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- PDB-4p6y: Crystal structure of the M42 aminopeptidase TmPep1050 from Thermo... -

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Basic information

Entry
Database: PDB / ID: 4p6y
TitleCrystal structure of the M42 aminopeptidase TmPep1050 from Thermotoga maritima
ComponentsAminopeptidase
KeywordsHYDROLASE / Aminopeptidase / M42 family / large self-assembled dodecamer / tetrahedral structure / metalloprotease / metal-binding hydrolase / hyperthermophilic
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 / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDutoit, R. / Demarez, M. / Van Elder, D. / Bauvois, C.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Fonds de la Recherche Scientifique (FNRS)IISN 4.4505.00 Belgium
Citation
Journal: To Be Published
Title: Crystal structure of the M42 aminopeptidase TmPep1050 from Thermotoga maritima
Authors: Dutoit, R. / Brandt, N. / Durisotti, V. / Oudjama, Y. / Demarez, M. / Van Elder, D. / Bauvois, C.
#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 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminopeptidase
B: Aminopeptidase
C: Aminopeptidase
D: Aminopeptidase
E: Aminopeptidase
F: Aminopeptidase
G: Aminopeptidase
H: Aminopeptidase
I: Aminopeptidase
J: Aminopeptidase
K: Aminopeptidase
L: Aminopeptidase


Theoretical massNumber of molelcules
Total (without water)433,32412
Polymers433,32412
Non-polymers00
Water40,0472223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area52260 Å2
ΔGint-207 kcal/mol
Surface area114090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.260, 114.570, 114.040
Angle α, β, γ (deg.)114.46, 91.71, 105.69
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Aminopeptidase / / Endoglucanase / Endoglucanase M


Mass: 36110.297 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_1050, THEMA_09110, Tmari_1054 / Plasmid: pCEC43 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0E0, cellulase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2223 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.75 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.75
Details: TmPep1050 (390 uM) in 50 mM MOPS pH 7.2 with 0.5 M ammonium sulfate and 1 mM cobalt chloride, was mixed 2:2 with well buffer (2.1M malic acid pH 6.75) with 500 uL well buffer in the well of ...Details: TmPep1050 (390 uM) in 50 mM MOPS pH 7.2 with 0.5 M ammonium sulfate and 1 mM cobalt chloride, was mixed 2:2 with well buffer (2.1M malic acid pH 6.75) with 500 uL well buffer in the well of the crystallization tray

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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: Apr 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.2→44.05 Å / Num. obs: 237152 / % possible obs: 93.54 % / Observed criterion σ(F): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 32.64 Å2 / Rmerge(I) obs: 0.08925 / Net I/σ(I): 8.56
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 2.22 / % possible all: 84.76

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1539) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLO

1ylo


Resolution: 2.2→44.045 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2474 11854 5 %Random selection
Rwork0.2118 ---
obs0.2136 237090 93.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37 Å2
Refinement stepCycle: LAST / Resolution: 2.2→44.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29969 0 0 2223 32192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00930442
X-RAY DIFFRACTIONf_angle_d1.25441103
X-RAY DIFFRACTIONf_dihedral_angle_d13.40611341
X-RAY DIFFRACTIONf_chiral_restr0.0544744
X-RAY DIFFRACTIONf_plane_restr0.0075329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2260.35522790.31065294X-RAY DIFFRACTION67
2.226-2.25220.35083940.30717506X-RAY DIFFRACTION93
2.2522-2.27970.33754000.29147599X-RAY DIFFRACTION95
2.2797-2.30850.33344020.28337651X-RAY DIFFRACTION96
2.3085-2.33890.3054090.26647785X-RAY DIFFRACTION96
2.3389-2.3710.31484030.27617654X-RAY DIFFRACTION96
2.371-2.40480.32334040.27427665X-RAY DIFFRACTION96
2.4048-2.44070.31594090.26587776X-RAY DIFFRACTION96
2.4407-2.47890.30614070.26147728X-RAY DIFFRACTION96
2.4789-2.51950.32134010.27117628X-RAY DIFFRACTION95
2.5195-2.56290.31424070.26537717X-RAY DIFFRACTION96
2.5629-2.60950.33254070.26757734X-RAY DIFFRACTION96
2.6095-2.65970.30324030.25997656X-RAY DIFFRACTION96
2.6597-2.7140.30224000.25457597X-RAY DIFFRACTION95
2.714-2.7730.2894010.25557637X-RAY DIFFRACTION95
2.773-2.83750.29373960.24987525X-RAY DIFFRACTION94
2.8375-2.90840.2924020.24377630X-RAY DIFFRACTION95
2.9084-2.98710.30933980.25547558X-RAY DIFFRACTION94
2.9871-3.07490.28154010.23797625X-RAY DIFFRACTION94
3.0749-3.17420.27343940.24457486X-RAY DIFFRACTION93
3.1742-3.28760.25563910.22447425X-RAY DIFFRACTION93
3.2876-3.41920.2453890.22157384X-RAY DIFFRACTION92
3.4192-3.57470.24283900.19717411X-RAY DIFFRACTION92
3.5747-3.76310.23333840.19787308X-RAY DIFFRACTION91
3.7631-3.99870.21983900.17057394X-RAY DIFFRACTION92
3.9987-4.30720.18543950.16017507X-RAY DIFFRACTION94
4.3072-4.74020.16973980.15357563X-RAY DIFFRACTION94
4.7402-5.4250.18524010.15497624X-RAY DIFFRACTION95
5.425-6.83090.20474050.18037687X-RAY DIFFRACTION96
6.8309-44.05340.18093940.16577482X-RAY DIFFRACTION93

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