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- PDB-6lvh: Crystal structure of methionine aminopeptidase from Pyrococcus fu... -

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Basic information

Entry
Database: PDB / ID: 6lvh
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
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsAddlagatta, A. / Sandeep, C.B.
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: Addlagatta, A. / Sandeep, C.B.
History
DepositionFeb 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 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)33,1084
Polymers32,8311
Non-polymers2763
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-2 kcal/mol
Surface area12670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.658, 133.658, 62.520
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: 32831.332 Da / Num. of mol.: 1 / Mutation: N53G
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
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: 4.9 Å3/Da / Density % sol: 74.91 %
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: ROTATING ANODE / Type: RIGAKU R-AXIS IV / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.2→25 Å / Num. obs: 10354 / % possible obs: 97 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.045 / Rrim(I) all: 0.086 / Χ2: 0.981 / Net I/σ(I): 10.8 / Num. measured all: 36517
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.2-3.312.50.3988960.8230.2910.4960.84986
3.31-3.453.10.29110180.8730.1960.3530.88795
3.45-3.63.40.20810410.9490.1310.2470.87898
3.6-3.793.60.15310140.970.0950.1810.95297.6
3.79-4.033.70.11910450.9830.0720.1390.96298.3
4.03-4.343.80.08210580.9930.0490.0960.99698.7
4.34-4.773.80.06210580.9950.0370.0731.04598.9
4.77-5.463.80.0610500.9970.0360.071.04598.8
5.46-6.853.80.05910710.9950.0360.0691.09499.2
6.85-253.70.03611030.9980.0220.0430.98498.8

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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
REFMAC5.8.0238refinement
DENZO2.3.1data reduction
SCALEPACK2.2.0data scaling
MOLREP11.7.01phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WKM

1wkm


Resolution: 3.2→24.45 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.913 / SU B: 14.898 / SU ML: 0.245 / SU R Cruickshank DPI: 1.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.151 / ESU R Free: 0.342
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2137 492 4.8 %RANDOM
Rwork0.1621 ---
obs0.1646 9862 96.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 155.21 Å2 / Biso mean: 77.141 Å2 / Biso min: 5.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 3.2→24.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2308 0 18 14 2340
Biso mean--93.36 42.71 -
Num. residues----295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132364
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172359
X-RAY DIFFRACTIONr_angle_refined_deg1.741.6443187
X-RAY DIFFRACTIONr_angle_other_deg1.2091.5765465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3285294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59122.385109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.41515441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9361514
X-RAY DIFFRACTIONr_chiral_restr0.0730.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022578
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02456
LS refinement shellResolution: 3.201→3.284 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 30 -
Rwork0.273 628 -
all-658 -
obs--83.61 %

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