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- PDB-4x85: Crystal Structure of lipase from Geobacillus stearothermophilus T... -

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Basic information

Entry
Database: PDB / ID: 4x85
TitleCrystal Structure of lipase from Geobacillus stearothermophilus T6 methanol stable variant H86Y/A269T/R374W
ComponentsLipase
KeywordsHYDROLASE
Function / homologytriacylglycerol lipase / triglyceride lipase activity / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / triacylglycerol lipase
Function and homology information
Biological speciesGeobacillus stearothermophilus T6 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.192 Å
AuthorsKanteev, M. / Dror, A. / Gihaz, S. / Fishman, A.
Funding support Israel, 1items
OrganizationGrant numberCountry
Ministry of Environmental Protection132-2-2 Israel
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2015
Title: Structural insights into methanol-stable variants of lipase T6 from Geobacillus stearothermophilus.
Authors: Dror, A. / Kanteev, M. / Kagan, I. / Gihaz, S. / Shahar, A. / Fishman, A.
History
DepositionDec 10, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0353
Polymers43,9301
Non-polymers1052
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area15470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.696, 71.391, 113.564
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Lipase /


Mass: 43929.984 Da / Num. of mol.: 1 / Mutation: H86Y, A269T, R374W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus T6 (bacteria)
Plasmid: pET9a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q93A71, triacylglycerol lipase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2M sodium citrate , 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.56 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jun 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.56 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. all: 21348 / Num. obs: 69491 / % possible obs: 93.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.3
Reflection shellHighest resolution: 2.192 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 4.8 / % possible all: 92.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å24.85 Å
Translation2.5 Å24.85 Å

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Processing

Software
NameVersionClassification
PHASER2.3.0phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.192→24.848 Å / FOM work R set: 0.8489 / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 1050 5.23 %
Rwork0.2009 19035 -
obs0.2026 20085 93.81 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.392 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso max: 111.49 Å2 / Biso mean: 28.28 Å2 / Biso min: 10.09 Å2
Baniso -1Baniso -2Baniso -3
1--2.8438 Å2-0 Å20 Å2
2---4.7404 Å2-0 Å2
3---7.5841 Å2
Refinement stepCycle: final / Resolution: 2.192→24.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3108 0 2 259 3369
Biso mean--32.83 33.44 -
Num. residues----391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.023210
X-RAY DIFFRACTIONf_angle_d1.2914375
X-RAY DIFFRACTIONf_chiral_restr0.084451
X-RAY DIFFRACTIONf_plane_restr0.006570
X-RAY DIFFRACTIONf_dihedral_angle_d13.5241130
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1917-2.29140.32131200.24142306242692
2.2914-2.41210.25281180.22292336245494
2.4121-2.56310.28161170.23252365248294
2.5631-2.76080.27461270.22852366249394
2.7608-3.03820.23861480.21872367251595
3.0382-3.47680.23381680.20152341250994
3.4768-4.37650.19881240.17192426255094
4.3765-24.84960.20061280.18272528265694
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)
10.2185-0.31830.22020.2728-0.16150.14880.03490.04640.0019-0.0418-0.1665-0.15050.01650.1179-0.03250.1551-0.04110.00180.17980.01620.17119.4746-8.3861-17.5857
20.1786-0.06060.10230.24850.09660.3611-0.1062-0.22940.14380.0616-0.197-0.0881-0.2902-0.3463-0.01930.25330.01280.0020.28090.04970.287825.9782-17.5155-13.0059
30.2236-0.25190.14390.2609-0.0932-0.0029-0.082-0.0117-0.1707-0.09740.03380.16490.0789-0.0397-0.01130.163-0.02330.01990.14790.0180.122215.102-22.9633-10.5067
40.05390.14390.03620.58460.10150.1557-0.01240.05810.0897-0.0163-0.008-0.02220.00770.02740.00340.1673-0.0029-0.00060.16160.01540.116911.8221-10.7945-26.6709
50.10770.02870.03280.22810.14820.2658-0.0474-0.0897-0.1073-0.0173-0.03140.01190.13260.058100.1594-0.01680.01670.183-0.00390.173810.6122-18.5295-31.1392
60.5084-0.01320.19930.9909-0.10360.31790.04630.00880.05360.1137-0.04090.16170.00630.0227-00.1808-0.00370.01730.17120.00960.2-2.2719-5.172-16.1502
70.4760.0712-0.06740.21480.27650.35980.03480.06480.03810.22880.15330.0101-0.0238-0.03590.00120.2568-0.0123-0.02290.1686-0.0080.195310.913.3134-7.4772
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:86)A5 - 86
2X-RAY DIFFRACTION2chain 'A' and (resseq 87:107)A87 - 107
3X-RAY DIFFRACTION3chain 'A' and (resseq 108:149)A108 - 149
4X-RAY DIFFRACTION4chain 'A' and (resseq 150:212)A150 - 212
5X-RAY DIFFRACTION5chain 'A' and (resseq 213:254)A213 - 254
6X-RAY DIFFRACTION6chain 'A' and (resseq 255:360)A255 - 360
7X-RAY DIFFRACTION7chain 'A' and (resseq 361:395)A361 - 395

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