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- PDB-6khk: Lipase (Closed form) -

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Basic information

Entry
Database: PDB / ID: 6khk
TitleLipase (Closed form)
ComponentsHydrolase, alpha/beta domain protein
KeywordsHYDROLASE / Lipase
Function / homologySerine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold / hydrolase activity / Hydrolase, alpha/beta domain protein
Function and homology information
Biological speciesCutibacterium acnes HL110PA4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsKim, H.J. / Kwon, A.R.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)2017R1D1A1B03033857 Korea, Republic Of
National Research Foundation (Korea)2018R1A5A2024425 Korea, Republic Of
CitationJournal: To Be Published
Title: Closed, blocked, and open states of lysophospholipase from type II Cutibacterium acnes
Authors: Kim, H.J. / Lee, B.J. / Kwon, A.R.
History
DepositionJul 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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: Hydrolase, alpha/beta domain protein
B: Hydrolase, alpha/beta domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,86412
Polymers68,9432
Non-polymers92110
Water9,386521
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-14 kcal/mol
Surface area22310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.304, 93.336, 129.676
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Hydrolase, alpha/beta domain protein


Mass: 34471.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cutibacterium acnes HL110PA4 (bacteria)
Gene: HMPREF9578_02569 / Production host: Escherichia coli (E. coli) / References: UniProt: E6DAE5
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 30 % (w/v) PEG 8K and 0.1 M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 63275 / % possible obs: 92.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 21
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.295 / Num. unique obs: 3120

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→38.39 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.543 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2216 3129 5 %RANDOM
Rwork0.1794 ---
obs0.1814 60081 92.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.3 Å2 / Biso mean: 16.791 Å2 / Biso min: 6.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.75→38.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4709 0 60 521 5290
Biso mean--29.35 28.25 -
Num. residues----619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134883
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174402
X-RAY DIFFRACTIONr_angle_refined_deg1.7281.6336622
X-RAY DIFFRACTIONr_angle_other_deg1.4921.57610171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6865620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.93522.045269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59115729
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1271535
X-RAY DIFFRACTIONr_chiral_restr0.0870.2621
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025603
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021058
LS refinement shellResolution: 1.75→1.796 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 251 -
Rwork0.255 4245 -
all-4496 -
obs--89.74 %

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