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- PDB-6kvr: Fatty acid amide hydrolase -

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Basic information

Entry
Database: PDB / ID: 6kvr
TitleFatty acid amide hydrolase
ComponentsFatty acid amide hydrolase
KeywordsHYDROLASE / fatty acid
Function / homology
Function and homology information


indoleacetamide hydrolase activity / amidase / amidase activity
Similarity search - Function
Amidase, conserved site / Amidases signature. / Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsMin, C.A. / Yun, J.S. / Chang, J.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Korea)Bokhyeon Research Fund 2017 Korea, Republic Of
CitationJournal: Crystals / Year: 2019
Title: Comparison of Candida Albicans Fatty Acid Amide Hydrolase Structure with Homologous Amidase Signature Family Enzymes
Authors: Min, C.A. / Yun, J.S. / Choi, E.H. / Hwang, U.W. / Cho, D.H. / Yoon, J.H. / Chang, J.H.
History
DepositionSep 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty acid amide hydrolase
B: Fatty acid amide hydrolase


Theoretical massNumber of molelcules
Total (without water)128,2572
Polymers128,2572
Non-polymers00
Water10,971609
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-7 kcal/mol
Surface area39420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.874, 68.753, 100.979
Angle α, β, γ (deg.)90.000, 99.628, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Fatty acid amide hydrolase / Uncharacterized protein CaJ7.0332


Mass: 64128.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: CaJ7.0332, CaO19.5169 / Production host: Escherichia coli (E. coli) / References: UniProt: G1UA68
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop
Details: 100mM Tris/HCl (pH 8.5), 200mM Lithium sulfate, 30% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9897 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 2, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9897 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 58215 / % possible obs: 99.8 % / Redundancy: 7 % / Biso Wilson estimate: 29.83 Å2 / CC1/2: 0.9 / Net I/σ(I): 32.4
Reflection shellResolution: 2.2→2.28 Å / Num. unique obs: 5814 / CC1/2: 0.899

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→28.11 Å / SU ML: 0.2445 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.0423
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2176 3894 3.44 %
Rwork0.171 109407 -
obs0.1726 58195 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.5 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8962 0 0 609 9571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00779168
X-RAY DIFFRACTIONf_angle_d0.925112434
X-RAY DIFFRACTIONf_chiral_restr0.05411360
X-RAY DIFFRACTIONf_plane_restr0.00831614
X-RAY DIFFRACTIONf_dihedral_angle_d6.26111230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.220.35141070.24663057X-RAY DIFFRACTION76.35
2.22-2.250.29971400.24313898X-RAY DIFFRACTION100
2.25-2.280.27631450.23674005X-RAY DIFFRACTION99.88
2.28-2.310.28331410.22643941X-RAY DIFFRACTION99.9
2.31-2.340.21561380.22053971X-RAY DIFFRACTION99.83
2.34-2.380.30221420.22023950X-RAY DIFFRACTION99.78
2.38-2.420.29921400.22023929X-RAY DIFFRACTION99.73
2.42-2.460.28471390.21253949X-RAY DIFFRACTION99.93
2.46-2.50.24271410.19953984X-RAY DIFFRACTION99.71
2.5-2.540.25341450.1963996X-RAY DIFFRACTION99.86
2.54-2.590.2731400.21133870X-RAY DIFFRACTION99.78
2.59-2.650.31691400.19853969X-RAY DIFFRACTION99.81
2.65-2.70.27881380.20953924X-RAY DIFFRACTION99.88
2.7-2.770.26511410.2033930X-RAY DIFFRACTION99.73
2.77-2.840.27111430.20744010X-RAY DIFFRACTION99.81
2.84-2.910.24431410.19143939X-RAY DIFFRACTION99.9
2.91-30.22721400.19383973X-RAY DIFFRACTION99.68
3-3.090.22311430.18243972X-RAY DIFFRACTION99.61
3.09-3.20.23081350.18573871X-RAY DIFFRACTION99.48
3.2-3.330.19841420.16683947X-RAY DIFFRACTION99.61
3.33-3.480.1721410.15343981X-RAY DIFFRACTION99.45
3.48-3.670.17781410.14893911X-RAY DIFFRACTION99.12
3.67-3.90.19321390.14093943X-RAY DIFFRACTION99.2
3.9-4.20.17561420.13463904X-RAY DIFFRACTION99.09
4.2-4.620.18121400.12893930X-RAY DIFFRACTION99
4.62-5.280.17471370.13183928X-RAY DIFFRACTION98.78
5.28-6.640.19271370.16463893X-RAY DIFFRACTION99.14
6.64-28.110.1881360.14483832X-RAY DIFFRACTION96.31

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