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- PDB-3wj2: Crystal structure of ESTFA (FE-lacking apo form) -

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Basic information

Entry
Database: PDB / ID: 3wj2
TitleCrystal structure of ESTFA (FE-lacking apo form)
ComponentsCarboxylesterase
KeywordsHYDROLASE / ALPHA/BETA-HYDRORASE FOLD / CARBOXYLESTERASE
Function / homology
Function and homology information


carboxylesterase / carboxylesterase activity
Similarity search - Function
Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine active site. / : / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesFerroplasma acidiphilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsOhara, K. / Unno, H. / Oshima, Y. / Furukawa, K. / Fujino, N. / Hirooka, K. / Hemmi, H. / Takahashi, S. / Nishino, T. / Kusunoki, M. / Nakayama, T.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural insights into the low pH adaptation of a unique carboxylesterase from Ferroplasma: altering the pH optima of two carboxylesterases.
Authors: Ohara, K. / Unno, H. / Oshima, Y. / Hosoya, M. / Fujino, N. / Hirooka, K. / Takahashi, S. / Yamashita, S. / Kusunoki, M. / Nakayama, T.
History
DepositionOct 3, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carboxylesterase
B: Carboxylesterase
C: Carboxylesterase
D: Carboxylesterase


Theoretical massNumber of molelcules
Total (without water)138,5144
Polymers138,5144
Non-polymers00
Water17,709983
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10010 Å2
ΔGint-25 kcal/mol
Surface area43190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.804, 137.360, 76.878
Angle α, β, γ (deg.)90.00, 91.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Carboxylesterase


Mass: 34628.492 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ferroplasma acidiphilum (archaea) / Gene: est / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q2PCE5, carboxylesterase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 983 / 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: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 13% PEG 3350, 100MM SODIUM ACETATE, PH 8.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2008
RadiationMonochromator: SI(111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.61→50 Å / Num. obs: 166739 / % possible obs: 99 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.058
Reflection shellResolution: 1.61→1.67 Å / % possible all: 93.1

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→46.37 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.751 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 8382 5 %RANDOM
Rwork0.188 ---
obs0.19 158320 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å2-0 Å2-0.02 Å2
2--0.03 Å2-0 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.61→46.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9444 0 0 983 10427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0229648
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3951.97313013
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37851191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95123.846455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.117151659
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9741564
X-RAY DIFFRACTIONr_chiral_restr0.1710.21383
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0217400
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5321.55959
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.41829564
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.55133689
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.3324.53449
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.61→1.65 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 546 -
Rwork0.299 10768 -
obs--91.13 %

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