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- PDB-5l6z: Crystal structure of D62A mutant of Thermotoga maritima TmPEP1050... -

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Basic information

Entry
Database: PDB / ID: 5l6z
TitleCrystal structure of D62A mutant of Thermotoga maritima TmPEP1050 aminopeptidase
Componentsleucylaminopeptidase
KeywordsHYDROLASE / leucylaminopeptidase / M42 family / tetrahedral structure
Function / homology
Function and homology information


cellulase / cellulase activity / 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
CITRIC ACID / Endoglucanase / Endoglucanase M
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.501 Å
AuthorsDutoit, R. / Van Elder, D. / Bauvois, C.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Commission communautaire francaise Belgium
Citation
Journal: Proteins / Year: 2020
Title: M42 aminopeptidase catalytic site: the structural and functional role of a strictly conserved aspartate residue
Authors: Dutoit, R. / Brandt, N. / Van Gompel, T. / 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
DepositionJun 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 2.0Feb 24, 2021Group: Atomic model / Database references / Category: atom_site / citation / citation_author
Item: _atom_site.occupancy / _citation.country ..._atom_site.occupancy / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 2.1Jan 10, 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: leucylaminopeptidase
B: leucylaminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3715
Polymers72,1332
Non-polymers2383
Water14,772820
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-29 kcal/mol
Surface area27140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.180, 113.960, 267.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-436-

HOH

21B-553-

HOH

31B-703-

HOH

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Components

#1: Protein leucylaminopeptidase / Endoglucanase M


Mass: 36066.285 Da / Num. of mol.: 2 / Mutation: D62A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_1050, Tmari_1054 / Plasmid: pCEC85 / Details (production host): pBAD-TOPO + TM_1050 / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061
References: UniProt: Q9X0E0, UniProt: R4P256*PLUS, cellulase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 820 / 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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: 0.1M sodium acetate, 5% PEG3350 (v/v) pH5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.49→48.04 Å / Num. obs: 103936 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.091 / Net I/σ(I): 14.48
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.49-1.530.4933.51177.3
1.53-1.570.4254.671100
1.57-1.620.3615.611100
1.62-1.670.3186.541100
1.67-1.720.2747.721100
1.72-1.780.2349.161100
1.78-1.850.19611.321100
1.85-1.920.16313.71100
1.92-2.010.13516.03199.8
2.01-2.110.11718.11100
2.11-2.220.10419.69199.9
2.22-2.360.09920.791100
2.36-2.520.09221.491100
2.52-2.720.08522.56199.8
2.72-2.980.07724.25199.9
2.98-3.330.06925.42199.8
3.33-3.850.06326.57199.9
3.85-4.710.05527.89199.9
4.71-6.660.04627.681100
6.660.03725.52197

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.58 Å48 Å
Translation4.58 Å48 Å

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Processing

Software
NameVersionClassification
PHENIXv1.10.1-2155-000refinement
XSCALEdata scaling
PHASER2.6.0phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P6Y

4p6y


Resolution: 1.501→48 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.39
RfactorNum. reflection% reflection
Rfree0.2152 5159 5 %
Rwork0.1833 --
obs0.1849 103177 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.66 Å2 / Biso mean: 20.1971 Å2 / Biso min: 4.41 Å2
Refinement stepCycle: final / Resolution: 1.501→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4678 0 28 820 5526
Biso mean--31.85 33.24 -
Num. residues----623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065099
X-RAY DIFFRACTIONf_angle_d0.8216946
X-RAY DIFFRACTIONf_chiral_restr0.057791
X-RAY DIFFRACTIONf_plane_restr0.006929
X-RAY DIFFRACTIONf_dihedral_angle_d14.043107
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.501-1.51810.25241640.23563121328595
1.5181-1.53590.24281680.228331743342100
1.5359-1.55470.27751730.222732913464100
1.5547-1.57430.25251680.220431943362100
1.5743-1.59510.2551700.215732403410100
1.5951-1.61690.2761710.215932373408100
1.6169-1.640.26841720.208832803452100
1.64-1.66450.23251680.211631823350100
1.6645-1.69050.25921740.209833173491100
1.6905-1.71820.27181680.216131763344100
1.7182-1.74780.22591720.219432703442100
1.7478-1.77960.26951720.208932613433100
1.7796-1.81390.2441700.205432483418100
1.8139-1.85090.26031720.208732533425100
1.8509-1.89110.24081710.203432713442100
1.8911-1.93510.23391710.202632493420100
1.9351-1.98350.24591700.195832313401100
1.9835-2.03710.21911720.201532733445100
2.0371-2.09710.26721730.200332763449100
2.0971-2.16480.19331700.193132423412100
2.1648-2.24210.21031740.18332943468100
2.2421-2.33190.20971720.182132823454100
2.3319-2.4380.19821730.186432853458100
2.438-2.56660.22011720.181132603432100
2.5666-2.72740.22561730.181132993472100
2.7274-2.93790.21421750.175233123487100
2.9379-3.23350.18541750.16433263501100
3.2335-3.70130.19331740.150733103484100
3.7013-4.66260.15991790.136334043583100
4.6626-48.02430.18711830.17473460364398

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