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- PDB-1c22: E. COLI METHIONINE AMINOPEPTIDASE: TRIFLUOROMETHIONINE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1c22
TitleE. COLI METHIONINE AMINOPEPTIDASE: TRIFLUOROMETHIONINE COMPLEX
ComponentsMETHIONINE AMINOPEPTIDASE
KeywordsHYDROLASE / PRODUCT COMPLEX
Function / homology
Function and homology information


: / methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloaminopeptidase activity / ferrous iron binding / proteolysis / metal ion binding / 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
: / 2-AMINO-4-TRIFLUOROMETHYLSULFANYL-BUTYRIC ACID / Methionine aminopeptidase / Methionine aminopeptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.75 Å
AuthorsLowther, W.T. / Zhang, Y. / Sampson, P.B. / Honek, J.F. / Matthews, B.W.
CitationJournal: Biochemistry / Year: 1999
Title: Insights into the mechanism of Escherichia coli methionine aminopeptidase from the structural analysis of reaction products and phosphorus-based transition-state analogues.
Authors: Lowther, W.T. / Zhang, Y. / Sampson, P.B. / Honek, J.F. / Matthews, B.W.
History
DepositionJul 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METHIONINE AMINOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5555
Polymers29,2111
Non-polymers3444
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.128, 67.604, 48.826
Angle α, β, γ (deg.)90.00, 111.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein METHIONINE AMINOPEPTIDASE


Mass: 29210.580 Da / Num. of mol.: 1 / Mutation: R175Q
Source method: isolated from a genetically manipulated source
Details: TRIFLUOROMETHIONINE COMPLEX / Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET28B / Production host: Escherichia coli (E. coli)
References: UniProt: P07906, UniProt: P0AE18*PLUS, methionyl aminopeptidase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Fragment: TRIFLUOROMETHIONINE / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MF3 / 2-AMINO-4-TRIFLUOROMETHYLSULFANYL-BUTYRIC ACID / TRIFLUOROMETHIONINE


Type: L-peptide linking / Mass: 203.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8F3NO2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE ARE FOUR ADDITIONAL RESIDUES ON THE C-TERMINUS LEFT OVER FROM A THROMBIN DIGEST OF THE HIS- ...THERE ARE FOUR ADDITIONAL RESIDUES ON THE C-TERMINUS LEFT OVER FROM A THROMBIN DIGEST OF THE HIS-TAGGED PROTEIN. THESE RESIDUES, L-V-P-R (RESIDUES 265-268), WERE NOT SEEN IN THE ELECTRON DENSITY AND ARE NOT A PART OF THE SEQRES.

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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: 2.06 Å3/Da / Density % sol: 40.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: HEPES, CoCl2, K2SO4, Methionine, PEG4000, NaCl, N-octanoyl sucrose, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
225 mMHEPES1drop
325 mM1dropK2SO4
4100 mM1dropNaCl
51 mM1dropCoCl2
615 mMmethionine1drop
748.8 mMN-octanoyl sucrose1drop
824-26 %PEG40001reservoir
90.1 MHEPES1reservoir
102 mM1reservoirCoCl2

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 18, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.75→27.1 Å / Num. all: 24021 / Num. obs: 116107 / % possible obs: 99.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 35.2
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 4.5 / % possible all: 100
Reflection
*PLUS
Num. obs: 24021 / Num. measured all: 116107
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
TNTphasing
RefinementResolution: 1.75→27.1 Å / Stereochemistry target values: TNT /
RfactorNum. reflection
all0.163 24021
obs-116107
Solvent computationSolvent model: TNT / Bsol: 221.4 Å2 / ksol: 0.842 e/Å3
Refinement stepCycle: LAST / Resolution: 1.75→27.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1987 0 15 103 2105
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.1
X-RAY DIFFRACTIONt_bond_d0.011
X-RAY DIFFRACTIONt_trig_c_planes0.009
X-RAY DIFFRACTIONt_gen_planes0.013
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 24021 / Rfactor all: 0.163
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.1
X-RAY DIFFRACTIONt_planar_d0.009
X-RAY DIFFRACTIONt_plane_restr0.013

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