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

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Basic information

Entry
Database: PDB / ID: 4zwp
TitleCrystal structure of organophosphate anhydrolase/prolidase mutant Y212F
ComponentsOPAA organophosphate prolidase anhydrolase
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 / aminopeptidase activity / response to toxic substance / proteolysis ...diisopropyl-fluorophosphatase / diisopropyl-fluorophosphatase activity / Xaa-Pro dipeptidase / proline dipeptidase activity / aryldialkylphosphatase / aryldialkylphosphatase activity / metalloexopeptidase activity / aminopeptidase activity / response to toxic substance / proteolysis / metal ion binding / cytosol
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 / molecular replacement / Resolution: 2.397 Å
AuthorsDaczkowski, C.M. / Pegan, S.D. / Harvey, S.P.
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 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Sep 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_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.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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_value_order / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)102,02815
Polymers100,7792
Non-polymers1,24913
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-47 kcal/mol
Surface area34010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.493, 68.179, 142.479
Angle α, β, γ (deg.)90.000, 110.500, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-503-

BA

21A-781-

HOH

31B-632-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein OPAA organophosphate prolidase anhydrolase / 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

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Non-polymers , 5 types, 390 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ba
#4: Chemical ChemComp-M44 / N,N'-bis(1-methylethyl)phosphorodiamidic acid


Mass: 180.185 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H17N2O2P
#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.: 377 / 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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 4% PEG 4,000, 20% Isopropanol, 11 mM BaCl2, 790 uM mipafox

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.397→50 Å / Num. obs: 37080 / % possible obs: 98.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 10.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZWO

