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- PDB-6nw5: Crystal structure of TmPep1050 aminopeptidase with its metal cofactors -

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Basic information

Entry
Database: PDB / ID: 6nw5
TitleCrystal structure of TmPep1050 aminopeptidase with its metal cofactors
ComponentsAminopeptidase
KeywordsHYDROLASE / M42 aminopeptidase / metal ion binding / TET-aminopeptidase / MH clan
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
: / HYDROXIDE ION / Endoglucanase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsDutoit, R.
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
DepositionFeb 6, 2019Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Derived calculations / Other
Category: citation / citation_author ...citation / citation_author / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_database_status.process_site
Revision 1.2Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,35738
Polymers144,4414
Non-polymers2,91634
Water26,5541474
1
A: Aminopeptidase
B: Aminopeptidase
C: Aminopeptidase
D: Aminopeptidase
hetero molecules

A: Aminopeptidase
B: Aminopeptidase
C: Aminopeptidase
D: Aminopeptidase
hetero molecules

A: Aminopeptidase
B: Aminopeptidase
C: Aminopeptidase
D: Aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)442,071114
Polymers433,32412
Non-polymers8,748102
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Unit cell
Length a, b, c (Å)131.152, 131.152, 285.610
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-870-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Aminopeptidase / / Endoglucanase / Endoglucanase M


Mass: 36110.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_1050, THEMA_09110, Tmari_1054 / Plasmid: pCEC43 / Details (production host): pBAD-TOPO w/ TM1050 / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: Q9X0E0

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Non-polymers , 5 types, 1508 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-OH / HYDROXIDE ION / Hydroxide


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1474 / 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: 3.27 Å3/Da / Density % sol: 62.42 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: TmPep1050 (1 mM in 50 mM MOPS 0.5 M ammonium sulfate 1 mM CoCl2 pH7.2) was crystallised in 0.18 M tri-ammonium citrate pH7.5 PEG3350 40%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 10, 2018
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→47.602 Å / Num. obs: 201316 / % possible obs: 99.8 % / Redundancy: 10.345 % / Biso Wilson estimate: 20.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.087 / Χ2: 1.133 / Net I/av σ(I): 2.17 / Net I/σ(I): 15.81
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.7410.4090.672.81145870.8710.70497.6
1.74-1.7910.2120.5573.47145720.9140.587100
1.79-1.849.7240.4624.24141810.9360.488100
1.84-1.910.7020.3765.69137010.9640.395100
1.9-1.9610.620.3087.24133340.9750.324100
1.96-2.0310.4450.2429.08128680.9860.254100
2.03-2.119.8520.19310.86124370.9890.204100
2.11-2.1910.5640.15813.87119050.9920.166100
2.19-2.2910.8940.13716.24115020.9940.144100
2.29-2.410.8750.12417.9109100.9950.13100
2.4-2.5310.720.10920.13104510.9950.115100
2.53-2.6910.5960.09822.3398310.9960.103100
2.69-2.8710.2060.08625.0492470.9960.091100
2.87-3.19.3380.07726.7886530.9970.082100
3.1-3.49.9510.06830.6779360.9980.072100
3.4-3.810.0760.06134.0871620.9980.064100
3.8-4.399.2890.05334.8763300.9980.056100
4.39-5.3710.7680.04638.853280.9990.049100
5.37-7.611.310.04138.6741430.9990.042100
7.6-47.60210.5970.0340.12223810.03299.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDS20180808data reduction
XSCALE20180808data scaling
PHASER2.8.2phasing
PHENIX1.14-3260-00refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P6Y

4p6y


Resolution: 1.7→47.602 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 15.7
RfactorNum. reflection% reflection
Rfree0.1636 9715 4.82 %
Rwork0.1426 --
obs0.1436 201316 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.66 Å2 / Biso mean: 24.5868 Å2 / Biso min: 11.14 Å2
Refinement stepCycle: final / Resolution: 1.7→47.602 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10061 0 134 1474 11669
Biso mean--41.49 38.22 -
Num. residues----1324
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6989-1.71820.3095960.2703121381273494
1.7182-1.73840.23465960.18411288613482100
1.7384-1.75960.21456920.18251270413396100
1.7596-1.78190.19225900.17691285013440100
1.7819-1.80530.20066580.16751287213530100
1.8053-1.83010.18067280.16161276513493100
1.8301-1.85620.18776480.16271270413352100
1.8562-1.88390.19667120.15961272613438100
1.8839-1.91340.17817120.15561281713529100
1.9134-1.94470.18157780.16041269313471100
1.9447-1.97830.19446880.15351272413412100
1.9783-2.01420.18256420.14941284413486100
2.0142-2.0530.16877060.1471279813504100
2.053-2.09490.16226780.14761281313491100
2.0949-2.14040.15555460.13951287413420100
2.1404-2.19020.17277200.14111275513475100
2.1902-2.2450.1745400.14281287413414100
2.245-2.30570.16036480.13991281013458100
2.3057-2.37360.15636720.13981271013382100
2.3736-2.45020.16395740.13931295513529100
2.4502-2.53770.17026120.14521286713479100
2.5377-2.63930.15937000.14561281813518100
2.6393-2.75940.16365840.14481281613400100
2.7594-2.90490.16126640.14451282213486100
2.9049-3.08690.19486740.15251270213376100
3.0869-3.32520.16887140.15161278213496100
3.3252-3.65970.14875920.13361293213524100
3.6597-4.1890.13375960.11391288413480100
4.189-5.27660.11655720.11241287613448100
5.2766-47.62030.1615950.15061282413419100

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