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- PDB-7yii: Carboxylesterase - RoCE -

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Basic information

Entry
Database: PDB / ID: 7yii
TitleCarboxylesterase - RoCE
ComponentsNon-heme haloperoxidase
KeywordsHYDROLASE / alpha/beta hydrolase / dimer / ester hydrolase / acyltransferase
Function / homologyAlpha/beta hydrolase family / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / Alpha/beta hydrolase fold-1 / peroxidase activity / Alpha/Beta hydrolase fold / hydrolase activity / Non-heme haloperoxidase
Function and homology information
Biological speciesRhodococcus opacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsDou, Z. / Jia, P. / Ni, Y. / Xu, G.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22078127 China
CitationJournal: To Be Published
Title: Carboxylesterase - RoCE
Authors: Dou, Z. / Jia, P. / Ni, Y. / Xu, G.C.
History
DepositionJul 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-heme haloperoxidase
B: Non-heme haloperoxidase


Theoretical massNumber of molelcules
Total (without water)56,8112
Polymers56,8112
Non-polymers00
Water8,197455
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-13 kcal/mol
Surface area20050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.677, 90.472, 131.358
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Non-heme haloperoxidase


Mass: 28405.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus opacus (bacteria) / Gene: R1CP_28090 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1B1KCC1, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris buffer (pH 6.5), 25% PEG 300 (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 18-ID / Wavelength: 0.987 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Nov 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.78→24.34 Å / Num. obs: 55437 / % possible obs: 98.5 % / Redundancy: 1 % / Rmerge(I) obs: 0.029 / Net I/σ(I): 13.7
Reflection shellResolution: 1.78→1.82 Å / Rmerge(I) obs: 0.01 / Num. unique obs: 2642

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RNC

4rnc


Resolution: 1.78→24.34 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.988 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1886 2731 4.9 %RANDOM
Rwork0.1565 ---
obs0.158 52737 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.69 Å2 / Biso mean: 20.428 Å2 / Biso min: 10.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.19 Å2
Refinement stepCycle: final / Resolution: 1.78→24.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3967 0 0 455 4422
Biso mean---34.57 -
Num. residues----546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134082
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153798
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.6275566
X-RAY DIFFRACTIONr_angle_other_deg1.5891.5768722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1565548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.4821.111198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.61315578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1871532
X-RAY DIFFRACTIONr_chiral_restr0.0940.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024766
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02914
LS refinement shellResolution: 1.782→1.828 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 158 -
Rwork0.189 3309 -
all-3467 -
obs--84.11 %

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