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- PDB-6idy: Crystal structure of Aspergillus fumigatus lipase B -

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Basic information

Entry
Database: PDB / ID: 6idy
TitleCrystal structure of Aspergillus fumigatus lipase B
Componentslipase aflb
KeywordsLIPID BINDING PROTEIN / lipase
Function / homologyAlpha/Beta hydrolase fold / Uncharacterized protein / Lipase, putative
Function and homology information
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWang, Y.H. / Lan, D.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31725022 China
CitationJournal: To Be Published
Title: Crystal structure of Aspergillus fumigatus lipase B
Authors: Wang, Y.H. / Lan, D.M.
History
DepositionSep 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: lipase aflb
B: lipase aflb
C: lipase aflb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,6608
Polymers140,3483
Non-polymers3125
Water10,665592
1
A: lipase aflb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9193
Polymers46,7831
Non-polymers1362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area15420 Å2
MethodPISA
2
B: lipase aflb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8232
Polymers46,7831
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area15660 Å2
MethodPISA
3
C: lipase aflb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9193
Polymers46,7831
Non-polymers1362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area15270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.190, 152.190, 134.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein lipase aflb


Mass: 46782.676 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (mold) / Gene: CDV57_02421 / Production host: Komagataella pastoris GS115 (fungus) / References: UniProt: A0A229Y729, UniProt: Q4WG73*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 1.7 M Ammonia Sulfate, 0.1 M Tris.Cl, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97737 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 31, 2017
RadiationMonochromator: MD2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97737 Å / Relative weight: 1
ReflectionResolution: 2.15→47.799 Å / Num. obs: 86274 / % possible obs: 99.9 % / Redundancy: 11.14 % / Biso Wilson estimate: 31.25 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.15 / Rrim(I) all: 0.157 / Net I/σ(I): 14.59
Reflection shellResolution: 2.15→2.28 Å / Redundancy: 10.86 % / Rmerge(I) obs: 0.808 / Mean I/σ(I) obs: 3.32 / Num. unique obs: 13718 / CC1/2: 0.856 / Rrim(I) all: 0.848 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K6G

4k6g


Resolution: 2.15→31.48 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.179 / SU Rfree Blow DPI: 0.146 / SU Rfree Cruickshank DPI: 0.145
RfactorNum. reflection% reflectionSelection details
Rfree0.197 4276 4.98 %RANDOM
Rwork0.173 ---
obs0.174 85809 100 %-
Displacement parametersBiso mean: 32.62 Å2
Baniso -1Baniso -2Baniso -3
1--2.7711 Å20 Å20 Å2
2---2.7711 Å20 Å2
3---5.5423 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: 1 / Resolution: 2.15→31.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9474 0 13 592 10079
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0089711HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9713274HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3144SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1632HARMONIC5
X-RAY DIFFRACTIONt_it9711HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.81
X-RAY DIFFRACTIONt_other_torsion15.13
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1311SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12479SEMIHARMONIC4
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 299 4.74 %
Rwork0.1934 6005 -
all0.1951 6304 -
obs--99.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.67590.17390.11280.94960.04280.72920.0022-0.00110.00860.09660.0228-0.1254-0.0270.1292-0.0251-0.0743-0.0295-0.0236-0.02680.01-0.0645-9.088736.4001-36.6729
20.6372-0.04920.07950.76380.23771.04960.0067-0.029-0.02820.0334-0.0204-0.03440.0536-0.04030.0137-0.06030.0038-0.0142-0.04050.0032-0.0788-40.418533.386612.3772
30.7778-0.42360.14571.8119-0.13740.95970.05780.0480.1776-0.2305-0.0437-0.0675-0.2839-0.0003-0.01410.05110.01350.0111-0.18630.0345-0.1219-39.749464.9542-10.625
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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