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- PDB-4zi5: Crystal Structure of Dienelactone Hydrolase-like Promiscuous Phos... -

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Basic information

Entry
Database: PDB / ID: 4zi5
TitleCrystal Structure of Dienelactone Hydrolase-like Promiscuous Phospotriesterase P91 from Metagenomic Libraries
ComponentsP91
KeywordsHYDROLASE / Metagenomic Libraries / alpha/beta Hydrolase / Promiscuity / Phosphotriesterase
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.702 Å
AuthorsColin, P.-Y. / Fischer, G. / Hyvonen, M. / Hollfelder, F.
CitationJournal: Nat Commun / Year: 2015
Title: Ultrahigh-throughput discovery of promiscuous enzymes by picodroplet functional metagenomics.
Authors: Colin, P.Y. / Kintses, B. / Gielen, F. / Miton, C.M. / Fischer, G. / Mohamed, M.F. / Hyvonen, M. / Morgavi, D.P. / Janssen, D.B. / Hollfelder, F.
History
DepositionApr 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / software / struct_conn / struct_ncs_dom_lim
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P91
B: P91
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8185
Polymers53,7342
Non-polymers843
Water8,215456
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-8 kcal/mol
Surface area18050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.613, 73.414, 113.057
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: -1 - 237 / Label seq-ID: 12 - 250

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein P91


Mass: 26867.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Plasmid: pASKIBA5+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: aryldialkylphosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.56 % / Description: shard-like plates
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris pH=8.5, 0.2M MgCl2, 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.91882 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91882 Å / Relative weight: 1
ReflectionResolution: 1.702→61.57 Å / Num. obs: 45156 / % possible obs: 87.6 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 12.5
Reflection shellResolution: 1.702→1.708 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 2 / Rsym value: 0.454 / % possible all: 55.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDS(VERSION January 10data reduction
Aimless(version 0.3.8)data scaling
PHASERphasing
autoPROCdata reduction
CCP46.4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F67

3f67


Resolution: 1.702→61.57 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.654 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20744 2180 4.8 %RANDOM
Rwork0.18263 ---
obs0.18385 42939 87.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.248 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å20 Å2-0 Å2
2--0.26 Å20 Å2
3---1.21 Å2
Refinement stepCycle: LAST / Resolution: 1.702→61.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3586 0 3 456 4045
Refine LS restraints NCS

Ens-ID: 1 / Number: 28118 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.702→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 137 -
Rwork0.318 2650 -
obs--73.83 %

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