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- PDB-2mat: E.COLI METHIONINE AMINOPEPTIDASE AT 1.9 ANGSTROM RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 2mat
TitleE.COLI METHIONINE AMINOPEPTIDASE AT 1.9 ANGSTROM RESOLUTION
ComponentsPROTEIN (METHIONINE AMINOPEPTIDASE)
KeywordsHYDROLASE / HYDROLASE(ALPHA-AMINOACYLPEPTIDE)
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 aminopeptidase / Methionine aminopeptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLowther, W.T. / Orville, A.M. / Madden, D.T. / Lim, S. / Rich, D.H. / Matthews, B.W.
Citation
Journal: Biochemistry / Year: 1999
Title: Escherichia coli methionine aminopeptidase: implications of crystallographic analyses of the native, mutant, and inhibited enzymes for the mechanism of catalysis.
Authors: Lowther, W.T. / Orville, A.M. / Madden, D.T. / Lim, S. / Rich, D.H. / Matthews, B.W.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: The anti-angiogenic agent fumagillin covalently modifies a conserved active-site histidine in the Escherichia coli methionine aminopeptidase.
Authors: Lowther, W.T. / McMillen, D.A. / Orville, A.M. / Matthews, B.W.
#2: 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.
History
DepositionMar 29, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 18, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2019Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_ref_seq_dif.details
Revision 1.5Aug 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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.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

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Assembly

Deposited unit
A: PROTEIN (METHIONINE AMINOPEPTIDASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5425
Polymers29,3421
Non-polymers2004
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.299, 67.683, 48.863
Angle α, β, γ (deg.)90.00, 111.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (METHIONINE AMINOPEPTIDASE)


Mass: 29341.775 Da / Num. of mol.: 1 / Mutation: R175Q
Source method: isolated from a genetically manipulated source
Details: SITE-DIRECTED MUTANT / Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET28B / Cell line (production host): BL21(DE3) / 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.: 3 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGLN 175, SITE-DIRECTED MUTANT

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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: 2.05 Å3/Da / Density % sol: 39.4 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.1
Details: CRYSTALS OF THE CO(II)-SUBSTITUTED ENZYME WERE GROWN AT ROOM TEMPERATURE BY VAPOR DIFFUSION IN 20-30 UL SITTING DROPS AFTER MIXING THE PROTEIN, 12 MG/ML SOLUTION IN STORAGE BUFFER(25 MM ...Details: CRYSTALS OF THE CO(II)-SUBSTITUTED ENZYME WERE GROWN AT ROOM TEMPERATURE BY VAPOR DIFFUSION IN 20-30 UL SITTING DROPS AFTER MIXING THE PROTEIN, 12 MG/ML SOLUTION IN STORAGE BUFFER(25 MM HEPES PH 6.8, 25 MM K2SO4, 100 MM NACL, 1 MM COCL2, 15 MM METHIONINE),CONTAINING 48.8 MM N-OCTANOYL SUCROSE, 1:1 WITH WELL SOLUTIONS (24-26% PEG4000, 0.1M HEPES PH7.0-7.2,FRESH 2 MM COCL2)., pH 7.1, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Details: drop consists of 1:1 mixture of well and protein solutions
PH range low: 7.2 / PH range high: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
248.8 mMN-octanoyl sucrose1drop
324-26 %PEG40001reservoir
40.1 MHEPES1reservoir
52 mM1reservoirCoCl2

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 10, 1998
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→35.5 Å / Num. obs: 18444 / % possible obs: 100 % / Redundancy: 5.1 % / Biso Wilson estimate: 15.5 Å2 / Rsym value: 0.077 / Net I/σ(I): 22.7
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 6.1 / Rsym value: 0.251 / % possible all: 100
Reflection
*PLUS
Num. measured all: 94123 / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.251

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5F PRERELEASErefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MAT

1mat


Resolution: 1.9→35.5 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
all0.155 18444 -
obs-18444 100 %
Solvent computationSolvent model: TNT / Bsol: 212.2 Å2 / ksol: 0.825 e/Å3
Refinement stepCycle: LAST / Resolution: 1.9→35.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1991 0 4 96 2091
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01220260.8
X-RAY DIFFRACTIONt_angle_deg2.327381.3
X-RAY DIFFRACTIONt_dihedral_angle_d16.412240
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.008512
X-RAY DIFFRACTIONt_gen_planes0.0132955
X-RAY DIFFRACTIONt_it4.120261
X-RAY DIFFRACTIONt_nbd0.0131810
Software
*PLUS
Name: TNT / Version: 5F / Classification: refinement
Refine LS restraints
*PLUS
Type: t_plane_restr / Dev ideal: 0.013 / Weight: 5

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