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- PDB-6a0w: Crystal structure of lipase from Rhizopus microsporus var. chinensis -

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Basic information

Entry
Database: PDB / ID: 6a0w
TitleCrystal structure of lipase from Rhizopus microsporus var. chinensis
ComponentsLipase
KeywordsHYDROLASE / Rhizopus microsporus var. chinensis / lipase / N-terminal polypeptide segment
Function / homology
Function and homology information


lipid metabolic process
Similarity search - Function
: / Fungal lipase-like domain / Lipase (class 3) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesRhizopus chinensis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, M. / Yu, X.W. / Xu, Y. / Huang, C.H. / Guo, R.T.
CitationJournal: Biochemistry / Year: 2019
Title: Structural Basis by Which the N-Terminal Polypeptide Segment ofRhizopus chinensisLipase Regulates Its Substrate Binding Affinity.
Authors: Zhang, M. / Yu, X.W. / Xu, Y. / Guo, R.T. / Swapna, G.V.T. / Szyperski, T. / Hunt, J.F. / Montelione, G.T.
History
DepositionJun 6, 2018Deposition site: PDBJ / Processing site: PDBJ
SupersessionOct 9, 2019ID: 4L3W
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6524
Polymers33,3641
Non-polymers2883
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-19 kcal/mol
Surface area11640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.225, 86.225, 101.151
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Lipase


Mass: 33363.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizopus chinensis (fungus) / Production host: Komagataella pastoris (fungus) / References: UniProt: A3FM73
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
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: 3.25 Å3/Da / Density % sol: 62.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25mM Tris pH 8.0, 150mM NaCl, 0.25M (NH4)2SO4, 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 30238 / % possible obs: 100 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 25.72
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LGY

1lgy


Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.925 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.124 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20829 1421 4.8 %RANDOM
Rwork0.1676 ---
obs0.16959 28451 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.055 Å2
Baniso -1Baniso -2Baniso -3
1-1.94 Å20.97 Å20 Å2
2--1.94 Å2-0 Å2
3----6.3 Å2
Refinement stepCycle: 1 / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 15 212 2444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192280
X-RAY DIFFRACTIONr_bond_other_d00.022072
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.9513110
X-RAY DIFFRACTIONr_angle_other_deg0.82534820
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9285285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33224.08693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.5515354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.267159
X-RAY DIFFRACTIONr_chiral_restr0.1180.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0212508
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02455
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_it4.1983.5561146
X-RAY DIFFRACTIONr_mcbond_other4.1913.5551145
X-RAY DIFFRACTIONr_mcangle_it5.1575.3041429
X-RAY DIFFRACTIONr_mcangle_other5.1575.3051430
X-RAY DIFFRACTIONr_scbond_it6.1583.9841134
X-RAY DIFFRACTIONr_scbond_other6.1443.9691130
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9525.7551675
X-RAY DIFFRACTIONr_long_range_B_refined9.13543.9012672
X-RAY DIFFRACTIONr_long_range_B_other9.05143.4482619
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 130 -
Rwork0.264 2041 -
obs--100 %

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