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- PDB-1mat: STRUCTURE OF THE COBALT-DEPENDENT METHIONINE AMINOPEPTIDASE FROM ... -

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Basic information

Entry
Database: PDB / ID: 1mat
TitleSTRUCTURE OF THE COBALT-DEPENDENT METHIONINE AMINOPEPTIDASE FROM ESCHERICHIA COLI: A NEW TYPE OF PROTEOLYTIC ENZYME
ComponentsMETHIONYL AMINOPEPTIDASE
KeywordsHYDROLASE(ALPHA-AMINOACYLPEPTIDE)
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
: / Methionine aminopeptidase / Methionine aminopeptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsRoderick, S.L. / Matthews, B.W.
Citation
Journal: Biochemistry / Year: 1993
Title: Structure of the cobalt-dependent methionine aminopeptidase from Escherichia coli: a new type of proteolytic enzyme.
Authors: Roderick, S.L. / Matthews, B.W.
#1: Journal: J.Biol.Chem. / Year: 1988
Title: Crystallization of Methionine Aminopeptidase from Escherichia Coli
Authors: Roderick, S.L. / Matthews, B.W.
#2: Journal: J.Bacteriol. / Year: 1987
Title: Processing of the Initiation Methionine from Proteins: Properties of the Escherichia Coli Methionine Aminopeptidase and its Gene Structure
Authors: Ben-Bassat, A. / Bauer, K. / Chang, S.-Y. / Myambo, K. / Boosman, A. / Chang, S.
History
DepositionDec 2, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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
Remark 700SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE ...SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW TWO SHEETS ARE DEFINED. STRANDS 2, 3, AND 4 OF 1A AND 1B ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METHIONYL AMINOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4893
Polymers29,3711
Non-polymers1182
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.000, 61.700, 54.500
Angle α, β, γ (deg.)90.00, 107.30, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO 181
2: FOLLOWING RESIDUES TRUNCATED TO ALA: GLU 12, LYS 13, LYS 117, GLU 123, VAL 194, LEU 195, AND LYS 218.
3: RESIDUE LEU 88 TRUNCATED TO GLY.
4: FOLLOWING RESIDUES TRUNCATED TO GAMMA CARBON: GLU 9, ARG 93, LYS 86, LEU 87, LYS 89, THR 119, GLU 167, LYS 211, LYS 226, ARG 228, AND GLU 264.
5: FOLLOWING RESIDUES TRUNCATED TO DELTA CARBON: ARG 19, LYS 155, ARG 189, AND LYS 196.
6: RESIDUE LYS 252 TRUNCATED TO EPSILON CARBON.
7: FOLLOWING RESIDUES TRUNCATED TO VAL: ILE 49, ILE 120, AND ILE 144.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.333795, 0.741892, 0.581532), (0.657432, -0.62533, 0.420413), (0.675552, 0.241987, -0.696475)
Vector: -63.26726, 52.73847, 76.57813)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR PORTIONS OF THE CHAIN WHEN APPLIED TO OTHER PORTIONS OF THE CHAIN AS FOLLOWS: APPLYING MTRIX TO YIELDS ----------------- ----------------- THR 119 - MET 139 ILE 11 - TYR 31 VAL 140 - ILE 144 VAL 32 - VAL 36 ASN 145 - ALA 159 SER 37 - ASN 51 GLY 198 - ASN 208 GLY 91 - ILE 101 LEU 230 - THR 241 PHE 105 - GLY 116

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Components

#1: Protein METHIONYL AMINOPEPTIDASE


Mass: 29370.838 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.27 %
Crystal grow
*PLUS
pH: 6.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
142 mg/mlprotein1drop
225 Msodium cacodylate1drop
325 mM1dropK2SO4
4100 mM1dropNaCl
51 mM1dropCoCl2
614 %(w/v)PEG40001drop
70.5 %(w/v)octyl beta-glucoside1drop
823-35 %PEG40001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 8054 / % possible obs: 93 % / Rmerge(I) obs: 0.035

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Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.182 / Highest resolution: 2.4 Å
Refinement stepCycle: LAST / Highest resolution: 2.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1965 0 2 15 1982
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.019
X-RAY DIFFRACTIONt_angle_deg2.9
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 52 Å / Num. reflection obs: 8387 / Rfactor obs: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg

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