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- PDB-6lh7: Crystal Structure of Vibrio cholerae Methionine Aminopeptidase wi... -

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Basic information

Entry
Database: PDB / ID: 6lh7
TitleCrystal Structure of Vibrio cholerae Methionine Aminopeptidase with Partially Occupied Metals
ComponentsMethionine aminopeptidaseMethionyl aminopeptidase
KeywordsHYDROLASE / peta-bread fold / metallo enzyme / MetAP
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: 1.473 Å
AuthorsPillalamarri, V. / Addlagatta, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, 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
DepositionDec 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methionine aminopeptidase
B: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,79612
Polymers67,1472
Non-polymers64910
Water9,908550
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 area11910 Å2
MethodPISA
2
B: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7144
Polymers33,5731
Non-polymers1403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-23 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.702, 50.293, 131.684
Angle α, β, γ (deg.)90.000, 97.241, 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 / 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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.39 Å3/Da / Density % sol: 49.41 %
Description: Rhomboid shaped crystals are observed within 12 hours
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: 0.1 M Hepes pH-7.3 , 10% PEG 3350, 5% Glycerol

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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: 1.47→49.31 Å / Num. obs: 108944 / % possible obs: 99.7 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.026 / Rrim(I) all: 0.067 / Net I/σ(I): 17.6 / Num. measured all: 684923 / Scaling rejects: 38
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
1.47-1.560.6763165852550.8410.2940.7392.797.7
8.07-49.315.60.02940327160.9990.0130.03246.698.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.503
Highest resolutionLowest resolution
Rotation48.18 Å1.67 Å

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Processing

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

6k26


Resolution: 1.473→48.226 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.016 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.059
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1765 5364 4.925 %
Rwork0.1518 --
all0.153 --
obs-108924 99.646 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.882 Å2
Baniso -1Baniso -2Baniso -3
1--0.755 Å2-0 Å20.026 Å2
2--0.544 Å20 Å2
3---0.198 Å2
Refinement stepCycle: LAST / Resolution: 1.473→48.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4378 0 30 550 4958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0134719
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174476
X-RAY DIFFRACTIONr_angle_refined_deg1.8831.6446425
X-RAY DIFFRACTIONr_angle_other_deg1.511.57910461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6245622
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05622.669251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.78215880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7511531
X-RAY DIFFRACTIONr_chiral_restr0.0960.2647
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025315
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02942
X-RAY DIFFRACTIONr_nbd_refined0.2250.2883
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.24157
X-RAY DIFFRACTIONr_nbtor_refined0.1670.22255
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.22093
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2369
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0580.24
X-RAY DIFFRACTIONr_metal_ion_refined0.1770.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1380.228
X-RAY DIFFRACTIONr_nbd_other0.1940.295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2170.234
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.3110.22
X-RAY DIFFRACTIONr_mcbond_it1.4671.4192306
X-RAY DIFFRACTIONr_mcbond_other1.4631.4182305
X-RAY DIFFRACTIONr_mcangle_it2.0692.1272899
X-RAY DIFFRACTIONr_mcangle_other2.0712.1282900
X-RAY DIFFRACTIONr_scbond_it2.8311.8042413
X-RAY DIFFRACTIONr_scbond_other2.8051.8032413
X-RAY DIFFRACTIONr_scangle_it4.262.573493
X-RAY DIFFRACTIONr_scangle_other4.2522.573493
X-RAY DIFFRACTIONr_lrange_it5.11318.3075316
X-RAY DIFFRACTIONr_lrange_other5.07217.8365189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.473-1.5110.233920.2197478X-RAY DIFFRACTION98.1419
1.511-1.5530.2253380.2027421X-RAY DIFFRACTION99.4616
1.553-1.5980.2213700.1847189X-RAY DIFFRACTION99.0046
1.598-1.6470.1813420.1677074X-RAY DIFFRACTION99.7847
1.647-1.7010.1943410.1656786X-RAY DIFFRACTION99.8599
1.701-1.7610.1853560.1546591X-RAY DIFFRACTION99.9712
1.761-1.8270.1843170.1496397X-RAY DIFFRACTION99.9851
1.827-1.9020.1753100.1446149X-RAY DIFFRACTION100
1.902-1.9860.1663420.1425888X-RAY DIFFRACTION99.9839
1.986-2.0830.1643020.1385617X-RAY DIFFRACTION99.9156
2.083-2.1960.1672790.145343X-RAY DIFFRACTION99.9111
2.196-2.3290.1632590.1325070X-RAY DIFFRACTION99.9625
2.329-2.490.1612560.1314804X-RAY DIFFRACTION99.9408
2.49-2.6890.1672350.1344410X-RAY DIFFRACTION99.957
2.689-2.9460.1732220.1454141X-RAY DIFFRACTION99.9084
2.946-3.2930.1482120.143696X-RAY DIFFRACTION99.9744
3.293-3.8020.1821700.153273X-RAY DIFFRACTION99.7104
3.802-4.6560.1551510.1412805X-RAY DIFFRACTION99.7974
4.656-6.580.2081100.1882180X-RAY DIFFRACTION99.7387
6.58-48.2260.256600.211248X-RAY DIFFRACTION98.941

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