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- PDB-4zwo: Crystal structure of organophosphate anhydrolase/prolidase mutant... -

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Basic information

Entry
Database: PDB / ID: 4zwo
TitleCrystal structure of organophosphate anhydrolase/prolidase mutant Y212F
Componentsorganophosphate anhydrolase/prolidase
KeywordsHYDROLASE / OPAA organophosphate prolidase anhydrolase
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 / : / Xaa-Pro dipeptidase, N-terminal domain / 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 / : / Xaa-Pro dipeptidase, N-terminal domain / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.141 Å
AuthorsDaczkowski, C.M. / Pegan, S.D. / Harvey, S.P.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)W-31-109-Eng-38 United States
Defense Threat Reduction Agency (DTRA)CB3742 United States
CitationJournal: Biochemistry / Year: 2015
Title: Engineering the Organophosphorus Acid Anhydrolase Enzyme for Increased Catalytic Efficiency and Broadened Stereospecificity on Russian VX.
Authors: Daczkowski, C.M. / Pegan, S.D. / Harvey, S.P.
History
DepositionMay 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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
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.ptnr2_symmetry / _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_symmetry
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: organophosphate anhydrolase/prolidase
B: organophosphate anhydrolase/prolidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,40812
Polymers100,7792
Non-polymers62910
Water12,827712
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-55 kcal/mol
Surface area34420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.391, 67.944, 140.450
Angle α, β, γ (deg.)90.000, 110.080, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-601-

HOH

21B-721-

HOH

31B-867-

HOH

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Components

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


Mass: 50389.578 Da / Num. of mol.: 2 / Mutation: Y212F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alteromonas sp. (bacteria) / Gene: pepQ, opaA / Plasmid: pSE420 / Production host: Escherichia coli (E. coli) / References: UniProt: Q44238, Xaa-Pro dipeptidase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID


Mass: 76.051 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 712 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 4% PEG 4,000, 20% Isopropanol, 11 mM BaCl2

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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 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 49830 / % possible obs: 99.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 18.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX1.9-1692refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L24

