8.006 Å2
Refinement stepCycle: LAST / Resolution: 2.103→19.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1714 0 0 236 1950

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