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- PDB-1bf6: PHOSPHOTRIESTERASE HOMOLOGY PROTEIN FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1bf6
TitlePHOSPHOTRIESTERASE HOMOLOGY PROTEIN FROM ESCHERICHIA COLI
ComponentsPHOSPHOTRIESTERASE HOMOLOGY PROTEIN
KeywordsPHOSPHOTRIESTERASE / HYPOTHETICAL PROTEIN
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds / catabolic process / Hydrolases; Acting on ester bonds / 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 homology protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.7 Å
AuthorsBuchbinder, J.L. / Stephenson, R.C. / Scanlan, T.S. / Fletterick, R.J.
Citation
Journal: Biochemistry / Year: 1998
Title: Biochemical characterization and crystallographic structure of an Escherichia coli protein from the phosphotriesterase gene family.
Authors: Buchbinder, J.L. / Stephenson, R.C. / Dresser, M.J. / Pitera, J.W. / Scanlan, T.S. / Fletterick, R.J.
#1: Journal: Biochemistry / Year: 1998
Title: Erratum. Biochemical Characterization and Crystallographic Structure of an Escherichia Coli Protein from the Phosphotriesterase Gene Family
Authors: Buchbinder, J.L. / Stephenson, R.C. / Dresser, M.J. / Pitera, J.W. / Scanlan, T.S. / Fletterick, R.J.
History
DepositionMay 27, 1998Processing site: BNL
Revision 1.0Jun 8, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_label_seq_id / _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: PHOSPHOTRIESTERASE HOMOLOGY PROTEIN
B: PHOSPHOTRIESTERASE HOMOLOGY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,30410
Polymers65,6402
Non-polymers6648
Water5,188288
1
A: PHOSPHOTRIESTERASE HOMOLOGY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3537
Polymers32,8201
Non-polymers5336
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHOSPHOTRIESTERASE HOMOLOGY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9513
Polymers32,8201
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.070, 80.800, 98.200
Angle α, β, γ (deg.)90.00, 97.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999993, -0.000858, -0.000305), (-0.000858, 0.999995, -0.001697), (0.000308, -0.001697, -0.999998)
Vector: 6.20002, 7.79165, -48.62572)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PHOSPHOTRIESTERASE HOMOLOGY PROTEIN


Mass: 32820.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P45548

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Non-polymers , 5 types, 296 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.7 Å3/Da / Density % sol: 51.24 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
21.5 Mammonium sulfate1reservoir
310 %MPD1reservoir
40.1 mM1reservoirZn(OAc)2
550 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 1, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 69475 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.08 / Net I/σ(I): 10.6
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3 / Rsym value: 0.3 / % possible all: 78
Reflection
*PLUS
Num. measured all: 286468
Reflection shell
*PLUS
% possible obs: 78 %

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MIR / Resolution: 1.7→50 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.01 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.241 7012 10 %RANDOM
Rwork0.204 ---
obs0.204 69458 98 %-
Displacement parametersBiso mean: 16.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4595 0 28 288 4911
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.7→1.78 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.36 679 8 %
Rwork0.32 6312 -
obs--77 %
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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