3l24


Resolution: 2.141→32.899 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2117 2526 5.07 %
Rwork0.1715 47295 -
obs0.1736 49821 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.89 Å2 / Biso mean: 29.7995 Å2 / Biso min: 12.85 Å2
Refinement stepCycle: final / Resolution: 2.141→32.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6953 0 23 712 7688
Biso mean--33.83 36.68 -
Num. residues----859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037209
X-RAY DIFFRACTIONf_angle_d0.6199787
X-RAY DIFFRACTIONf_chiral_restr0.0251031
X-RAY DIFFRACTIONf_plane_restr0.0031295
X-RAY DIFFRACTIONf_dihedral_angle_d12.7912602
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1414-2.18260.27191270.19642102222981
2.1826-2.22710.21681320.197226602792100
2.2271-2.27560.22431330.197426742807100
2.2756-2.32850.23391300.190926602790100
2.3285-2.38670.23851610.193826382799100
2.3867-2.45120.23811380.19826162754100
2.4512-2.52330.24761270.19426842811100
2.5233-2.60470.21391440.191426652809100
2.6047-2.69780.25871300.193326462776100
2.6978-2.80570.26161420.194326592801100
2.8057-2.93340.23691360.1926612797100
2.9334-3.08790.23451340.17926672801100
3.0879-3.28120.19891450.17826212766100
3.2812-3.53430.19171510.16432648279999
3.5343-3.88940.19761630.15062630279399
3.8894-4.45110.1721430.14392646278999
4.4511-5.60340.17991470.13632669281699
5.6034-32.90240.20451430.16582749289299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.4317-4.4426-3.09618.29264.6116.4290.24570.11350.7332-0.5444-0.0482-0.3683-0.79390.2625-0.20820.3147-0.0551-0.00470.15920.02730.2185119.4682-0.368246.5627
21.31760.48320.47611.84980.37531.16570.0642-0.13530.04390.0634-0.0446-0.21-0.03070.0816-0.02970.13920.015-0.03210.16520.00080.1972122.1775-20.349346.537
30.4471.34971.13587.63776.18485.2172-0.18460.3680.3256-1.34990.25030.1815-1.94571.151-0.0730.5663-0.04270.03870.6380.0990.4176127.7451-19.425326.7972
43.3455-1.3089-1.02642.9805-0.0811.42340.0172-0.0669-0.0656-0.0396-0.0651-0.20110.09030.20130.05080.1733-0.0031-0.07770.1857-0.03130.1557124.5139-21.646349.9818
54.75911.32512.05261.13840.83422.14790.02790.1961-0.05980.0212-0.0215-0.0051-0.0605-0.0989-0.00670.17770.03780.03480.12440.00910.133595.5535-13.938633.5262
64.7136-0.01911.46111.0351-0.15791.4373-0.0930.0971-0.0056-0.01130.05730.1094-0.0548-0.15040.04980.18960.0120.0180.1264-0.00420.141290.1666-11.246738.1398
72.99251.08560.22312.36230.7890.75970.2139-0.43680.29520.4422-0.27140.23750.0793-0.25390.04950.2916-0.00330.04590.2814-0.05590.188183.0096-13.028755.6649
85.2235-2.17940.25992.96480.27195.1050.0936-0.5164-0.19160.3-0.04670.00560.3372-0.0668-0.02420.2474-0.0419-0.00320.17380.010.1946103.8869-15.54857.476
95.08881.2131.44286.1006-1.03342.0830.2537-0.2517-0.23130.5352-0.12190.30210.1131-0.4275-0.1590.252-0.02470.03040.2437-0.050.146275.5423-24.640549.9524
107.84324.63213.74915.62412.28052.88160.0442-0.17740.4760.0939-0.16760.1416-0.0874-0.16220.10590.15940.04350.0610.1364-0.02670.150692.6233-6.46547.0385
115.5386-2.69070.57646.6403-1.90073.87710.12470.2603-0.86910.11890.010.02510.6808-0.1296-0.12350.3087-0.0896-0.02170.1936-0.06980.3416101.2319-54.185820.1816
120.92520.45490.52911.43561.01130.86390.0474-0.0953-0.08840.3133-0.0532-0.02430.4033-0.19740.0230.3162-0.05610.00210.18170.03250.1563101.5345-41.543434.6767
133.2251-3.6281-3.13144.87223.80433.1378-0.8661-0.3918-0.24-0.6351-1.08821.0683-1.1543-1.40981.97760.6886-0.0093-0.11580.5701-0.15470.943388.02-32.886539.591
144.2422-0.2091-0.38111.8134-0.32131.57430.0258-0.3688-0.65460.66970.01990.11880.3762-0.331-0.04390.4983-0.10580.02260.26780.04150.297898.4488-49.337637.1297
152.9824-0.1629-0.47861.1127-2.00025.22830.0473-0.2532-0.60290.4152-0.039-0.19740.62080.3311-0.020.4531-0.0107-0.07330.14730.02020.3161111.3923-50.674229.7028
162.21322.2532-0.28724.51990.07110.71060.08230.130.1533-0.0167-0.00370.1365-0.1204-0.0981-0.07920.15130.04420.01350.21570.01490.124107.3802-20.79917.3987
171.72350.6981-0.73051.1425-0.17521.1672-0.010.2442-0.0331-0.09290.0318-0.1014-0.0263-0.0427-0.02150.16140.0075-0.00610.2353-0.01070.1653120.6151-26.93536.71
189.20246.4496-1.85084.6029-1.98916.65380.3026-0.5979-0.47770.6568-0.6458-1.2934-0.00411.20070.35930.37010.0523-0.11110.47390.0110.582124.5015-45.564214.83
197.21435.91040.40965.58650.38961.3566-0.06340.2089-0.30970.01690.0999-0.3211-0.04640.0661-0.01710.14760.04520.01260.157-0.02090.1183125.4425-28.706511.1275
203.45241.7369-0.08652.89150.15561.3238-0.05660.37520.0514-0.06690.1238-0.05-0.0767-0.0382-0.06180.12020.00690.00180.24920.01040.0928118.8069-25.52685.3071
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:10)A2 - 10
2X-RAY DIFFRACTION2(chain A and resid 11:83)A11 - 83
3X-RAY DIFFRACTION3(chain A and resid 84:98)A84 - 98
4X-RAY DIFFRACTION4(chain A and resid 99:164)A99 - 164
5X-RAY DIFFRACTION5(chain A and resid 165:236)A165 - 236
6X-RAY DIFFRACTION6(chain A and resid 237:268)A237 - 268
7X-RAY DIFFRACTION7(chain A and resid 269:335)A269 - 335
8X-RAY DIFFRACTION8(chain A and resid 336:380)A336 - 380
9X-RAY DIFFRACTION9(chain A and resid 381:409)A381 - 409
10X-RAY DIFFRACTION10(chain A and resid 410:440)A410 - 440
11X-RAY DIFFRACTION11(chain B and resid 3:27)B3 - 27
12X-RAY DIFFRACTION12(chain B and resid 28:85)B28 - 85
13X-RAY DIFFRACTION13(chain B and resid 86:98)B86 - 98
14X-RAY DIFFRACTION14(chain B and resid 99:133)B99 - 133
15X-RAY DIFFRACTION15(chain B and resid 134:160)B134 - 160
16X-RAY DIFFRACTION16(chain B and resid 161:234)B161 - 234
17X-RAY DIFFRACTION17(chain B and resid 235:347)B235 - 347
18X-RAY DIFFRACTION18(chain B and resid 348:371)B348 - 371
19X-RAY DIFFRACTION19(chain B and resid 372:398)B372 - 398
20X-RAY DIFFRACTION20(chain B and resid 399:440)B399 - 440

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