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- PDB-2q92: E. coli methionine aminopeptidase Mn-form with inhibitor B23 -

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Basic information

Entry
Database: PDB / ID: 2q92
TitleE. coli methionine aminopeptidase Mn-form with inhibitor B23
ComponentsMethionine aminopeptidaseMethionyl aminopeptidase
KeywordsHYDROLASE / aminopeptidase / dinuclear / 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
5-(2-NITROPHENYL)-2-FUROIC ACID / : / Methionine aminopeptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYe, Q.-Z.
CitationJournal: Bmc Struct.Biol. / Year: 2007
Title: Structural analysis of inhibition of E. coli methionine aminopeptidase: implication of loop flexibility in selective inhibition of bacterial enzymes.
Authors: Ma, Z.Q. / Xie, S.X. / Huang, Q.Q. / Nan, F.J. / Hurley, T.D. / Ye, Q.Z.
History
DepositionJun 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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)29,4775
Polymers29,1111
Non-polymers3664
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.137, 60.984, 50.693
Angle α, β, γ (deg.)90.000, 104.930, 90.000
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.: 2 / 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-B23 / 5-(2-NITROPHENYL)-2-FUROIC ACID


Mass: 233.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H7NO5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 1.96 Å3/Da / Density % sol: 37.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10-15% PEG 20000, 0.1 M MES (pH 6.5), vapor diffusion, hanging drop, temperature 291K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→26.4 Å / Num. obs: 17799 / % possible obs: 100 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-23.50.2213.4904525800.221100
2-2.123.50.1554.8866924550.155100
2.12-2.273.60.1196.2820522980.119100
2.27-2.453.60.0928.1762121270.092100
2.45-2.693.60.07510718319820.075100
2.69-33.60.05712.7653017920.057100
3-3.473.70.04117.4584615960.041100
3.47-4.253.70.0322.1495813510.03100
4.25-6.013.70.02922.5377310270.029100
6.01-29.663.40.04113.620165910.04198.7

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Phasing

Phasing MRRfactor: 0.335 / Cor.coef. Fo:Fc: 0.708
Highest resolutionLowest resolution
Rotation3 Å26.36 Å
Translation3 Å26.36 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XNZ

1xnz


Resolution: 1.9→26.4 Å / FOM work R set: 0.849 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.238 1750 9.8 %
Rwork0.203 --
obs-17784 100 %
Solvent computationBsol: 35.672 Å2
Displacement parametersBiso mean: 21.767 Å2
Baniso -1Baniso -2Baniso -3
1-2.577 Å20 Å2-0.856 Å2
2---2.65 Å20 Å2
3---0.073 Å2
Refinement stepCycle: LAST / Resolution: 1.9→26.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2035 0 20 133 2188
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.318
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_scbond_it2.0922
X-RAY DIFFRACTIONc_mcangle_it1.8292
X-RAY DIFFRACTIONc_scangle_it3.0072.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 35

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.9-1.920.39500.274442492
1.92-1.940.287430.234470513
1.94-1.960.248500.223445495
1.96-1.980.253500.221459509
1.98-20.316420.216475517
2-2.020.25560.228452508
2.02-2.050.301430.232446489
2.05-2.070.264460.212442488
2.07-2.10.323610.227475536
2.1-2.130.299480.221456504
2.13-2.150.231530.216442495
2.15-2.190.321560.229441497
2.19-2.220.24470.221467514
2.22-2.250.239510.214450501
2.25-2.290.211470.206469516
2.29-2.330.244460.19459505
2.33-2.370.247480.222460508
2.37-2.420.354460.222473519
2.42-2.470.218470.174431478
2.47-2.520.277630.24469532
2.52-2.580.297510.208450501
2.58-2.640.247480.206469517
2.64-2.710.276490.2447496
2.71-2.790.256480.221453501
2.79-2.880.225450.191464509
2.88-2.990.235520.203461513
2.99-3.110.223430.228455498
3.11-3.250.226430.213479522
3.25-3.420.284610.217455516
3.42-3.630.221570.193446503
3.63-3.910.232660.187455521
3.91-4.310.193430.163462505
4.31-4.930.147440.161473517
4.93-6.20.205460.183475521
6.2-300.186610.186467528
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 DIFFRACTION5YE4.paramYE4.top

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