4zwo


Resolution: 2.397→48.936 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 23.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2259 1990 5.67 %
Rwork0.1726 33100 -
obs0.1756 35090 94.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.2 Å2 / Biso mean: 39.1694 Å2 / Biso min: 13.13 Å2
Refinement stepCycle: final / Resolution: 2.397→48.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6876 0 46 377 7299
Biso mean--59.48 40.34 -
Num. residues----850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077127
X-RAY DIFFRACTIONf_angle_d0.9569677
X-RAY DIFFRACTIONf_chiral_restr0.0371020
X-RAY DIFFRACTIONf_plane_restr0.0041277
X-RAY DIFFRACTIONf_dihedral_angle_d14.2212574
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3972-2.45710.2875880.22451572166064
2.4571-2.52360.25331400.21932205234589
2.5236-2.59780.28881490.21132416256596
2.5978-2.68170.2711410.21262439258099
2.6817-2.77750.26821510.20942454260599
2.7775-2.88870.32141490.209624652614100
2.8887-3.02020.25811450.20812487263299
3.0202-3.17940.27571530.203824862639100
3.1794-3.37850.25741470.18472474262199
3.3785-3.63930.21331410.16692439258097
3.6393-4.00540.21571420.16242300244292
4.0054-4.58460.19841420.13182379252195
4.5846-5.77460.16491520.13012450260297
5.7746-48.94640.18091500.15772534268498
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)
11.45830.54830.43983.74990.8961.6843-0.031-0.05430.02330.08950.0815-0.3818-0.07750.3072-0.06780.20910.0144-0.02630.29210.03160.284673.4061-18.6387179.8991
21.238-2.0216-3.29553.26745.35358.78470.09070.0072-0.2696-0.5508-0.1714-0.0657-1.07190.2710.00380.8683-0.1287-0.02450.49440.13490.716177.4121-15.3861163.2555
35.1124-0.5612-0.93643.5971-0.52733.31420.11890.1122-0.22430.2508-0.2033-0.73610.19320.88370.08490.33230.0286-0.10920.48310.0110.458581.2361-23.2413179.6467
47.4707-4.5002-5.78029.15635.877.4621-0.2199-0.2956-0.93680.5941-0.0738-0.16040.83710.12190.28850.323-0.0275-0.09950.43060.10550.387275.4598-30.5944188.1556
55.50840.88943.54621.6105-0.09074.14-0.2349-0.11790.44020.16990.01760.0348-0.6209-0.26390.22190.28430.09560.03790.2493-0.01850.270455.2758-8.9849178.082
65.52460.96460.24872.44350.78183.0855-0.0860.2231-0.1772-0.03840.00680.1461-0.1289-0.23860.08910.26630.0660.01060.2750.01380.258444.3016-17.7671166.2295
74.66090.8148-0.27241.01090.20051.2855-0.0139-0.34970.22350.2194-0.02720.2362-0.1361-0.3650.03890.37080.10030.01720.3345-0.01590.271538.2654-12.6374185.2695
87.43513.303-0.41322.57531.33236.1733-0.28190.68430.27290.8060.20950.62010.29480.87990.05650.66-0.00310.03810.61870.13790.509854.8479-19.0729195.8191
98.68155.70181.78876.01980.95920.94770.2993-0.34530.03420.3069-0.17780.2520.0051-0.2721-0.15440.37470.0929-0.00420.3582-0.01630.201336.743-20.2517186.2784
109.10725.0390.64945.630.2320.8226-0.01530.18010.41830.02130.07080.2217-0.1652-0.1489-0.03250.3290.133-0.00450.3146-0.0310.232238.7411-9.8716181.0085
112.00671.49221.052.09441.77792.2424-0.0529-0.049-0.22360.2216-0.06570.05520.4073-0.25670.12270.3261-0.04030.03370.26670.05250.283952.5814-45.4927163.5582
124.9538-1.2627-2.28449.55583.88498.4955-0.231-0.50610.4374-0.50730.65070.3319-0.4118-0.2082-0.42440.66130.1694-0.04520.57410.02990.693339.4149-33.9237172.7625
137.6896-1.7733-4.30585.25584.07966.78870.07420.3955-0.78060.5669-0.02460.48741.0896-1.4982-0.15260.4237-0.17530.08450.5087-00.4541.4156-47.5593161.5413
147.0921-2.2042-0.96545.4859-0.76893.33-0.2916-0.9078-0.58641.09910.28550.40640.4775-0.1083-0.02440.65-0.0826-0.01150.45250.07520.328753.9928-50.2943175.1207
151.50480.985-0.10942.0850.26571.1121-0.01140.1409-0.07190.08560.0334-0.03630.027-0.1107-0.03920.20820.01990.01690.2906-0.0130.175657.6391-32.317154.0232
166.5139-3.0094-4.95811.8152.39483.8832-0.2618-0.02020.07370.27630.1224-0.12520.2180.460.0810.3127-0.0087-0.03820.33810.03920.297669.8205-16.1179153.7535
171.91910.203-1.07880.8735-0.10821.5196-0.0460.227-0.0351-0.09790.0427-0.1913-0.08570.01190.01960.2605-0.0346-0.01140.3107-0.00270.22871.7404-26.6528140.6195
188.62465.9699-4.1795.7917-6.19778.67440.5414-1.0949-0.17780.3074-1.2871-0.9813-0.57910.65950.90230.69970.09790.00540.72910.05510.492174.0942-47.7674149.6081
195.25543.7743-0.51546.12770.52642.02620.10710.0396-0.09050.3357-0.0511-0.1551-0.05960.085-0.11860.2478-0.0093-0.01340.30650.01410.17775.2727-30.735144.608
202.46041.5137-0.35534.39940.17992.0064-0.11880.3920.1133-0.07290.185-0.0831-0.15870.0141-0.06790.2290.01440.00630.30840.03670.190470.7554-25.574138.9223
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:86)A3 - 86
2X-RAY DIFFRACTION2(chain A and resid 87:99)A87 - 99
3X-RAY DIFFRACTION3(chain A and resid 100:134)A100 - 134
4X-RAY DIFFRACTION4(chain A and resid 135:149)A135 - 149
5X-RAY DIFFRACTION5(chain A and resid 150:190)A150 - 190
6X-RAY DIFFRACTION6(chain A and resid 191:247)A191 - 247
7X-RAY DIFFRACTION7(chain A and resid 248:345)A248 - 345
8X-RAY DIFFRACTION8(chain A and resid 346:371)A346 - 371
9X-RAY DIFFRACTION9(chain A and resid 372:401)A372 - 401
10X-RAY DIFFRACTION10(chain A and resid 402:440)A402 - 440
11X-RAY DIFFRACTION11(chain B and resid 2:85)B2 - 85
12X-RAY DIFFRACTION12(chain B and resid 86:98)B86 - 98
13X-RAY DIFFRACTION13(chain B and resid 99:108)B99 - 108
14X-RAY DIFFRACTION14(chain B and resid 109:134)B109 - 134
15X-RAY DIFFRACTION15(chain B and resid 135:216)B135 - 216
16X-RAY DIFFRACTION16(chain B and resid 217:231)B217 - 231
17X-RAY DIFFRACTION17(chain B and resid 232:347)B232 - 347
18X-RAY DIFFRACTION18(chain B and resid 348:369)B348 - 369
19X-RAY DIFFRACTION19(chain B and resid 370:397)B370 - 397
20X-RAY DIFFRACTION20(chain B and resid 398:440)B398 - 440

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