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- PDB-4j5n: Crystal Structure of a Deinococcus radiodurans PTE-like lactonase... -

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Basic information

Entry
Database: PDB / ID: 4j5n
TitleCrystal Structure of a Deinococcus radiodurans PTE-like lactonase (drPLL) mutant Y28L/D71N/E101G/E179D/V235L/L270M
ComponentsPhosphotriesterase, putative
KeywordsHYDROLASE / Metalloenzyme / Tim Barrel / Nerve agent / Phosphotriesterase / Lactonase
Function / homology
Function and homology information


lactonohydrolase activity / 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: 2.05 Å
AuthorsMeier, M.M. / Rajendran, C. / Malisi, C. / Fox, N.G. / Xu, C. / Schlee, S. / Barondeau, D.P. / Hocker, B. / Sterner, R. / Raushel, F.M.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Molecular engineering of organophosphate hydrolysis activity from a weak promiscuous lactonase template.
Authors: Meier, M.M. / Rajendran, C. / Malisi, C. / Fox, N.G. / Xu, C. / Schlee, S. / Barondeau, D.P. / Hocker, B. / Sterner, R. / Raushel, F.M.
History
DepositionFeb 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphotriesterase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8223
Polymers34,7041
Non-polymers1182
Water3,783210
1


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

A: Phosphotriesterase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6446
Polymers69,4082
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area3910 Å2
ΔGint-75 kcal/mol
Surface area22280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.655, 61.655, 203.670
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 Phosphotriesterase, putative


Mass: 34704.102 Da / Num. of mol.: 1 / Mutation: Y28L, D71N, E101G, E179D, V235L, L270M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: Dr0930 (gi 15805954), DR_0930 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21DE3 Rosetta 2 cells / 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.: 210 / 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: 3.22 Å3/Da / Density % sol: 61.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2 uL of protein (~10 mg/mL) and 2 uL of well solution (0.1 M imidazole pH 8.0, 10% PEG 8000, 0.2 M Ca(OAc)2 ) were mixed and placed on a siliconized coverslip over 500 uL of the well ...Details: 2 uL of protein (~10 mg/mL) and 2 uL of well solution (0.1 M imidazole pH 8.0, 10% PEG 8000, 0.2 M Ca(OAc)2 ) were mixed and placed on a siliconized coverslip over 500 uL of the well solution. Cryo 14% EG, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2010
RadiationMonochromator: Si(111), side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 29424 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.4 % / Biso Wilson estimate: 38.6 Å2 / Rsym value: 0.137 / Net I/σ(I): 36.5
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 19.1 % / Mean I/σ(I) obs: 7.8 / Num. unique all: 1417 / Rsym value: 0.473 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
XFITdata reduction
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FDK

3fdk


Resolution: 2.05→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 1475 -RANDOM
Rwork0.2353 ---
all-29145 --
obs-29122 99.9 %-
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2431 0 2 210 2643
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_mcangle_it2.138
X-RAY DIFFRACTIONc_mcbond_it1.325
X-RAY DIFFRACTIONc_angle_deg1.593
X-RAY DIFFRACTIONc_bond_d0.0118
LS refinement shellResolution: 2.05→2.07 Å /
RfactorNum. reflection
Rfree0.432 49
Rwork0.365 -
obs-906

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