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- PDB-3gu9: R228A mutation in organophosphorus hydrolase from Deinococcus rad... -

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Basic information

Entry
Database: PDB / ID: 3gu9
TitleR228A mutation in organophosphorus hydrolase from Deinococcus radiodurans
ComponentsOrganophosphorus hydrolase
KeywordsHYDROLASE / mutant / amidohydrolase / alpha-beta barrel
Function / homology
Function and homology information


lactonohydrolase activity / catabolic process / zinc ion binding
Similarity search - Function
Aryldialkylphosphatase, zinc-binding site / Phosphotriesterase family signature 1. / Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Phosphotriesterase, putative
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsHawwa, R. / Larsen, S. / Ratia, K. / Mesecar, A.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structure-based and random mutagenesis approaches increase the organophosphate-degrading activity of a phosphotriesterase homologue from Deinococcus radiodurans.
Authors: Hawwa, R. / Larsen, S.D. / Ratia, K. / Mesecar, A.D.
History
DepositionMar 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Organophosphorus hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6473
Polymers35,5291
Non-polymers1182
Water6,197344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Organophosphorus hydrolase
hetero molecules

A: Organophosphorus hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2946
Polymers71,0582
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+5/31
Buried area3580 Å2
ΔGint-70 kcal/mol
Surface area23240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.200, 61.200, 206.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Organophosphorus hydrolase / Phosphotriesterase / putative


Mass: 35528.926 Da / Num. of mol.: 1 / Mutation: R228A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: DR_0930 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RVU2
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsWATER MOLECULES 1001-1345 IN THE PDB FILE CORRESPOND TO WATER MOLECULES 1-345 IN THE RELEVANT PUBLICATION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.6 M succinic acid, pH 7.0, 16% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorDate: Aug 26, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.06→20 Å / Num. obs: 50401 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.113
Reflection shellResolution: 2.06→2.18 Å / Rmerge(I) obs: 0.498 / % possible all: 85.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→20 Å / σ(F): 0
RfactorNum. reflection
Rfree0.221 2575
Rwork0.186 -
all-52976
obs-50401
Refinement stepCycle: LAST / Resolution: 2.06→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2499 0 2 344 2845
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.42

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