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- PDB-6m00: crystal structure of Methionine aminopeptidase from Pyrococcus fu... -

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Basic information

Entry
Database: PDB / ID: 6m00
Titlecrystal structure of Methionine aminopeptidase from Pyrococcus furiosus
ComponentsMethionine aminopeptidase
KeywordsHYDROLASE / Methionine aminopeptidase
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 / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / Methionine aminopeptidase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsSandeep, C.B. / Addlagatta, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)EMR/2015/000461 India
CitationJournal: To Be Published
Title: crystal structure of Methionine aminopeptidase from Pyrococcus furiosus
Authors: sandeep, C.B. / Addlagatta, A.
History
DepositionFeb 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)33,0063
Polymers32,8881
Non-polymers1182
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-26 kcal/mol
Surface area12940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.684, 137.684, 61.332
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Methionine aminopeptidase / MetAP / Peptidase M


Mass: 32888.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: map, PF0541 / Production host: Escherichia coli (E. coli) / References: UniProt: P56218, methionyl aminopeptidase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 5.1 Å3/Da / Density % sol: 75.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.1 M sodium acetate, 2M NaCl , 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97949 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.85→45.86 Å / Num. obs: 14342 / % possible obs: 92.7 % / Redundancy: 6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.074 / Rrim(I) all: 0.196 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.85-34.21.732719917320.2910.8861.9590.876.9
9.01-45.867.30.04233174520.9990.0150.04420.290.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.414
Highest resolutionLowest resolution
Rotation24.44 Å3.41 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
DENZO2.3.1data reduction
SCALEPACK2.2.0data scaling
MOLREP11.4.03phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WKM

1wkm


Resolution: 3.2→45.79 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.903 / SU B: 24.705 / SU ML: 0.373 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.726 / ESU R Free: 0.448
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2764 477 4.6 %RANDOM
Rwork0.2425 ---
obs0.2441 9793 92.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 99.21 Å2 / Biso mean: 55.423 Å2 / Biso min: 37.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å20 Å2
2--0.03 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 3.2→45.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2304 0 2 0 2306
Biso mean--67.43 --
Num. residues----294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192345
X-RAY DIFFRACTIONr_bond_other_d0.0020.022373
X-RAY DIFFRACTIONr_angle_refined_deg1.881.9883167
X-RAY DIFFRACTIONr_angle_other_deg1.04935471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0275293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.01424.27196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.3415439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0461514
X-RAY DIFFRACTIONr_chiral_restr0.0960.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212581
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02481
LS refinement shellResolution: 3.2→3.282 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.435 35 -
Rwork0.391 689 -
obs--88.73 %

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