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- PDB-1wr8: Crystal structure of hypothetical protein PH1421 from Pyrococcus ... -

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Basic information

Entry
Database: PDB / ID: 1wr8
TitleCrystal structure of hypothetical protein PH1421 from Pyrococcus horikoshii.
ComponentsPhosphoglycolate phosphatase
KeywordsHYDROLASE / alpha / beta core domain / had superfamily / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


phosphoglycolate phosphatase / phosphoglycolate phosphatase activity / carbohydrate metabolic process / magnesium ion binding
Similarity search - Function
Phosphoglycolate phosphatase / Hypothetical Protein Ta0175; Chain: A, domain 2 - #10 / Hypothetical Protein Ta0175; Chain: A, domain 2 / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD-like superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Phosphoglycolate phosphatase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsYamamoto, H. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structure of a haloacid dehalogenase superfamily phosphatase PH1421 from Pyrococcus horikoshii OT3: oligomeric state and thermoadaptation mechanism.
Authors: Yamamoto, H. / Takio, K. / Sugahara, M. / Kunishima, N.
History
DepositionOct 13, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 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 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Phosphoglycolate phosphatase
B: Phosphoglycolate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3403
Polymers51,2812
Non-polymers591
Water10,233568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-14 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.795, 81.772, 86.949
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer in asymmetric unit.

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Components

#1: Protein Phosphoglycolate phosphatase / PGP / Haloacid dehalogenase-like hydrolase


Mass: 25640.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH1421 / Plasmid: pET 11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: O50129, phosphoglycolate phosphatase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 2.2 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 4.6
Details: ammonium acetate, sodium acetate, PEG 4000, glycerol, potassium dihydrogen phosphate, pH 4.6, MICROBATCH, temperature 291K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1.0000, 1.590996, 1.591394, 1.594101
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jul 4, 2004 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.5909961
31.5913941
41.5941011
ReflectionResolution: 1.6→40 Å / Num. all: 60470 / Num. obs: 59382 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 19.403 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.039 / Net I/σ(I): 19.1
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 6.2 / Rsym value: 0.27 / % possible all: 96.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.6→37 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2117 3003 -RANDOM
Rwork0.1973 ---
obs0.1973 59331 97.7 %-
Displacement parametersBiso mean: 22.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.16 Å2-3.85 Å21.69 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.6→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3600 0 4 568 4172
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.27 481 -
Rwork0.234 --
obs-8895 93.8 %

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