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

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Basic information

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


N-acylneuraminate-9-phosphatase activity / N-acetylneuraminate biosynthetic process / dephosphorylation / metal ion binding
Similarity search - Function
Hypothetical cof family signature 1. / HAD-superfamily hydrolase, subfamily IA, CTE7 / HAD-superfamily hydrolase,subfamily IIIA / Haloacid dehalogenase-like hydrolase / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Glyceraldehyde 3-phosphate phosphatase
Similarity search - Component
Biological speciesThermococcus onnurineus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.703 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 1.1Apr 29, 2015Group: Data collection
Revision 1.2Jun 17, 2015Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / 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_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _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)27,2004
Polymers26,7611
Non-polymers4393
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-7 kcal/mol
Surface area10860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.540, 61.702, 37.575
Angle α, β, γ (deg.)90.00, 107.35, 90.00
Int Tables number5
Space group name H-MC121

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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-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.53 Å3/Da / Density % sol: 51.45 %
Crystal growTemperature: 287 K / Method: evaporation / pH: 9.5 / Details: 1.0M sodium citrate, 0.1M CHES (pH 9.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 28848 / % possible obs: 98.3 % / Redundancy: 3.5 % / Net I/σ(I): 21.7
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 2.7 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.14data extraction
HKL-2000data scaling
HKL-2000data processing
SOLVEphasing
RESOLVEphasing
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementResolution: 1.703→29.242 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1875 2007 6.96 %
Rwork0.1615 --
obs0.1633 28842 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.703→29.242 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1772 0 27 198 1997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071943
X-RAY DIFFRACTIONf_angle_d1.0632646
X-RAY DIFFRACTIONf_dihedral_angle_d11.431772
X-RAY DIFFRACTIONf_chiral_restr0.045284
X-RAY DIFFRACTIONf_plane_restr0.005335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7031-1.74570.23411390.21961806X-RAY DIFFRACTION94
1.7457-1.79290.24871450.19661905X-RAY DIFFRACTION97
1.7929-1.84570.22551380.18321881X-RAY DIFFRACTION98
1.8457-1.90520.181460.1681899X-RAY DIFFRACTION98
1.9052-1.97330.18771420.16041910X-RAY DIFFRACTION98
1.9733-2.05230.16481400.15361901X-RAY DIFFRACTION99
2.0523-2.14570.21611430.1611916X-RAY DIFFRACTION98
2.1457-2.25880.1981400.15751919X-RAY DIFFRACTION99
2.2588-2.40020.20111460.16271912X-RAY DIFFRACTION99
2.4002-2.58550.19241470.16331933X-RAY DIFFRACTION99
2.5855-2.84540.21681390.17261949X-RAY DIFFRACTION99
2.8454-3.25670.19761430.16231957X-RAY DIFFRACTION100
3.2567-4.10130.15251480.14651954X-RAY DIFFRACTION100
4.1013-29.24590.16511510.15321993X-RAY DIFFRACTION100

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