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- PDB-4pbf: Phosphotriesterase variant Rev12 -

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Basic information

Entry
Database: PDB / ID: 4pbf
TitlePhosphotriesterase variant Rev12
ComponentsPhosphotriesterase variant PTE-revR12
KeywordsHYDROLASE / Phosphotriesterase / arylesterase / evolution
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds / catabolic process / zinc ion binding
Similarity search - Function
Aryldialkylphosphatase, zinc-binding site / Phosphotriesterase family signature 1. / Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / Phosphotriesterase variant PTE-revR12
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCampbell, E. / Kaltenbach, M. / Tokuriki, N. / Jackson, C.J.
CitationJournal: Nat. Chem. Biol. / Year: 2016
Title: The role of protein dynamics in the evolution of new enzyme function.
Authors: Campbell, E. / Kaltenbach, M. / Correy, G.J. / Carr, P.D. / Porebski, B.T. / Livingstone, E.K. / Afriat-Jurnou, L. / Buckle, A.M. / Weik, M. / Hollfelder, F. / Tokuriki, N. / Jackson, C.J.
History
DepositionApr 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Derived calculations
Category: atom_type / citation ...atom_type / citation / citation_author / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id
Revision 1.4Nov 15, 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: Phosphotriesterase variant PTE-revR12
B: Phosphotriesterase variant PTE-revR12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,44710
Polymers72,6752
Non-polymers7728
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-173 kcal/mol
Surface area23090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.696, 123.696, 112.132
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Phosphotriesterase variant PTE-revR12


Mass: 36337.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevundimonas diminuta (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A060GTM0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 3.41 Å3/Da / Density % sol: 63.9 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 100 mM Nal Cacodylate, 35% 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.27
11H+L, -K, -L20.142
11H, -K, -H-L30.091
11-H-L, K, H40.176
11L, K, -H-L50.208
11L, -K, H60.113
ReflectionResolution: 1.9→48.33 Å / Num. obs: 76542 / % possible obs: 97.6 % / Redundancy: 11 % / Rmerge(I) obs: 0.163 / Net I/σ(I): 14.6
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 10.4 % / Rmerge(I) obs: 1.322 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GY0

4gy0


Resolution: 1.9→48.33 Å / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.73 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1728 3943 5.16 %
Rwork0.1405 --
obs0.1567 76478 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5056 0 30 345 5431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065366
X-RAY DIFFRACTIONf_angle_d0.977313
X-RAY DIFFRACTIONf_dihedral_angle_d13.0561973
X-RAY DIFFRACTIONf_chiral_restr0.036846
X-RAY DIFFRACTIONf_plane_restr0.005957
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9004-1.93310.42362120.32413588X-RAY DIFFRACTION94
1.9331-1.96830.22141970.22273600X-RAY DIFFRACTION95
1.9683-2.00610.24391740.1823624X-RAY DIFFRACTION95
2.0061-2.04710.19931830.17873633X-RAY DIFFRACTION95
2.0471-2.09160.2791730.22743591X-RAY DIFFRACTION95
2.0916-2.14020.21641500.16943714X-RAY DIFFRACTION96
2.1402-2.19380.20652110.16583570X-RAY DIFFRACTION94
2.1938-2.25310.24012130.19923613X-RAY DIFFRACTION94
2.2531-2.31940.20621900.16283615X-RAY DIFFRACTION95
2.3194-2.39420.19882340.14973584X-RAY DIFFRACTION94
2.3942-2.47980.17972070.14813603X-RAY DIFFRACTION95
2.4798-2.5790.16392030.14783630X-RAY DIFFRACTION95
2.579-2.69640.19162070.14313618X-RAY DIFFRACTION95
2.6964-2.83850.14351950.13753621X-RAY DIFFRACTION95
2.8385-3.01630.15542010.13753636X-RAY DIFFRACTION95
3.0163-3.24910.17322160.13983586X-RAY DIFFRACTION94
3.2491-3.57580.17291770.14223662X-RAY DIFFRACTION95
3.5758-4.09280.15272190.13593623X-RAY DIFFRACTION94
4.0928-5.15450.16681910.12653674X-RAY DIFFRACTION95
5.1545-38.7370.16671890.14113715X-RAY DIFFRACTION95

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