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- PDB-8ik1: EstL5 in complex of PMSF -

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Basic information

Entry
Database: PDB / ID: 8ik1
TitleEstL5 in complex of PMSF
ComponentsGDSL family lipase
KeywordsHYDROLASE / Esterase / Complex / PMSF / Hexandiol
Function / homologySGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / HEXANE-1,6-DIOL / GDSL family lipase
Function and homology information
Biological speciesGeobacillus sp. PA-3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsChen, R. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0907702 China
CitationJournal: To Be Published
Title: EstL5 in complex of PMSF
Authors: Chen, R. / Zhang, Y.
History
DepositionFeb 28, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 2.0Jun 21, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GDSL family lipase
B: GDSL family lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0244
Polymers51,7882
Non-polymers2362
Water73941
1
A: GDSL family lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0122
Polymers25,8941
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GDSL family lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0122
Polymers25,8941
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.153, 105.153, 128.001
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein GDSL family lipase


Mass: 25894.061 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus sp. PA-3 (bacteria) / Gene: GEPA3_1571 / Production host: Escherichia (bacteria) / References: UniProt: A0A0Q0YZM0
#2: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL / 1,6-Hexanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.39 Å3/Da / Density % sol: 63.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.01 M CoCl2-6H2O, pH 4.8 0.1 M Sodium acetate and 1 M 1,6-Hexanediol

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.35→105.15 Å / Num. obs: 29348 / % possible obs: 96.3 % / Redundancy: 8.7 % / CC1/2: 0.999 / Rrim(I) all: 0.047 / Net I/σ(I): 20.7
Reflection shellResolution: 2.35→2.47 Å / Redundancy: 7.8 % / Num. unique obs: 4241 / CC1/2: 0.87 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.1refinement
XDSdata reduction
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→29.51 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2497 1467 5.01 %
Rwork0.2107 --
obs0.2126 29305 95.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3230 0 16 41 3287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023293
X-RAY DIFFRACTIONf_angle_d0.5064451
X-RAY DIFFRACTIONf_dihedral_angle_d12.1741233
X-RAY DIFFRACTIONf_chiral_restr0.04503
X-RAY DIFFRACTIONf_plane_restr0.002584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.430.36141330.3332768X-RAY DIFFRACTION96
2.43-2.530.31941260.29142803X-RAY DIFFRACTION97
2.53-2.640.31281510.24812767X-RAY DIFFRACTION97
2.64-2.780.31691580.25362741X-RAY DIFFRACTION96
2.78-2.960.29561480.26132771X-RAY DIFFRACTION96
2.96-3.180.28781610.26552785X-RAY DIFFRACTION96
3.18-3.50.26661400.23632761X-RAY DIFFRACTION95
3.5-4.010.28141430.21182784X-RAY DIFFRACTION95
4.01-5.050.21021460.17462786X-RAY DIFFRACTION94
5.05-29.510.20671610.17862872X-RAY DIFFRACTION92
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)
12.8751-0.0438-2.87252.98551.6225.05260.15010.03750.191-0.2866-0.1422-0.3105-0.42340.5229-0.00020.4438-00.04190.50050.04860.463446.7909-1.56547.2243
26.5507-2.78613.33258.42240.88386.6785-0.02410.06470.41890.0554-0.1252-0.4296-0.58930.40440.12120.4755-0.06050.06410.3383-0.02480.419140.04267.932317.066
36.1033.6319-5.44553.3142-2.79025.07320.0694-1.0304-0.76321.024-0.5054-0.8184-0.330.53560.40690.6009-0.0485-0.08550.59220.05370.556638.1903-6.030332.4834
44.17241.1884-2.04135.5293-3.46343.98330.0343-0.3427-0.08740.8223-0.11840.1972-0.7184-0.7205-0.03280.55440.02830.06040.5017-0.07120.519529.36222.131425.5708
55.3957-0.2636-0.12538.4809-0.4794.8652-0.3903-0.1968-0.56940.56560.1624-0.3373-0.2393-0.1414-0.06190.3582-0.02460.06220.4754-0.05630.4737.2097-8.757119.2547
68.0957-5.04623.47737.4057-4.73178.247-0.6542-0.12540.9610.3579-0.3325-0.51570.0614-0.46820.76040.5596-0.04430.09570.4212-0.03530.436229.8134-10.28924.5373
76.34740.689-0.06491.98970.94842.7038-0.19630.0876-0.9221-0.05420.1681-0.41570.38050.18690.02270.49930.02770.09040.3899-0.05060.507542.0958-12.308614.7534
85.76610.2607-1.47054.1383-0.19453.3747-0.20050.4946-0.9455-0.2904-0.11260.09080.6257-0.35040.28580.7635-0.20920.18170.5737-0.2230.7326.0763-31.275810.0855
94.78320.33130.06154.8918-1.0653.3475-0.26370.7363-0.1767-0.4140.11060.28140.1271-0.34890.13490.5039-0.13160.04890.5552-0.13050.470126.0852-17.31068.6827
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 52 through 96 )
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 145 )
4X-RAY DIFFRACTION4chain 'A' and (resid 146 through 170 )
5X-RAY DIFFRACTION5chain 'A' and (resid 171 through 190 )
6X-RAY DIFFRACTION6chain 'A' and (resid 191 through 211 )
7X-RAY DIFFRACTION7chain 'A' and (resid 212 through 258 )
8X-RAY DIFFRACTION8chain 'B' and (resid 52 through 179 )
9X-RAY DIFFRACTION9chain 'B' and (resid 180 through 258 )

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