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- PDB-1c21: E. COLI METHIONINE AMINOPEPTIDASE: METHIONINE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1c21
TitleE. COLI METHIONINE AMINOPEPTIDASE: METHIONINE COMPLEX
ComponentsMETHIONINE AMINOPEPTIDASEMethionyl aminopeptidase
KeywordsHYDROLASE / PRODUCT COMPLEX
Function / homology
Function and homology information


: / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / 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
: / METHIONINE / Methionine aminopeptidase / Methionine aminopeptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.8 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)29,5015
Polymers29,2111
Non-polymers2904
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.242, 67.588, 48.927
Angle α, β, γ (deg.)90.00, 111.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein METHIONINE AMINOPEPTIDASE / Methionyl aminopeptidase


Mass: 29210.580 Da / Num. of mol.: 1 / Fragment: METHIONINE / Mutation: R175Q
Source method: isolated from a genetically manipulated source
Details: METHIONINE 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 / 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-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.07 Å3/Da / Density % sol: 40.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: K2SO4, NaCl, methionine, N-octanoyl sucrose, PEG 4000, HEPES, CoCl2, 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: Apr 23, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→24.8 Å / Num. all: 21097 / Num. obs: 85232 / % possible obs: 95.1 % / Redundancy: 4 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 35.2
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 4.4 / % possible all: 90.2
Reflection
*PLUS
Num. obs: 21097 / Num. measured all: 85232
Reflection shell
*PLUS
% possible obs: 90.2 %

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Processing

Software
NameClassification
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
TNTphasing
RefinementResolution: 1.8→24.8 Å / Stereochemistry target values: TNT /
RfactorNum. reflection
all0.163 21097
obs-85232
Solvent computationSolvent model: TNT / Bsol: 204.6 Å2 / ksol: 0.834 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→24.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1980 0 12 97 2089
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.05
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_trig_c_planes0.006
X-RAY DIFFRACTIONt_gen_planes0.012
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Rfactor all: 0.163 / Num. reflection obs: 21097
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.05
X-RAY DIFFRACTIONt_planar_d0.006
X-RAY DIFFRACTIONt_plane_restr0.012

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