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- PDB-7srv: Metal dependent activation of Plasmodium falciparum M17 aminopept... -

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Basic information

Entry
Database: PDB / ID: 7srv
TitleMetal dependent activation of Plasmodium falciparum M17 aminopeptidase (inactive form), spacegroup P22121
ComponentsM17 leucyl aminopeptidase
KeywordsPEPTIDE BINDING PROTEIN / Malaria / enzyme / metallo aminopeptidase
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / leucyl aminopeptidase / metallodipeptidase activity / peptide catabolic process / metalloaminopeptidase activity / carboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / zinc ion binding ...Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / leucyl aminopeptidase / metallodipeptidase activity / peptide catabolic process / metalloaminopeptidase activity / carboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / zinc ion binding / metal ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Peptidase M17, leucine aminopeptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Zn peptidases / Aminopeptidase / Macro domain-like ...Peptidase M17, leucine aminopeptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Zn peptidases / Aminopeptidase / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / CARBONATE ION / PHOSPHATE ION / Leucine aminopeptidase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsWebb, C.T. / McGowan, S.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: J.Biol.Chem. / Year: 2022
Title: A metal ion-dependent conformational switch modulates activity of the Plasmodium M17 aminopeptidase.
Authors: Webb, C.T. / Yang, W. / Riley, B.T. / Hayes, B.K. / Sivaraman, K.K. / Malcolm, T.R. / Harrop, S. / Atkinson, S.C. / Kass, I. / Buckle, A.M. / Drinkwater, N. / McGowan, S.
History
DepositionNov 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: M17 leucyl aminopeptidase
B: M17 leucyl aminopeptidase
C: M17 leucyl aminopeptidase
D: M17 leucyl aminopeptidase
E: M17 leucyl aminopeptidase
F: M17 leucyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,21953
Polymers351,4676
Non-polymers2,75347
Water34,3371906
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.542, 172.670, 179.395
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-1409-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 96 through 101 or (resid 102...
d_2ens_1(chain "B" and (resid 96 through 101 or (resid 102...
d_3ens_1(chain "C" and (resid 96 through 101 or (resid 102...
d_4ens_1(chain "D" and (resid 96 through 117 or (resid 118...
d_5ens_1(chain "E" and (resid 96 through 110 or (resid 111...
d_6ens_1(chain "F" and (resid 96 through 101 or (resid 102...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROGLUA11 - 39
d_12ens_1GLYGLYA41 - 51
d_13ens_1GLUVALA53 - 68
d_14ens_1GLUILEA70 - 143
d_15ens_1VALTHRA145 - 170
d_16ens_1GLULEUA177 - 238
d_17ens_1TYRGLYA240 - 262
d_18ens_1METALAA264 - 302
d_19ens_1SERASPA306 - 314
d_110ens_1SERCYSA316 - 345
d_111ens_1ASNTYRA347 - 354
d_112ens_1PROGLUA356 - 422
d_113ens_1LEUILEA424 - 425
d_114ens_1LYSLEUA427 - 429
d_115ens_1SERILEA431 - 445
d_116ens_1GLUALAA447 - 450
d_117ens_1LEUASPA452 - 518
d_118ens_1ZNZNB
d_119ens_1CO3CO3C
d_21ens_1PROGLUD11 - 39
d_22ens_1GLYGLYD41 - 51
d_23ens_1GLUVALD53 - 68
d_24ens_1GLUILED70 - 143
d_25ens_1VALTHRD145 - 170
d_26ens_1GLULEUD177 - 238
d_27ens_1TYRGLYD240 - 262
d_28ens_1METALAD264 - 302
d_29ens_1SERASPD306 - 314
d_210ens_1SERCYSD316 - 345
d_211ens_1ASNTYRD347 - 354
d_212ens_1PROGLUD356 - 422
d_213ens_1LEUILED424 - 425
d_214ens_1LYSLEUD427 - 429
d_215ens_1SERILED431 - 445
d_216ens_1GLUALAD447 - 450
d_217ens_1LEUASPD452 - 518
d_218ens_1ZNZNE
d_219ens_1CO3CO3F
d_31ens_1PROGLUG11 - 39
d_32ens_1GLYGLYG41 - 51
d_33ens_1GLUVALG53 - 68
d_34ens_1GLUILEG70 - 143
d_35ens_1VALTHRG145 - 170
d_36ens_1GLULEUG177 - 238
d_37ens_1TYRGLYG240 - 262
d_38ens_1METALAG264 - 302
d_39ens_1SERASPG305 - 313
d_310ens_1SERCYSG315 - 344
d_311ens_1ASNTYRG346 - 353
d_312ens_1PROGLUG355 - 421
d_313ens_1LEUILEG423 - 424
d_314ens_1LYSLEUG426 - 428
d_315ens_1SERILEG430 - 444
d_316ens_1GLUALAG446 - 449
d_317ens_1LEUASPG451 - 517
d_318ens_1ZNZNH
d_319ens_1CO3CO3I
d_41ens_1PROGLUJ2 - 30
d_42ens_1GLYGLYJ32 - 42
d_43ens_1GLUVALJ44 - 59
d_44ens_1GLUILEJ61 - 134
d_45ens_1VALTHRJ136 - 161
d_46ens_1GLULEUJ165 - 226
d_47ens_1TYRGLYJ228 - 250
d_48ens_1METALAJ252 - 290
d_49ens_1SERASPJ294 - 302
d_410ens_1SERCYSJ304 - 333
d_411ens_1ASNTYRJ335 - 342
d_412ens_1PROGLUJ344 - 410
d_413ens_1LEUILEJ412 - 413
d_414ens_1LYSLEUJ415 - 417
d_415ens_1SERILEJ419 - 433
d_416ens_1GLUALAJ435 - 438
d_417ens_1LEUASPJ440 - 506
d_418ens_1ZNZNK
d_419ens_1CO3CO3L
d_51ens_1PROGLUM7 - 35
d_52ens_1GLYGLYM37 - 47
d_53ens_1GLUVALM49 - 64
d_54ens_1GLUILEM66 - 139
d_55ens_1VALTHRM141 - 166
d_56ens_1GLULEUM169 - 230
d_57ens_1TYRGLYM232 - 254
d_58ens_1METASPM256 - 303
d_59ens_1SERCYSM305 - 334
d_510ens_1ASNTYRM336 - 343
d_511ens_1PROGLUM345 - 411
d_512ens_1LEUILEM413 - 414
d_513ens_1LYSLEUM416 - 418
d_514ens_1SERILEM420 - 434
d_515ens_1GLUALAM436 - 439
d_516ens_1LEUASPM441 - 507
d_517ens_1ZNZNN
d_518ens_1CO3CO3O
d_61ens_1PROGLUP1 - 29
d_62ens_1GLYVALP31 - 57
d_63ens_1GLUILEP59 - 132
d_64ens_1VALTHRP134 - 159
d_65ens_1GLULEUP161 - 222
d_66ens_1TYRGLYP224 - 246
d_67ens_1METALAP248 - 286
d_68ens_1SERASPP289 - 297
d_69ens_1SERCYSP299 - 328
d_610ens_1ASNTYRP330 - 337
d_611ens_1PROGLUP339 - 405
d_612ens_1LEUILEP407 - 408
d_613ens_1LYSLEUP410 - 412
d_614ens_1SERILEP414 - 428
d_615ens_1GLUALAP430 - 433
d_616ens_1LEUASPP435 - 501
d_617ens_1ZNZNQ
d_618ens_1CO3CO3R

