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

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Basic information

Entry
Database: PDB / ID: 1xgs
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 / RIGID-BODY REFINEMENT / Resolution: 1.75 Å
AuthorsTahirov, T.H. / Tsukihara, T.
CitationJournal: 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.
History
DepositionApr 25, 1997Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METHIONINE AMINOPEPTIDASE
B: METHIONINE AMINOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0126
Polymers65,7772
Non-polymers2364
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.903, 83.286, 70.267
Angle α, β, γ (deg.)90.00, 105.87, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.956232, -0.267113, 0.11946), (-0.279453, 0.712624, -0.643485), (0.086753, -0.648704, -0.75608)
Vector: 30.8395, 27.2631, 60.3591)

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Components

#1: Protein METHIONINE AMINOPEPTIDASE


Mass: 32888.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: CONTAIN TWO COBALT IONS IN ACTIVE SITE / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: P56218
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.9 %
Description: DATA WERE COLLECTED USING 2 DEGREE OSCILLATION. LOW-HUMIDITY FORM CRYSTAL FORM USED FOR DATA COLLECTION WAS OBTAINED BY WATER-MEDIATED TRANSFORMATION OF NATIVE MONOCLINIC PFMAP CRYSTAL.
Crystal growpH: 8.5
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 20% ETHANOL IN ...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 20% ETHANOL IN 0.1 M TRIS BUFFER AT PH 8.5, THEN EQUILIBRATED AGAINST RESERVOIR SOLUTION. OBTAINED CRYSTALS WERE TRANSFORMED TO LOW-HUMIDITY FORM BY CONTROLLING THE RELATIVE HUMIDITY USING THE SATURATED SALT SOLUTIONS (AMMONIUM SULFATE AT LAST STAGE).
PH range: 4.5-8.5
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Tahirov, T., (1998) J. Struct. Biol., 121, 68. / pH: 4.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
22 mM1dropCoCl2
320 mMpotassium acetate1drop
420 %ethanol1reservoir
50.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Dec 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→100 Å / Num. obs: 49955 / % possible obs: 84.6 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 9.7
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 1.6 / % possible all: 62.4
Reflection
*PLUS
Num. measured all: 192734
Reflection shell
*PLUS
% possible obs: 62.4 %

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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: RIGID-BODY REFINEMENT
Starting model: STRUCTURE OF NATIVE MONOCLINIC PFMAP CRYSTAL DETERMINED BY MIR METHOD

Resolution: 1.75→15 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
Details: PARAMETER AND TOPOLOGY FILES ARE MODIFIED TO INCLUDE THE COBALT IONS IN THE REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.235 4521 7.8 %RANDOM
Rwork0.187 ---
obs0.187 45327 78.3 %-
Displacement parametersBiso mean: 20 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.75→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4624 0 4 206 4834
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.61
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.32
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.43
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: 1.75→1.83 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.319 353 4.5 %
Rwork0.299 3110 -
obs--48.3 %
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_deg24.32
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.43

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