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- PDB-5ne7: Crystal structure of H60A mutant of Thermotoga maritima TmPEP1050... -

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Basic information

Entry
Database: PDB / ID: 5ne7
TitleCrystal structure of H60A mutant of Thermotoga maritima TmPEP1050 aminopeptidase
ComponentsAMINOPEPTIDASE
KeywordsLYASE / aminopeptidase / M42 family / tetrahedral structure / metal ion binding
Function / homology
Function and homology information


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
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.84 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 2.0Jan 29, 2020Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.1Jan 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2793
Polymers72,0862
Non-polymers1921
Water9,008500
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Size exclusion chromatography with a Superdex 75 column (GE healthcare). The apparent molecular weight is 68.4 kDa.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-6 kcal/mol
Surface area27730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.630, 114.220, 267.960
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-543-

HOH

21B-640-

HOH

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Components

#1: Protein AMINOPEPTIDASE / Endoglucanase M


Mass: 36043.227 Da / Num. of mol.: 2 / Mutation: H60A
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 (E. coli) / Variant (production host): M1061 / References: UniProt: Q9X0E0, leucyl aminopeptidase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 2.26 Å3/Da / Density % sol: 45.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: TmPep1050 H60A (230 uM in 50 mM MOPS 0.5 M ammonium sulfate 1 mM cobalt chloride pH7.2) crystallised in 0.1 M sodium citrate 5 % PEG3350 pH 4.5

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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
ReflectionResolution: 1.84→43.46 Å / Num. obs: 57222 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 12.015 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.091 / Χ2: 1.003 / Net I/σ(I): 16.52
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.84-1.899.8480.6062.6338180.8910.63791.7
1.89-1.9411.1570.6813.241240.90.71599.8
1.94-1.9911.6450.4314.5739560.9520.451100
1.99-2.0611.8520.3565.7938720.9730.373100
2.06-2.1211.5420.3286.9437950.9720.343100
2.12-2.211.2230.2588.4936430.9850.271100
2.2-2.2811.9950.23610.2634890.9850.24699.9
2.28-2.3712.0610.18412.1334250.990.193100
2.37-2.4813.4720.16514.5432170.9930.172100
2.48-2.613.3290.14316.6531190.9940.149100
2.6-2.7413.1730.11520.1829880.9960.12100
2.74-2.9112.9440.09723.5428270.9970.101100
2.91-3.1112.7180.08326.9526380.9970.086100
3.11-3.3612.3690.07130.8724900.9980.074100
3.36-3.6811.6430.06533.5722930.9980.068100
3.68-4.1110.7410.0634.7920930.9980.063100
4.11-4.7511.8110.05139.1518710.9990.053100
4.75-5.8213.6250.04741.7115630.9990.048100
5.82-8.2213.6220.04241.9912630.9990.044100
8.22-43.4612.3470.03443.87380.9990.03598.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.98 Å43.46 Å
Translation5.98 Å43.46 Å

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Processing

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

4p6y


Resolution: 1.84→43.46 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.21
RfactorNum. reflection% reflection
Rfree0.1952 2862 5 %
Rwork0.167 --
obs0.1684 57213 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.23 Å2 / Biso mean: 33.2333 Å2 / Biso min: 14.5 Å2
Refinement stepCycle: final / Resolution: 1.84→43.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4730 0 13 500 5243
Biso mean--55.6 41.23 -
Num. residues----633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045009
X-RAY DIFFRACTIONf_angle_d0.6726818
X-RAY DIFFRACTIONf_chiral_restr0.053796
X-RAY DIFFRACTIONf_plane_restr0.004893
X-RAY DIFFRACTIONf_dihedral_angle_d10.5733105
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 (%)
1.8392-1.87090.29651240.28482346247088
1.8709-1.90490.26041440.238327272871100
1.9049-1.94150.24851410.225726812822100
1.9415-1.98120.25481410.194826782819100
1.9812-2.02420.21431430.180627142857100
2.0242-2.07130.23531390.186226542793100
2.0713-2.12310.20511460.181827582904100
2.1231-2.18050.20231420.181427022844100
2.1805-2.24470.23391430.185627172860100
2.2447-2.31710.2411420.178726922834100
2.3171-2.39990.22371420.172627002842100
2.3999-2.4960.23121440.16827512895100
2.496-2.60960.19551420.169927002842100
2.6096-2.74720.19441450.166827502895100
2.7472-2.91930.20121440.167727382882100
2.9193-3.14460.20131440.169427282872100
3.1446-3.46090.17061460.158827762922100
3.4609-3.96140.17251460.146227722918100
3.9614-4.98980.15341480.13228162964100
4.9898-43.47250.18411560.173829513107100

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