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- PDB-9h0z: Crystal structure of TTL[Nle], thermophilic lipase TTL from Therm... -

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Basic information

Entry
Database: PDB / ID: 9h0z
TitleCrystal structure of TTL[Nle], thermophilic lipase TTL from Thermoanaerobacter thermohydrosulfuricus containing non-canonical amino acid Nle at the position of Met
ComponentsSerine aminopeptidase S33 domain-containing protein
KeywordsLIPID BINDING PROTEIN / lipase / thermophilic / non-canonical amino acid / Nle / ncAAs / norleucine
Function / homology: / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / Serine aminopeptidase S33 domain-containing protein
Function and homology information
Biological speciesThermoanaerobacter thermohydrosulfuricus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsHromic-Jahjefendic, A. / Pavkov-Keller, T. / Wiltschi, B. / Gruber, K.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Research Promotion Agency Austria
CitationJournal: To Be Published
Title: ncAA incorporation, lipase and OYE
Authors: Hromic-Jahjefendic, A. / Pavkov-Keller, T. / Gruber, K. / Wiltschi, B.
History
DepositionOct 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine aminopeptidase S33 domain-containing protein
B: Serine aminopeptidase S33 domain-containing protein
C: Serine aminopeptidase S33 domain-containing protein
D: Serine aminopeptidase S33 domain-containing protein
E: Serine aminopeptidase S33 domain-containing protein
F: Serine aminopeptidase S33 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,44512
Polymers179,8696
Non-polymers5766
Water2,198122
1
A: Serine aminopeptidase S33 domain-containing protein
B: Serine aminopeptidase S33 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1484
Polymers59,9562
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-32 kcal/mol
Surface area20350 Å2
MethodPISA
2
C: Serine aminopeptidase S33 domain-containing protein
D: Serine aminopeptidase S33 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1484
Polymers59,9562
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-31 kcal/mol
Surface area19610 Å2
MethodPISA
3
E: Serine aminopeptidase S33 domain-containing protein
F: Serine aminopeptidase S33 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1484
Polymers59,9562
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-34 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.900, 76.297, 187.790
Angle α, β, γ (deg.)90.000, 93.522, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Serine aminopeptidase S33 domain-containing protein


Mass: 29978.137 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter thermohydrosulfuricus (bacteria)
Gene: SAMN04244560_02687 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1G7VV58
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 8mg/ml protein concentration Index screen condition D4 containing 0.1 M Citric acid pH 3.5, 25% w/v Polyethylene glycol 3,350 drops: 0.5ul + 0.5ul

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.79→54.9 Å / Num. obs: 45722 / % possible obs: 99.37 % / Redundancy: 3.4 % / Biso Wilson estimate: 49.3 Å2 / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.1 / Rrim(I) all: 0.187 / Net I/σ(I): 8.13
Reflection shellResolution: 2.79→2.89 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.779 / Mean I/σ(I) obs: 1.56 / Num. unique obs: 4378 / CC1/2: 0.643 / CC star: 0.885 / Rpim(I) all: 0.516 / Rrim(I) all: 0.937 / % possible all: 96.06

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.16_3549refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→54.89 Å / SU ML: 0.4233 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.3348
RfactorNum. reflection% reflection
Rfree0.2633 2264 4.95 %
Rwork0.2136 43429 -
obs0.2161 45693 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.45 Å2
Refinement stepCycle: LAST / Resolution: 2.79→54.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11964 0 30 122 12116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003112225
X-RAY DIFFRACTIONf_angle_d0.590416404
X-RAY DIFFRACTIONf_chiral_restr0.04281791
X-RAY DIFFRACTIONf_plane_restr0.00312092
X-RAY DIFFRACTIONf_dihedral_angle_d4.08458281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.850.39461230.30122492X-RAY DIFFRACTION91.63
2.85-2.920.33661460.28882709X-RAY DIFFRACTION99.9
2.92-2.990.34221240.28332705X-RAY DIFFRACTION99.86
2.99-3.070.28561470.27222722X-RAY DIFFRACTION99.72
3.07-3.160.33561200.27312701X-RAY DIFFRACTION99.82
3.16-3.260.34291620.26832728X-RAY DIFFRACTION99.83
3.26-3.380.32861290.25162716X-RAY DIFFRACTION99.89
3.38-3.510.30571420.23542692X-RAY DIFFRACTION99.82
3.51-3.670.2971730.22132718X-RAY DIFFRACTION99.69
3.67-3.870.27181490.22052724X-RAY DIFFRACTION99.86
3.87-4.110.28041540.19922697X-RAY DIFFRACTION99.76
4.11-4.430.20221320.17032737X-RAY DIFFRACTION99.69
4.43-4.870.18421490.15792733X-RAY DIFFRACTION99.86
4.87-5.580.21341340.17542772X-RAY DIFFRACTION99.83
5.58-7.020.22441310.2112764X-RAY DIFFRACTION99.83
7.02-54.890.23781490.18752819X-RAY DIFFRACTION99.03

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