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- PDB-4xvc: Crystal structure of an esterase from the bacterial hormone-sensi... -

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Basic information

Entry
Database: PDB / ID: 4xvc
TitleCrystal structure of an esterase from the bacterial hormone-sensitive lipase (HSL) family
ComponentsEsterase E40
KeywordsHYDROLASE / Esterase
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / phenylmethanesulfonic acid
Function and homology information
Biological speciesenvironmental samples (Diatom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, Y. / Li, P.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Interdomain Hydrophobic Interactions Modulate the Thermostability of Microbial Esterases from the Hormone-Sensitive Lipase Family.
Authors: Li, P.Y. / Chen, X.L. / Ji, P. / Li, C.Y. / Wang, P. / Zhang, Y. / Xie, B.B. / Qin, Q.L. / Su, H.N. / Zhou, B.C. / Zhang, Y.Z. / Zhang, X.Y.
History
DepositionJan 27, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2May 6, 2015Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: cell / chem_comp_atom ...cell / chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _cell.Z_PDB / _citation.journal_id_CSD ..._cell.Z_PDB / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Esterase E40
B: Esterase E40
C: Esterase E40
D: Esterase E40
E: Esterase E40
F: Esterase E40
G: Esterase E40
H: Esterase E40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,77916
Polymers274,4018
Non-polymers1,3788
Water35,9041993
1
A: Esterase E40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4722
Polymers34,3001
Non-polymers1721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Esterase E40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4722
Polymers34,3001
Non-polymers1721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Esterase E40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4722
Polymers34,3001
Non-polymers1721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Esterase E40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4722
Polymers34,3001
Non-polymers1721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Esterase E40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4722
Polymers34,3001
Non-polymers1721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Esterase E40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4722
Polymers34,3001
Non-polymers1721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Esterase E40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4722
Polymers34,3001
Non-polymers1721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Esterase E40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4722
Polymers34,3001
Non-polymers1721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.630, 76.172, 130.186
Angle α, β, γ (deg.)74.04, 75.15, 72.60
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 2:297 )
211CHAIN B AND (RESSEQ 2:297 )
311CHAIN C AND (RESSEQ 2:297 )
411CHAIN D AND (RESSEQ 2:297 )
511CHAIN E AND (RESSEQ 2:297 )
611CHAIN F AND (RESSEQ 2:297 )
711CHAIN G AND (RESSEQ 2:297 )
811CHAIN H AND (RESSEQ 2:297 )

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Components

#1: Protein
Esterase E40


Mass: 34300.113 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) environmental samples (Diatom)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: carboxylesterase
#2: Chemical
ChemComp-PMS / phenylmethanesulfonic acid


Mass: 172.202 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H8O3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1993 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION AND THE SEQUENCE HAS BEEN SUBMITTED TO GENBANK UNDER THE ACCESSION NUMBER KP696774.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.15M ammonium sulfate, 0.1M MES, 12%(w/v) PEG 4,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 161567 / % possible obs: 97.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 24.417
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.248 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.6.4_486)refinement
HKL-2000data scaling
PHASERphasing
PHENIXmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H18

3h18


Resolution: 2→39.33 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 27.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 8110 5.02 %
Rwork0.196 --
obs0.198 161567 92.7 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.1 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.6547 Å27.1072 Å22.096 Å2
2---2.4328 Å21.3651 Å2
3----0.2219 Å2
Refinement stepCycle: LAST / Resolution: 2→39.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18048 0 80 1993 20121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818566
X-RAY DIFFRACTIONf_angle_d1.08825322
X-RAY DIFFRACTIONf_dihedral_angle_d13.5946858
X-RAY DIFFRACTIONf_chiral_restr0.0742829
X-RAY DIFFRACTIONf_plane_restr0.0053338
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2242X-RAY DIFFRACTIONPOSITIONAL
12B2242X-RAY DIFFRACTIONPOSITIONAL0.033
13C2221X-RAY DIFFRACTIONPOSITIONAL0.043
14D2214X-RAY DIFFRACTIONPOSITIONAL0.045
15E2220X-RAY DIFFRACTIONPOSITIONAL0.039
16F2236X-RAY DIFFRACTIONPOSITIONAL0.031
17G2227X-RAY DIFFRACTIONPOSITIONAL0.046
18H2227X-RAY DIFFRACTIONPOSITIONAL0.045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0011-2.02380.23912580.19074483X-RAY DIFFRACTION81
2.0238-2.04760.2712570.19764934X-RAY DIFFRACTION90
2.0476-2.07260.25152290.18785146X-RAY DIFFRACTION91
2.0726-2.09880.23062610.19014983X-RAY DIFFRACTION91
2.0988-2.12650.26562570.18835063X-RAY DIFFRACTION91
2.1265-2.15560.21392670.18425028X-RAY DIFFRACTION92
2.1556-2.18640.23042740.18775094X-RAY DIFFRACTION92
2.1864-2.2190.22592700.17975082X-RAY DIFFRACTION93
2.219-2.25370.21782890.18175110X-RAY DIFFRACTION92
2.2537-2.29060.24992670.19635038X-RAY DIFFRACTION92
2.2906-2.33010.24782650.19035208X-RAY DIFFRACTION93
2.3301-2.37250.23422660.18695045X-RAY DIFFRACTION92
2.3725-2.41810.24032660.19535175X-RAY DIFFRACTION93
2.4181-2.46750.25512750.20035117X-RAY DIFFRACTION93
2.4675-2.52110.22172800.19675136X-RAY DIFFRACTION93
2.5211-2.57970.25142950.20655134X-RAY DIFFRACTION94
2.5797-2.64420.24912620.20335186X-RAY DIFFRACTION93
2.6442-2.71570.23582810.20815139X-RAY DIFFRACTION93
2.7157-2.79560.23912760.19725162X-RAY DIFFRACTION93
2.7956-2.88580.25792860.20165130X-RAY DIFFRACTION94
2.8858-2.98890.2272690.20635202X-RAY DIFFRACTION94
2.9889-3.10860.22862700.21265205X-RAY DIFFRACTION94
3.1086-3.250.22062920.2165156X-RAY DIFFRACTION94
3.25-3.42120.23112830.2085166X-RAY DIFFRACTION94
3.4212-3.63540.2373070.19625160X-RAY DIFFRACTION94
3.6354-3.91590.20582250.19135040X-RAY DIFFRACTION91
3.9159-4.30950.23862990.18375297X-RAY DIFFRACTION97
4.3095-4.93210.19282650.17885376X-RAY DIFFRACTION97
4.9321-6.210.21322580.20045376X-RAY DIFFRACTION97
6.21-39.33820.22192610.21085086X-RAY DIFFRACTION92

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