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- PDB-4ao6: Native structure of a novel cold-adapted esterase from an Arctic ... -

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Basic information

Entry
Database: PDB / ID: 4ao6
TitleNative structure of a novel cold-adapted esterase from an Arctic intertidal metagenomic library
ComponentsESTERASE
KeywordsHYDROLASE / THERMO LABEL
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesUNIDENTIFIED (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsFu, J. / Leiros, H.-K.S. / Pascale, D.d. / Johnson, K.A. / Blencke, H.M. / Landfald, B.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2013
Title: Functional and Structural Studies of a Novel Cold-Adapted Esterase from an Arctic Intertidal Metagenomic Library.
Authors: Fu, J. / Leiros, H.-K.S. / De Pascale, D. / Johnson, K.A. / Blencke, H.M. / Landfald, B.
History
DepositionMar 23, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ESTERASE


Theoretical massNumber of molelcules
Total (without water)28,2941
Polymers28,2941
Non-polymers00
Water1,982110
1
A: ESTERASE

A: ESTERASE


Theoretical massNumber of molelcules
Total (without water)56,5882
Polymers56,5882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area1380 Å2
ΔGint-7.7 kcal/mol
Surface area18560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.860, 69.870, 54.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ESTERASE


Mass: 28294.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: A HIS-TAGGED CONSTRUCT / Source: (gene. exp.) UNIDENTIFIED (others)
Description: FROM A METAGENOMIC LIBRARY FROM INTERTIDAL ZONE AT SVALBARD ARCHIPELAGO
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): M15 (PREP4)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES MRGSHHHHHHGS ARE THE N-TERMINAL HIS TAG

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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: 1.86 Å3/Da / Density % sol: 34.02 % / Description: NONE
Crystal growDetails: 26-30% POLYETHYLENE GLYCOL (PEG) 3350, 3% GLYCEROL 0.1 M SODIUM MALONATE PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 28142 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 0
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.2 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata scaling
SCALAdata scaling
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.6→25 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.172 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21947 1420 5 %RANDOM
Rwork0.18715 ---
obs0.18877 26718 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.423 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2---0.59 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 0 110 1807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221764
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.9632396
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1785231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45323.67668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92115294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.1131511
X-RAY DIFFRACTIONr_chiral_restr0.0950.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211329
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_it0.8031.51121
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.41521791
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8213643
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8724.5604
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: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 104 -
Rwork0.285 1869 -
obs--95.87 %
Refinement TLS params.Method: refined / Origin x: 35.578 Å / Origin y: 16.6247 Å / Origin z: 14.9207 Å
111213212223313233
T0.0461 Å20.0002 Å20.005 Å2-0.0354 Å20.0127 Å2--0.0513 Å2
L1.2308 °20.7021 °20.3946 °2-2.3145 °20.2543 °2--0.9728 °2
S-0.0777 Å °-0.0252 Å °0.1732 Å °-0.2277 Å °-0.0031 Å °-0.0876 Å °-0.1664 Å °0.0281 Å °0.0808 Å °

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