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- PDB-5yr6: Human methionine aminopeptidase type 1b (F309L mutant) in complex... -

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Basic information

Entry
Database: PDB / ID: 5yr6
TitleHuman methionine aminopeptidase type 1b (F309L mutant) in complex with TNP470
ComponentsMethionine aminopeptidase 1
KeywordsHYDROLASE / Metal binding protein / Methionine Aminopeptidase
Function / homology
Function and homology information


N-terminal protein amino acid modification / peptidyl-methionine modification / methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloexopeptidase activity / metalloaminopeptidase activity / protein maturation / aminopeptidase activity / cytosolic ribosome / platelet aggregation ...N-terminal protein amino acid modification / peptidyl-methionine modification / methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloexopeptidase activity / metalloaminopeptidase activity / protein maturation / aminopeptidase activity / cytosolic ribosome / platelet aggregation / Inactivation, recovery and regulation of the phototransduction cascade / regulation of translation / proteolysis / metal ion binding / cytosol / cytoplasm
Similarity search - Function
MYND-like zinc finger / zf-MYND-like zinc finger, mRNA-binding / Zinc finger C6H2-type profile. / 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 ...MYND-like zinc finger / zf-MYND-like zinc finger, mRNA-binding / Zinc finger C6H2-type profile. / 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
: / Chem-TN4 / Methionine aminopeptidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsPillalamarri, V. / Arya, T. / Addlagatta, A.
Funding support India, 1items
OrganizationGrant numberCountry
Other governmentEMR/2015/000461 India
CitationJournal: Biochem. J. / Year: 2019
Title: Discovery of natural product ovalicin sensitive type 1 methionine aminopeptidases: molecular and structural basis.
Authors: Pillalamarri, V. / Arya, T. / Haque, N. / Bala, S.C. / Marapaka, A.K. / Addlagatta, A.
History
DepositionNov 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 2.0Feb 13, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_validate_close_contact ...atom_site / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _atom_site.occupancy
Revision 2.1Mar 20, 2019Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 2.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methionine aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6905
Polymers34,1451
Non-polymers5454
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-29 kcal/mol
Surface area12750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.439, 77.325, 47.759
Angle α, β, γ (deg.)90.000, 91.700, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 34144.891 Da / Num. of mol.: 1 / Fragment: UNP residues 81-384 / Mutation: F309L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METAP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P53582, methionyl aminopeptidase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-TN4 / (1R,2S,3S,4R)-4-hydroxy-2-methoxy-4-methyl-3-[(2R,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]cyclohexyl (chloroacetyl)carbamate / TNP-470 (Open form)


Mass: 403.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30ClNO6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.56 Å3/Da / Density % sol: 52.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 0.1M Bistris pH-6.2, 19% PEG 3350, 5% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.75→27 Å / Num. obs: 34902 / % possible obs: 99.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.038 / Rrim(I) all: 0.071 / Χ2: 1.018 / Net I/σ(I): 16.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.8130.50234630.7960.3390.6090.96799.9
1.81-1.893.10.3834730.8830.2520.4581.013100
1.89-1.973.10.2634700.9330.1720.3131.056100
1.97-2.073.10.18335190.9620.1190.2191.05100
2.07-2.23.10.14634430.9730.0950.1751.032100
2.2-2.373.20.11535000.9790.0740.1371.052100
2.37-2.613.20.09334950.9860.060.1111.04100
2.61-2.993.20.07235020.990.0460.0860.994100
2.99-3.773.30.05134960.9960.0320.0611.026100
3.77-273.30.03935410.9970.0250.0460.94999

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.411
Highest resolutionLowest resolution
Rotation25.6 Å2.06 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-3000data collection
DENZO2.3.1data reduction
SCALEPACK2.2.0data scaling
MOLREP11.5.05phasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GZ5

2gz5


Resolution: 1.75→25.61 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.691 / SU ML: 0.082 / SU R Cruickshank DPI: 0.1088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.105 / Details: MOLECULAR REPLCEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.2105 1722 4.9 %RANDOM
Rwork0.1801 ---
obs0.1816 33158 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 87.4 Å2 / Biso mean: 32.038 Å2 / Biso min: 15.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å2-0 Å20.64 Å2
2---1.94 Å2-0 Å2
3---1.63 Å2
Refinement stepCycle: final / Resolution: 1.75→25.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2393 0 26 168 2587
Biso mean--30.78 30.21 -
Num. residues----304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0142514
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172225
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.6783424
X-RAY DIFFRACTIONr_angle_other_deg1.0161.6475237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0555315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67521.185135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03615417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4971520
X-RAY DIFFRACTIONr_chiral_restr0.2750.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022834
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02455
LS refinement shellResolution: 1.745→1.79 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 122 -
Rwork0.328 2287 -
all-2409 -
obs--93.81 %

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