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- PDB-3l7g: Crystal structure of organophosphate anhydrolase/prolidase -

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Basic information

Entry
Database: PDB / ID: 3l7g
TitleCrystal structure of organophosphate anhydrolase/prolidase
ComponentsXaa-Pro dipeptidase
KeywordsHYDROLASE / Pita-bread / Detoxification / Dipeptidase / Manganese / Metal-binding / Metalloprotease / Protease
Function / homology
Function and homology information


diisopropyl-fluorophosphatase / diisopropyl-fluorophosphatase activity / Xaa-Pro dipeptidase / proline dipeptidase activity / aryldialkylphosphatase / aryldialkylphosphatase activity / metalloexopeptidase activity / response to toxic substance / proteolysis / metal ion binding
Similarity search - Function
: / Xaa-Pro dipeptidase, N-terminal domain / 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 ...: / Xaa-Pro dipeptidase, N-terminal domain / 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
N,N'-bis(1-methylethyl)phosphorodiamidic acid / : / Xaa-Pro dipeptidase
Similarity search - Component
Biological speciesAlteromonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsVyas, N.K. / Nickitenko, A. / Quiocho, F.A.
CitationJournal: Biochemistry / Year: 2010
Title: Structural insights into the dual activities of the nerve agent degrading organophosphate anhydrolase/prolidase.
Authors: Vyas, N.K. / Nickitenko, A. / Rastogi, V.K. / Shah, S.S. / Quiocho, F.A.
History
DepositionDec 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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_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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.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: Xaa-Pro dipeptidase
B: Xaa-Pro dipeptidase
C: Xaa-Pro dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,64617
Polymers177,5013
Non-polymers1,14514
Water5,585310
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Xaa-Pro dipeptidase
hetero molecules

A: Xaa-Pro dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,13412
Polymers118,3342
Non-polymers80010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area5220 Å2
ΔGint-38 kcal/mol
Surface area34280 Å2
MethodPISA
3
B: Xaa-Pro dipeptidase
hetero molecules

C: Xaa-Pro dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,07911
Polymers118,3342
Non-polymers7459
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-x+1/2,y+1/2,-z+1/21
Buried area5210 Å2
ΔGint-37 kcal/mol
Surface area33690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.354, 143.934, 219.213
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Xaa-Pro dipeptidase / X-Pro dipeptidase / Proline dipeptidase / Prolidase / Imidodipeptidase / Organophosphorus acid ...X-Pro dipeptidase / Proline dipeptidase / Prolidase / Imidodipeptidase / Organophosphorus acid anhydrolase 2 / OPAA-2 / DFPase / Phosphotriesterase / Paraoxon hydrolase


Mass: 59166.891 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alteromonas sp. (bacteria) / Strain: JD6.5 / Gene: opaA, pepQ / Plasmid: pT651 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue
References: UniProt: Q44238, Xaa-Pro dipeptidase, diisopropyl-fluorophosphatase, aryldialkylphosphatase
#2: Chemical ChemComp-M44 / N,N'-bis(1-methylethyl)phosphorodiamidic acid


Mass: 180.185 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H17N2O2P
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAS PER THE AUTHORS THE ELECTRON DENSITIES AT 211, 283 AND 439 FIT VERY CONVINCINGLY TO PRO, MET AND ...AS PER THE AUTHORS THE ELECTRON DENSITIES AT 211, 283 AND 439 FIT VERY CONVINCINGLY TO PRO, MET AND LEU RESPECTIVELY

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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: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 1mM Mipafox, 16% PEG 4000, 20 mM MnCl2, 1mM beta-mercaptoethanol, 270 mM ammonium acetate and 60 mM sodium acetate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2002 / Details: mirrors
RadiationMonochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.7→100 Å / Num. obs: 54263 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Biso Wilson estimate: 42.2 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 9.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.444 / % possible all: 97.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3L24

3l24


Resolution: 2.7→40.73 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3187018.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.259 5017 10.1 %RANDOM
Rwork0.204 ---
obs0.204 49599 91.4 %-
all-51982 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.14 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 42.7 Å2
Baniso -1Baniso -2Baniso -3
1-15.75 Å20 Å20 Å2
2---10.99 Å20 Å2
3----4.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.7→40.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10227 0 44 310 10581
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.3
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 792 10.4 %
Rwork0.309 6852 -
obs--85.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4MFPRODUCT.PARAMMFPRODUCT.TOP

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