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- PDB-6k26: Crystal structure of Vibrio cholerae methionine aminopeptidase -

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Basic information

Entry
Database: PDB / ID: 6k26
TitleCrystal structure of Vibrio cholerae methionine aminopeptidase
ComponentsMethionine aminopeptidaseMethionyl aminopeptidase
KeywordsHYDROLASE / MetAP / Methionine aminopeptidase
Function / homology
Function and homology information


: / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloaminopeptidase activity / transition metal ion binding / proteolysis / metal ion binding / cytosol
Similarity search - Function
Methionine aminopeptidase subfamily 1 signature. / Peptidase M24A, methionine aminopeptidase, subfamily 1 / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Methionine aminopeptidase / Methionine aminopeptidase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 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
DepositionMay 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.2Nov 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)66,9304
Polymers66,8842
Non-polymers462
Water5,729318
1
A: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4652
Polymers33,4421
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4652
Polymers33,4421
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.529, 50.010, 131.086
Angle α, β, γ (deg.)90.000, 97.250, 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: 33442.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: map / Variant: serotype O1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A085RSZ7, UniProt: Q9KPV1*PLUS, methionyl aminopeptidase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Hepes, 12 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 12, 2017 / Details: VariMax Cu-HF
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. obs: 53682 / % possible obs: 98.5 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.057 / Rrim(I) all: 0.101 / Χ2: 1.021 / Net I/σ(I): 8.9 / Num. measured all: 155933
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.922.80.53152600.6180.3660.6481.04397.8
1.92-1.992.80.37153020.8640.2560.4531.0198
1.99-2.082.90.27353330.9110.1870.3321.05498.2
2.08-2.192.90.21352970.9380.1450.2591.04398.1
2.19-2.332.90.17353390.9590.1170.211.02198.6
2.33-2.512.90.14453820.9730.0980.1751.02898.6
2.51-2.762.90.11353810.9810.0770.1370.96698.9
2.76-3.162.90.07953890.9890.0530.0950.98298.9
3.16-3.9830.05454320.9950.0370.0661.02298.9
3.98-402.90.04255670.9970.0290.0511.0498.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.579
Highest resolutionLowest resolution
Rotation34.63 Å2.01 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000v716data scaling
MOLREP11.6.03phasing
PDB_EXTRACT3.25data extraction
Coot0.8.9.2model building
HKL-2000v716data reduction
HKL-3000v703ndata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2MAT

2mat


Resolution: 1.85→34.66 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.1984 / WRfactor Rwork: 0.1585 / FOM work R set: 0.8588 / SU B: 2.772 / SU ML: 0.081 / SU R Cruickshank DPI: 0.1227 / SU Rfree: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2076 2658 5 %RANDOM
Rwork0.1658 ---
obs0.1679 51013 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.45 Å2 / Biso mean: 22.57 Å2 / Biso min: 6.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å2-0.14 Å2
2--0.92 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.85→34.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4378 0 2 326 4706
Biso mean--18.92 24.69 -
Num. residues----558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134612
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174344
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.6426270
X-RAY DIFFRACTIONr_angle_other_deg1.4211.57710139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8215598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35223.051236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52315848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9951526
X-RAY DIFFRACTIONr_chiral_restr0.080.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025195
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02907
LS refinement shellResolution: 1.851→1.899 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 192 -
Rwork0.263 3610 -
all-3802 -
obs--94.62 %

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