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- PDB-6ksg: Vibrio cholerae Methionine Aminopeptidase in holo form -

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Basic information

Entry
Database: PDB / ID: 6ksg
TitleVibrio cholerae Methionine Aminopeptidase in holo form
ComponentsMethionine aminopeptidaseMethionyl aminopeptidase
KeywordsHYDROLASE
Function / homology
Function and homology information


initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloaminopeptidase activity / transition metal ion binding / proteolysis / cytosol
Similarity search - Function
Methionine aminopeptidase subfamily 1 signature. / Peptidase M24A, methionine aminopeptidase, subfamily 1 / Peptidase M24, methionine aminopeptidase / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like
Similarity search - Domain/homology
NICKEL (II) ION / Methionine aminopeptidase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsPillalamarri, V. / Addlagatta, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (India)EMR/2015/000461 India
CitationJournal: Eur.J.Med.Chem. / Year: 2020
Title: Methionine aminopeptidases with short sequence inserts within the catalytic domain are differentially inhibited: Structural and biochemical studies of three proteins from Vibrio spp.
Authors: Pillalamarri, V. / Reddy, C.G. / Bala, S.C. / Jangam, A. / Kutty, V.V. / Addlagatta, A.
History
DepositionAug 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 27, 2021Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.3Nov 22, 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
B: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,98014
Polymers67,1472
Non-polymers83312
Water3,765209
1
A: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0828
Polymers33,5731
Non-polymers5097
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-23 kcal/mol
Surface area11870 Å2
MethodPISA
2
B: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8986
Polymers33,5731
Non-polymers3255
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-23 kcal/mol
Surface area11740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.508, 49.835, 131.221
Angle α, β, γ (deg.)90.000, 97.280, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Methionine aminopeptidase / Methionyl aminopeptidase / MetAP / Peptidase M


Mass: 33573.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: map, VC_2261 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9KPV1, methionyl aminopeptidase
#2: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.56 Å3/Da / Density % sol: 51.96 % / Mosaicity: 0.24 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9536 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 1.9→48 Å / Num. obs: 50007 / % possible obs: 99.6 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.032 / Rrim(I) all: 0.081 / Net I/σ(I): 15.8 / Num. measured all: 307534 / Scaling rejects: 125
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
1.9-1.955.80.7951891932470.8740.3550.8732.797.8
8.92-485.30.03628415390.9990.0170.0439.999.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.487
Highest resolutionLowest resolution
Rotation46.54 Å2.08 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
Aimless0.7.3data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6K26

6k26


Resolution: 1.9→46.58 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.2276 / WRfactor Rwork: 0.1867 / FOM work R set: 0.8286 / SU B: 3.566 / SU ML: 0.104 / SU R Cruickshank DPI: 0.153 / SU Rfree: 0.1456 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: MOLECULAR REPLCEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 2495 5 %RANDOM
Rwork0.1957 ---
obs0.1978 47497 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.75 Å2 / Biso mean: 28.019 Å2 / Biso min: 8.36 Å2
Baniso -1Baniso -2Baniso -3
1--1.61 Å2-0 Å2-0.26 Å2
2--0.67 Å20 Å2
3---0.98 Å2
Refinement stepCycle: final / Resolution: 1.9→46.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4378 0 42 214 4634
Biso mean--42.74 31.51 -
Num. residues----558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134548
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174254
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.6426156
X-RAY DIFFRACTIONr_angle_other_deg1.381.5769918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9555572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50723.276232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34515816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1041524
X-RAY DIFFRACTIONr_chiral_restr0.0740.2618
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025064
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02880
LS refinement shellResolution: 1.903→1.952 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 167 -
Rwork0.288 3452 -
all-3619 -
obs--98.18 %

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