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- PDB-8khm: Crystal structure of human methionine aminopeptidase 12 (MAP12) i... -

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Basic information

Entry
Database: PDB / ID: 8khm
TitleCrystal structure of human methionine aminopeptidase 12 (MAP12) in the unbound form
ComponentsMethionine aminopeptidase 1D, mitochondrial
KeywordsHYDROLASE / Methionine aminopeptidase / Metal-activated proteases / Mitochondrial-targeted protein
Function / homology
Function and homology information


methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloexopeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / post-translational protein modification / mitochondrion / proteolysis / metal ion binding
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
TRIETHYLENE GLYCOL / Methionine aminopeptidase 1D, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsLee, Y. / Lee, E. / Hahn, H. / Kim, H. / Heo, Y. / Jang, D.M. / Kim, H.J. / Kim, H.S.
Funding support Korea, Republic Of, 5items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2023-00207997 Korea, Republic Of
Other governmentICR-21-05
Other governmentICR-22-05
Other privateNCC-2210390
Other privateNCC-2210730
CitationJournal: Sci Rep / Year: 2023
Title: Structural insights into N-terminal methionine cleavage by the human mitochondrial methionine aminopeptidase, MetAP1D.
Authors: Lee, Y. / Kim, H. / Lee, E. / Hahn, H. / Heo, Y. / Jang, D.M. / Kwak, K. / Kim, H.J. / Kim, H.S.
History
DepositionAug 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methionine aminopeptidase 1D, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7194
Polymers34,3851
Non-polymers3343
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-1 kcal/mol
Surface area12080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.398, 81.204, 48.893
Angle α, β, γ (deg.)90.00, 102.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Methionine aminopeptidase 1D, mitochondrial / MAP 1D / MetAP 1D / Methionyl aminopeptidase type 1D / mitochondrial / Peptidase M 1D


Mass: 34384.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METAP1D, MAP1D / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6UB28, methionyl aminopeptidase
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 43.65 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES pH 7.2, 0.1M Carboxylic acids, 17% (v/v) MPD, 17% (w/v) PEG 1000, 17% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97957 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 1.39→27.67 Å / Num. obs: 58324 / % possible obs: 99.3 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.073 / Net I/σ(I): 12.83
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.39-1.480.88193010.7651.0231
1.48-1.580.54788190.90.641
1.58-1.710.32582710.9370.3831
1.71-1.870.19576210.9790.2251
1.87-2.090.10868600.9920.1251
2.09-2.410.06360520.9970.0731
2.41-2.940.04251160.9980.051
2.94-4.140.02739920.9990.0311
4.14-27.670.02222920.9990.0251

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→27.67 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2081 2958 5.08 %
Rwork0.1889 --
obs0.1899 58269 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.39→27.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2210 0 22 261 2493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062346
X-RAY DIFFRACTIONf_angle_d0.8953203
X-RAY DIFFRACTIONf_dihedral_angle_d6.31328
X-RAY DIFFRACTIONf_chiral_restr0.078355
X-RAY DIFFRACTIONf_plane_restr0.007425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.420.40961100.38992483X-RAY DIFFRACTION95
1.42-1.440.39331430.36962688X-RAY DIFFRACTION100
1.44-1.470.36941380.34392611X-RAY DIFFRACTION100
1.47-1.50.33261600.32532622X-RAY DIFFRACTION99
1.5-1.530.33531030.30732653X-RAY DIFFRACTION99
1.53-1.560.29331640.29362615X-RAY DIFFRACTION100
1.56-1.60.32991300.26882656X-RAY DIFFRACTION100
1.6-1.640.26881350.2492642X-RAY DIFFRACTION100
1.64-1.680.23231460.23792656X-RAY DIFFRACTION100
1.68-1.730.24671470.22052630X-RAY DIFFRACTION100
1.73-1.790.24481210.20492649X-RAY DIFFRACTION100
1.79-1.850.23591350.19042660X-RAY DIFFRACTION100
1.85-1.920.24321460.20842603X-RAY DIFFRACTION99
1.92-2.010.18821620.18372615X-RAY DIFFRACTION100
2.01-2.120.21131440.17752620X-RAY DIFFRACTION99
2.12-2.250.20611200.16622672X-RAY DIFFRACTION99
2.25-2.420.21291630.17062624X-RAY DIFFRACTION99
2.42-2.670.19351580.16092626X-RAY DIFFRACTION99
2.67-3.050.1591440.15282617X-RAY DIFFRACTION98
3.05-3.840.16091380.14362660X-RAY DIFFRACTION99
3.84-27.670.1611510.15352709X-RAY DIFFRACTION100

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