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- PDB-5ne8: Crystal structure of H307A mutant of Thermotoga maritima TmPEP105... -

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Basic information

Entry
Database: PDB / ID: 5ne8
TitleCrystal structure of H307A mutant of Thermotoga maritima TmPEP1050 aminopeptidase
ComponentsAMINOPEPTIDASE
KeywordsLYASE / aminopeptidase / M42 family / tetrahedral structure / metal ion binding
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / cellulase / aminopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase M42, domain 2 / Peptidase M42, domain 2 / : / M42 glutamyl aminopeptidase / Peptidase M42 / Zn peptidases / Elongation Factor Tu (Ef-tu); domain 3 / Aminopeptidase / Beta Barrel / 3-Layer(aba) Sandwich ...Peptidase M42, domain 2 / Peptidase M42, domain 2 / : / M42 glutamyl aminopeptidase / Peptidase M42 / Zn peptidases / Elongation Factor Tu (Ef-tu); domain 3 / Aminopeptidase / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsDutoit, R.
Funding support Belgium, 1items
OrganizationGrant numberCountry
BAG-Belgium20151139 Belgium
Citation
Journal: J.Biol.Chem. / Year: 2019
Title: How metal cofactors drive dimer-dodecamer transition of the M42 aminopeptidase TmPep1050 ofThermotoga maritima.
Authors: Dutoit, R. / Van Gompel, T. / Brandt, N. / Van Elder, D. / Van Dyck, J. / Sobott, F. / Droogmans, L.
#1: Journal: PLoS ONE / Year: 2012
Title: Functional characterization of two M42 aminopeptidases erroneously annotated as cellulases.
Authors: Dutoit, R. / Brandt, N. / Legrain, C. / Bauvois, C.
History
DepositionMar 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AMINOPEPTIDASE
B: AMINOPEPTIDASE


Theoretical massNumber of molelcules
Total (without water)72,0862
Polymers72,0862
Non-polymers00
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Size exclusion chromatography with superdex 75 column (GE Healthcare). The apparent molecular weight is 67.3 kDa
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-4 kcal/mol
Surface area27300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.790, 138.650, 61.250
Angle α, β, γ (deg.)90.000, 110.510, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein AMINOPEPTIDASE / Endoglucanase M


Mass: 36043.230 Da / Num. of mol.: 2 / Mutation: H307A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Gene: TM_1050, Tmari_1054 / Plasmid: pBAD-TOPO / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: Q9X0E0, leucyl aminopeptidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: TmPep1050 H307A (230 uM) was crystallised in 0.1 M sodium citrate 10 % PEG3350 pH4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 25, 2016
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
Reflection twinOperator: h,-k,-h-l / Fraction: 0.4
ReflectionResolution: 1.75→40.107 Å / Num. obs: 67094 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.732 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.06 / Χ2: 1.008 / Net I/σ(I): 17.96
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.75-1.796.7860.5632.3848790.8410.60997.2
1.79-1.847.1190.473.2348030.8780.507100
1.84-1.97.0120.3614.4446780.9390.3999.6
1.9-1.956.8580.3345.5845970.9460.36199.9
1.95-2.026.820.2237.7944240.9720.24299.9
2.02-2.096.6530.1859.4742550.9770.20199.7
2.09-2.176.2580.1511.5541890.9820.16499.7
2.17-2.266.3360.12614.1239980.9870.13899.7
2.26-2.366.3420.09817.0737640.9910.10799.9
2.36-2.476.9870.08120.8536450.9930.08899.4
2.47-2.616.9930.07223.9534690.9940.07899.6
2.61-2.766.9010.06227.6332960.9950.06799.7
2.76-2.966.8230.05430.9630780.9960.05999.8
2.96-3.196.7760.04834.4928900.9970.05299.7
3.19-3.56.5640.04537.1126380.9970.04899.8
3.5-3.916.0870.04337.6224220.9970.04799.7
3.91-4.516.1890.03939.6821110.9970.04299.9
4.51-5.536.9190.03642.4117940.9980.03999.4
5.53-7.827.3450.03443.0713920.9980.03699.8
7.82-40.1076.9110.03443.737720.9970.03798.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.75 Å40.11 Å
Translation1.75 Å40.11 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155refinement
XSCALE20160617data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.22data extraction
XDS20160617data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P6Y

4p6y


Resolution: 1.75→40.107 Å / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 37.47
RfactorNum. reflection% reflection
Rfree0.185 3363 5.01 %
Rwork0.1646 --
obs0.1686 67094 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.27 Å2 / Biso mean: 28.9339 Å2 / Biso min: 13.61 Å2
Refinement stepCycle: final / Resolution: 1.75→40.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4621 0 0 335 4956
Biso mean---34.04 -
Num. residues----617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124837
X-RAY DIFFRACTIONf_angle_d1.2636567
X-RAY DIFFRACTIONf_chiral_restr0.067763
X-RAY DIFFRACTIONf_plane_restr0.007860
X-RAY DIFFRACTIONf_dihedral_angle_d10.4132993
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.749-1.77920.40511650.36443117328293
1.7792-1.81150.36631670.34893174334195
1.8115-1.84630.33531670.31993176334395
1.8463-1.8840.30211650.29153148331395
1.884-1.9250.31231690.27533209337895
1.925-1.96980.24321690.25343209337895
1.9698-2.0190.22211670.23693175334295
2.019-2.07360.24831670.23373167333495
2.0736-2.13460.2671700.21863227339795
2.1346-2.20350.22631660.21243151331795
2.2035-2.28230.23021670.21223182334995
2.2823-2.37360.22681680.19833185335395
2.3736-2.48170.20711670.19333173334095
2.4817-2.61250.22311680.18363193336195
2.6125-2.77610.19421690.17743204337395
2.7761-2.99040.20631660.1693163332995
2.9904-3.29120.17921700.15593232340295
3.2912-3.76720.15361680.13423191335995
3.7672-4.7450.12441690.09813219338895
4.745-40.08810.13281710.11753231340295

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