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- PDB-2p98: E. coli methionine aminopeptidase monometalated with inhibitor YE7 -

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Basic information

Entry
Database: PDB / ID: 2p98
TitleE. coli methionine aminopeptidase monometalated with inhibitor YE7
ComponentsMethionine aminopeptidaseMethionyl aminopeptidase
KeywordsHYDROLASE / monometalated / mononuclear / Mn(II)-form / enzyme-inhibitor complex / metalloenzyme
Function / homology
Function and homology information


initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloaminopeptidase activity / ferrous iron binding / proteolysis / cytosol
Similarity search - Function
Methionine aminopeptidase subfamily 1 signature. / Peptidase M24A, methionine aminopeptidase, subfamily 1 / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / IMIDAZO[2,1-A]ISOQUINOLINE-2-CARBOHYDRAZIDE / Methionine aminopeptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsYe, Q.
CitationJournal: J.Med.Chem. / Year: 2007
Title: Inhibition of Monometalated Methionine Aminopeptidase: Inhibitor Discovery and Crystallographic Analysis.
Authors: Huang, M. / Xie, S.X. / Ma, Z.Q. / Huang, Q.Q. / Nan, F.J. / Ye, Q.Z.
History
DepositionMar 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4154
Polymers29,1111
Non-polymers3043
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.190, 60.270, 50.610
Angle α, β, γ (deg.)90.00, 104.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Methionine aminopeptidase / Methionyl aminopeptidase / MAP / Peptidase M


Mass: 29110.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: map / Plasmid: pGEMEX-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AE18, methionyl aminopeptidase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-YE7 / IMIDAZO[2,1-A]ISOQUINOLINE-2-CARBOHYDRAZIDE


Mass: 226.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10N4O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 1.94 Å3/Da / Density % sol: 36.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG 20000, 0.1 M MES (pH 6.5), vapor diffusion, hanging drop, temperature 291K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 23375 / % possible obs: 95.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.793.70.24931228833040.24992.7
1.79-1.93.70.1664.51176631470.16693.3
1.9-2.033.70.1017.31115329800.10194.6
2.03-2.193.80.0739.81053828100.07395.7
2.19-2.43.80.05213.8984026100.05295.6
2.4-2.693.80.0417.9894223790.0497.2
2.69-3.13.80.0416.2801421250.0497.7
3.1-3.83.80.02822.6681618120.02898.2
3.8-5.383.70.02130.7534514260.02199.2
5.38-19.893.50.02917.127687820.02997.1

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Phasing

Phasing MRRfactor: 0.333 / Cor.coef. Fo:Fc: 0.707
Highest resolutionLowest resolution
Rotation3 Å19.89 Å
Translation3 Å19.89 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→20 Å / FOM work R set: 0.852 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.238 2308 9.4 %
Rwork0.207 --
obs-23359 95.2 %
Solvent computationBsol: 33.677 Å2
Displacement parametersBiso mean: 23.304 Å2
Baniso -1Baniso -2Baniso -3
1-2.735 Å20 Å2-0.478 Å2
2---3.428 Å20 Å2
3---0.693 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2035 0 19 158 2212
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.352
X-RAY DIFFRACTIONc_mcbond_it1.1531.5
X-RAY DIFFRACTIONc_scbond_it1.9732
X-RAY DIFFRACTIONc_mcangle_it1.6462
X-RAY DIFFRACTIONc_scangle_it2.8242.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 46

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.7-1.710.352570.382427484
1.71-1.730.312580.367446504
1.73-1.740.346430.326447490
1.74-1.750.306410.305452493
1.75-1.770.392490.305426475
1.77-1.780.384570.287437494
1.78-1.80.358540.273431485
1.8-1.810.318540.268433487
1.81-1.830.296440.286478522
1.83-1.840.315430.266429472
1.84-1.860.303400.256455495
1.86-1.880.331460.241451497
1.88-1.90.292620.265436498
1.9-1.920.235500.233443493
1.92-1.940.268530.206459512
1.94-1.960.22500.202437487
1.96-1.980.261460.213447493
1.98-2.010.3590.227446505
2.01-2.030.256560.227445501
2.03-2.060.234450.218448493
2.06-2.080.222480.203454502
2.08-2.110.272540.204468522
2.11-2.140.243410.21455496
2.14-2.170.284400.203468508
2.17-2.210.241430.228485528
2.21-2.240.279470.221422469
2.24-2.280.292440.241477521
2.28-2.320.242530.217474527
2.32-2.370.274450.224462507
2.37-2.420.271450.214461506
2.42-2.470.28560.198453509
2.47-2.530.228430.236482525
2.53-2.590.207520.219448500
2.59-2.660.269530.214470523
2.66-2.740.278490.206472521
2.74-2.830.275480.217466514
2.83-2.930.25480.207464512
2.93-3.040.271510.209471522
3.04-3.180.205480.211489537
3.18-3.350.238580.203459517
3.35-3.560.228540.197478532
3.56-3.830.196550.168470525
3.83-4.210.173640.17475539
4.21-4.810.157480.153478526
4.81-6.040.245550.185488543
6.04-200.173590.162489548
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein_1.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5YE7.paramYE7.top

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