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- PDB-1xgo: METHIONINE AMINOPEPTIDASE FROM HYPERTHERMOPHILE PYROCOCCUS FURIOSUS -

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Basic information

Entry
Database: PDB / ID: 1xgo
TitleMETHIONINE AMINOPEPTIDASE FROM HYPERTHERMOPHILE PYROCOCCUS FURIOSUS
ComponentsMETHIONINE AMINOPEPTIDASE
KeywordsAMINOPEPTIDASE / HYPERTHERMOPHILE
Function / homology
Function and homology information


methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloaminopeptidase activity / proteolysis / metal ion binding / cytoplasm
Similarity search - Function
Methionine aminopeptidase, archaeal / Peptidase M24A, methionine aminopeptidase, subfamily 2 / : / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 ...Methionine aminopeptidase, archaeal / Peptidase M24A, methionine aminopeptidase, subfamily 2 / : / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Methionine aminopeptidase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsTahirov, T.H. / Tsukihara, T.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Crystal structure of methionine aminopeptidase from hyperthermophile, Pyrococcus furiosus.
Authors: Tahirov, T.H. / Oki, H. / Tsukihara, T. / Ogasahara, K. / Yutani, K. / Ogata, K. / Izu, Y. / Tsunasawa, S. / Kato, I.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Crystallization and Preliminary X-Ray Analysis of Methionine Aminopeptidase from the Hyperthermophilic Bacterium Pyrococcus Furiosus
Authors: Tahirov, T.H. / Oki, H. / Tsukihara, T. / Ogasahara, K. / Izu, Y. / Tsunasawa, S. / Kato, I. / Yutani, K.
History
DepositionNov 18, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 28, 2016Group: Other
Revision 1.4Aug 9, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.5May 22, 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


Theoretical massNumber of molelcules
Total (without water)32,8881
Polymers32,8881
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.916, 138.916, 63.907
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein METHIONINE AMINOPEPTIDASE


Mass: 32888.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: TWO COBALT IONS IN ACTIVE SITE REMOVED BY THE REDUCTION OF PH TO 2.6
Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: P56218, methionyl aminopeptidase

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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: 5.412 Å3/Da / Density % sol: 77.4 %
Crystal growpH: 2.6
Details: PROTEIN SOLUTION CONTAINING 16 MG/ML PFMAP, 2 MM COCL2 AND 30 MM L-METHIONINE IN 20 MM POTASSIUM ACETATE AT PH4.5 WAS MIXED WITH EQUAL AMOUNT OF RESERVOIR SOLUTION CONTAINING 10% PEG6000 AND ...Details: PROTEIN SOLUTION CONTAINING 16 MG/ML PFMAP, 2 MM COCL2 AND 30 MM L-METHIONINE IN 20 MM POTASSIUM ACETATE AT PH4.5 WAS MIXED WITH EQUAL AMOUNT OF RESERVOIR SOLUTION CONTAINING 10% PEG6000 AND 2.0 M SODIUM CHLORIDE AT PH 2.6, THEN EQUILIBRATED AGAINST RESERVOIR SOLUTION.
PH range: 2.6-4.5
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 %(v/v)PEG60001reservoir
22.0 Msodium chloride1reservoir

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 7571 / % possible obs: 84.3 % / Observed criterion σ(I): 1 / Redundancy: 3.65 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 6.1
Reflection shellResolution: 3.5→3.63 Å / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 1.9 / % possible all: 64.9
Reflection
*PLUS
Num. measured all: 59765
Reflection shell
*PLUS
% possible obs: 64.9 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MONOCLINIC CRYSTAL FORM, PDB ENTRY 1XGM

1xgm


Resolution: 3.5→15 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.274 788 8.8 %RANDOM
Rwork0.182 ---
obs0.182 7163 80.3 %-
Displacement parametersBiso mean: 31.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 3.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2312 0 0 0 2312
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.27
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.21
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.03
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3.5→3.66 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.293 65 5.9 %
Rwork0.221 516 -
obs--52.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.21
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.03

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