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- PDB-4ygq: Crystal structure of HAD phosphatase from Thermococcus onnurineus -

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Basic information

Entry
Database: PDB / ID: 4ygq
TitleCrystal structure of HAD phosphatase from Thermococcus onnurineus
ComponentsHydrolase
KeywordsHYDROLASE / HAD phosphatase / substrate selectivity
Function / homology
Function and homology information


small molecule biosynthetic process / cellular biosynthetic process / organonitrogen compound biosynthetic process / phosphatase activity / metal ion binding
Similarity search - Function
Hypothetical cof family signature 1. / HAD-superfamily hydrolase, subfamily IA, CTE7 / HAD-superfamily hydrolase,subfamily IIIA / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
TERTIARY-BUTYL ALCOHOL / Glyceraldehyde 3-phosphate phosphatase
Similarity search - Component
Biological speciesThermococcus onnurineus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsNgo, T.D. / Le, B.V. / Subramani, V.K. / Nguyen, C.M.T. / Lee, H.S. / Cho, Y. / Kim, K.K. / Hwang, H.Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Structural basis for the substrate selectivity of a HAD phosphatase from Thermococcus onnurineus NA1
Authors: Ngo, T.D. / Le, B.V. / Subramani, V.K. / Nguyen, C.M.T. / Lee, H.S. / Cho, Y. / Kim, K.K. / Hwang, H.Y.
History
DepositionFeb 26, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8352
Polymers26,7611
Non-polymers741
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint5 kcal/mol
Surface area10590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.193, 62.991, 37.541
Angle α, β, γ (deg.)90.00, 106.50, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-450-

HOH

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Components

#1: Protein Hydrolase /


Mass: 26760.705 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus onnurineus (strain NA1) (archaea)
Strain: NA1 / Gene: TON_0338 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YTD6
#2: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL / Tert-Butyl alcohol


Mass: 74.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.09 %
Crystal growTemperature: 287 K / Method: evaporation / Details: 35% t-butanol and 1.0 M trisodium citrate (pH 5.6)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1.0000, 0.9795, 0.9796, 0.9718
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97951
30.97961
40.97181
ReflectionResolution: 2→50 Å / Num. obs: 17464 / % possible obs: 94.7 % / Redundancy: 3.1 % / Net I/σ(I): 17.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementResolution: 2→33 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2025 899 5.15 %
Rwork0.1659 --
obs0.1679 17457 94.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1772 0 5 130 1907
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071842
X-RAY DIFFRACTIONf_angle_d1.042497
X-RAY DIFFRACTIONf_dihedral_angle_d12.28706
X-RAY DIFFRACTIONf_chiral_restr0.043271
X-RAY DIFFRACTIONf_plane_restr0.006317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9983-2.12350.26661390.19532685X-RAY DIFFRACTION93
2.1235-2.28740.23831410.17792789X-RAY DIFFRACTION95
2.2874-2.51750.24271570.172821X-RAY DIFFRACTION97
2.5175-2.88160.2181490.18322800X-RAY DIFFRACTION96
2.8816-3.62980.20911580.16572778X-RAY DIFFRACTION95
3.6298-330.15971550.14672685X-RAY DIFFRACTION91

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