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- PDB-2evo: crystal structure of methionine amino peptidase in complex with N... -

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Basic information

Entry
Database: PDB / ID: 2evo
Titlecrystal structure of methionine amino peptidase in complex with N-cyclopentyl-N-(thiazol-2-yl)oxalamide
ComponentsMethionine aminopeptidaseMethionyl aminopeptidase
KeywordsHYDROLASE / methionine aminopeptidase / complex
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
: / N1-CYCLOPENTYL-N2-(THIAZOL-2-YL)OXALAMIDE / Methionine aminopeptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHuang, W.-J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Structural analysis of metalloform-selective inhibition of methionine aminopeptidase.
Authors: Xie, S.X. / Huang, W.J. / Ma, Z.Q. / Huang, M. / Hanzlik, R.P. / Ye, Q.Z.
History
DepositionOct 31, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_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
B: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,57410
Polymers58,7422
Non-polymers8328
Water4,738263
1
A: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7875
Polymers29,3711
Non-polymers4164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7875
Polymers29,3711
Non-polymers4164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.200, 63.400, 75.300
Angle α, β, γ (deg.)90.00, 108.50, 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: 29370.838 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: map / Plasmid: pGEMEX-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P0AE18, methionyl aminopeptidase
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-CT0 / N1-CYCLOPENTYL-N2-(THIAZOL-2-YL)OXALAMIDE


Mass: 239.294 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N3O2S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 1.9 Å3/Da / Density % sol: 35.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7.5
Details: 15% PEG 8000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 7, 2004 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 43944 / Num. obs: 48408 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.7→2.1 Å / % possible all: 89.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
XDSdata reduction
AMoREphasing
CNSrefinement
CrystalClear(MSC/RIGAKU)data reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2mat

2mat


Resolution: 1.7→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.241 1758 RANDOM
Rwork0.213 --
all0.232 48408 -
obs0.23 43944 -
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4042 0 38 263 4343
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.005
X-RAY DIFFRACTIONc_angle_deg1.35

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