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- PDB-3l24: Crystal Structure of the Nerve Agent Degrading Organophosphate An... -

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Basic information

Entry
Database: PDB / ID: 3l24
TitleCrystal Structure of the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in Complex with Inhibitors
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
GLYCOLIC ACID / : / Xaa-Pro dipeptidase
Similarity search - Component
Biological speciesAlteromonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsVyas, N.K. / Nichitenko, A. / Rastogi, V.K. / Shah, S.S. / 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 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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)178,27816
Polymers177,5013
Non-polymers77813
Water7,764431
1
A: Xaa-Pro dipeptidase
hetero molecules

A: Xaa-Pro dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,81610
Polymers118,3342
Non-polymers4828
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area5930 Å2
ΔGint-55 kcal/mol
Surface area34620 Å2
MethodPISA
2
B: Xaa-Pro dipeptidase
hetero molecules

C: Xaa-Pro dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,87011
Polymers118,3342
Non-polymers5379
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-x+1/2,y+1/2,-z+1/21
Buried area6180 Å2
ΔGint-61 kcal/mol
Surface area33990 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID / Glycolic acid


Mass: 76.051 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 16% PEG 4000, 20mM 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: 1.0715, 1.8924, 1.8934, 1.8100
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2002 / Details: Mirrors
RadiationMonochromator: KOHZU / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.07151
21.89241
31.89341
41.811
ReflectionResolution: 2.2→47.1 Å / Num. all: 99490 / Num. obs: 99490 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0.9 / Redundancy: 7 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 6.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 0.9 / Num. unique all: 14417 / Rsym value: 0.5 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→47.1 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 4197465.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 8726 10 %RANDOM
Rwork0.235 ---
all0.239 87268 --
obs0.239 87212 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.25 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso mean: 47.3 Å2
Baniso -1Baniso -2Baniso -3
1-14.36 Å20 Å20 Å2
2---10.09 Å20 Å2
3----4.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.3→47.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10227 0 25 431 10683
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.76
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 1397 9.7 %
Rwork0.298 12989 -
obs-1397 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4glycolate_new.param

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