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- PDB-3f4c: Crystal structure of organophosphorus hydrolase from Geobacillus ... -

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Basic information

Entry
Database: PDB / ID: 3f4c
TitleCrystal structure of organophosphorus hydrolase from Geobacillus stearothermophilus strain 10, with glycerol bound
ComponentsOrganophosphorus hydrolase
KeywordsHYDROLASE / ALPHA-BETA BARREL / AMIDOHYDROLASE / BINUCLEAR METAL ENZYME / GLYCEROL-BOUND
Function / homology
Function and homology information


catabolic process / zinc ion binding
Similarity search - Function
Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Organophosphorus hydrolase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsHawwa, R. / Aikens, J. / Turner, R.J. / Santarsiero, B. / Mesecar, A.
CitationJournal: Arch.Biochem.Biophys. / Year: 2009
Title: Structural basis for thermostability revealed through the identification and characterization of a highly thermostable phosphotriesterase-like lactonase from Geobacillus stearothermophilus.
Authors: Hawwa, R. / Aikens, J. / Turner, R.J. / Santarsiero, B.D. / Mesecar, A.D.
History
DepositionOct 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 6, 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 / 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_asym_id / _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_asym_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.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 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: Organophosphorus hydrolase
B: Organophosphorus hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9738
Polymers74,5532
Non-polymers4206
Water7,927440
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-11.9 kcal/mol
Surface area23760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.212, 156.761, 49.990
Angle α, β, γ (deg.)90.00, 116.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Organophosphorus hydrolase


Mass: 37276.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: 10 / Production host: Escherichia coli (E. coli) / References: UniProt: D0VX06*PLUS
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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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: 2.22 Å3/Da / Density % sol: 44.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M Ammonium acetate, 0.1 M Sodium citrate, 30% w/v PEG 4000. Cryoprotectant: 0.35 M Ammonium acetate, 0.25 M Sodium citrate pH 5.0, 30% PEG 4000, 30% Glycerol, pH 5.6, VAPOR DIFFUSION, ...Details: 0.2 M Ammonium acetate, 0.1 M Sodium citrate, 30% w/v PEG 4000. Cryoprotectant: 0.35 M Ammonium acetate, 0.25 M Sodium citrate pH 5.0, 30% PEG 4000, 30% Glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 25, 2005 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→20 Å / Num. all: 35079 / Num. obs: 35079 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 29
Reflection shellResolution: 2.07→2.14 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 6.7 / % possible all: 54.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ZC1

2zc1


Resolution: 2.07→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2518 1742 RANDOM
Rwork0.191 --
all0.191 35079 -
obs0.191 35079 -
Solvent computationBsol: 72.5295 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.097 Å20 Å2-0.769 Å2
2---12.056 Å20 Å2
3---3.959 Å2
Refinement stepCycle: LAST / Resolution: 2.07→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5096 0 16 440 5552
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.62313
X-RAY DIFFRACTIONc_bond_d0.012421
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d1.01
LS refinement shellResolution: 2.07→2.09 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 18 -
Rwork0.2843 --
obs-338 54.3 %

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