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- PDB-3rva: Crystal structure of organophosphorus acid anhydrolase from Alter... -

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Basic information

Entry
Database: PDB / ID: 3rva
TitleCrystal structure of organophosphorus acid anhydrolase from Alteromonas macleodii
ComponentsOrganophosphorus acid anhydrolase
KeywordsHYDROLASE / organophosphorus acid anhydrolase / pita-bread fold / binuclear metal center / bi-functional / prolidase / nerve agents / Xaa-Pro dipeptides
Function / homology
Function and homology information


phosphoric triester hydrolase activity / Xaa-Pro dipeptidase / proline dipeptidase activity / metalloexopeptidase activity / metal ion binding
Similarity search - Function
Xaa-Pro dipeptidase / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 ...Xaa-Pro dipeptidase / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / NICKEL (II) ION / PHOSPHATE ION / Xaa-Pro dipeptidase
Similarity search - Component
Biological speciesAlteromonas macleodii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsStepankova, A. / Koval, T. / Ostergaard, L.H. / Duskova, J. / Skalova, T. / Hasek, J. / Dohnalek, J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Organophosphorus acid anhydrolase from Alteromonas macleodii: structural study and functional relationship to prolidases.
Authors: Stepankova, A. / Duskova, J. / Skalova, T. / Hasek, J. / Koval, T. / Ostergaard, L.H. / Dohnalek, J.
History
DepositionMay 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Sep 13, 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_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 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: Organophosphorus acid anhydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7865
Polymers51,5231
Non-polymers2644
Water8,359464
1
A: Organophosphorus acid anhydrolase
hetero molecules

A: Organophosphorus acid anhydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,57310
Polymers103,0462
Non-polymers5278
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5450 Å2
ΔGint-74 kcal/mol
Surface area36090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.770, 49.190, 97.340
Angle α, β, γ (deg.)90.00, 125.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Organophosphorus acid anhydrolase


Mass: 51522.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: construct with C-terminal non-cleavable HIS tag / Source: (gene. exp.) Alteromonas macleodii (bacteria) / Plasmid: pET-30(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: F8UVJ4*PLUS, diisopropyl-fluorophosphatase, Xaa-Pro dipeptidase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 2.54 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.056 M Sodium phosphate monobasic monohydrate, 1.344 M Potassium phosphate dibasic, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 19, 2010 / Details: 2 mirrors and a double-crystal monochromator
RadiationMonochromator: KMC-1, Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. all: 48066 / Num. obs: 48066 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 4.4 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 16.65
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 2 / Num. unique all: 2405 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.6.0111refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3L24

3l24


Resolution: 1.8→40 Å / Cor.coef. Fo:Fc: 0.969 / SU B: 1.788 / SU ML: 0.055 / Isotropic thermal model: isotropic / Cross valid method: Rfree throughout / σ(F): 0
Stereochemistry target values: CCP4 6.1.3 stereochemistry library
Details: HYDROGENS HAVE BEEN GENERATED AND USED ONLY IN REFINEMENT. STRUCTURE SOLUTION AND REFINEMENT WERE PERFORMED USING FREE R FOR CROSS-VALIDATION THROUGHOUT: FREE R = 0.185 (FREE R = 0.2610 FOR ...Details: HYDROGENS HAVE BEEN GENERATED AND USED ONLY IN REFINEMENT. STRUCTURE SOLUTION AND REFINEMENT WERE PERFORMED USING FREE R FOR CROSS-VALIDATION THROUGHOUT: FREE R = 0.185 (FREE R = 0.2610 FOR THE HIGHEST RESOLUTION SHELL) FROM A RANDOM TEST SET COMPRISING 5% OF REFLECTIONS (47975 TOTAL). FINAL REFINEMENT WAS PERFORMED USING ALL REFLECTIONS.
RfactorNum. reflection% reflectionSelection details
Rwork0.1559 ---
all0.1563 47975 --
obs0.1563 47975 99.43 %-
Rfree-2371 -random
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.099 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å2-1.39 Å2
2--0.05 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3579 0 8 464 4051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223776
X-RAY DIFFRACTIONr_bond_other_d0.0010.022543
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.9455151
X-RAY DIFFRACTIONr_angle_other_deg0.8736204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5045.043466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39724.279201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.06415627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6821524
X-RAY DIFFRACTIONr_chiral_restr0.0870.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214249
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02778
LS refinement shellResolution: 1.802→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.24 3274 -
Rfree-159 -
obs-3274 95.34 %

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