NCS oper:
IDCodeMatrixVector
1given(-0.161785979733, 0.758910110445, -0.630777885651), (-0.773245705957, -0.494629330134, -0.396778154628), (-0.613120196194, 0.42355314901, 0.666848074889)-107.093051421, 366.159394404, -61.3340337189
2given(-0.174140005111, -0.773780958544, -0.609047031694), (0.761691463516, -0.497838393302, 0.414708389789), (-0.624100451071, -0.391688603804, 0.676075931108)228.675376567, 289.037349702, 117.13310387
3given(-0.623940384341, 0.760867491197, 0.178266815835), (0.743586782179, 0.507873651758, 0.434905795797), (0.24036866301, 0.403912137338, -0.882653890919)-118.818977561, 69.4528900994, -33.4738883503
4given(-0.604457587377, -0.776161694271, 0.179454867331), (-0.760060067723, 0.494406599956, -0.421747326456), (0.238620448653, -0.391324850049, -0.888777330504)216.054702299, 149.560125744, 140.208476199
5given(0.5332759513, 0.0113748566998, 0.845864866513), (0.0104645269664, -0.999921788099, 0.00684918679935), (0.845876618332, 0.0051990690995, -0.533353275269)-14.716335365, 436.640155961, 22.1868424885

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
M17 leucyl aminopeptidase


Mass: 58577.777 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Escherichia coli (E. coli) / References: UniProt: Q8IL11, leucyl aminopeptidase

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Non-polymers , 8 types, 1953 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CO3
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1906 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20 % PEG3350, 0.2 M calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953724 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953724 Å / Relative weight: 1
ReflectionResolution: 2→49.19 Å / Num. obs: 233061 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 36.46 Å2 / CC1/2: 0.997 / Net I/σ(I): 7.1
Reflection shellResolution: 2→2.03 Å / Num. unique obs: 11469 / CC1/2: 0.244

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KQZ

3kqz


Resolution: 2.03→49.19 Å / SU ML: 0.2689 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.1964
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2188 11027 4.95 %
Rwork0.1885 211802 -
obs0.19 222829 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.81 Å2
Refinement stepCycle: LAST / Resolution: 2.03→49.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23466 0 120 1906 25492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002424065
X-RAY DIFFRACTIONf_angle_d0.608232666
X-RAY DIFFRACTIONf_chiral_restr0.06183764
X-RAY DIFFRACTIONf_plane_restr0.00314165
X-RAY DIFFRACTIONf_dihedral_angle_d5.89963310
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.691606431562
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.459263222782
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.956698417195
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.788939330326
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.713033011848
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.050.35333740.3286964X-RAY DIFFRACTION99.82
2.05-2.080.3733630.32577010X-RAY DIFFRACTION99.81
2.08-2.10.35023430.30576979X-RAY DIFFRACTION99.95
2.1-2.130.32643930.28826968X-RAY DIFFRACTION99.97
2.13-2.160.31533410.287034X-RAY DIFFRACTION99.99
2.16-2.190.30184000.27177003X-RAY DIFFRACTION99.95
2.19-2.220.32133420.26256974X-RAY DIFFRACTION100
2.22-2.250.28653930.25266986X-RAY DIFFRACTION100
2.25-2.290.29323930.25286966X-RAY DIFFRACTION100
2.29-2.320.26493800.24687014X-RAY DIFFRACTION100
2.32-2.360.27123700.23097007X-RAY DIFFRACTION100
2.36-2.410.27813250.22917027X-RAY DIFFRACTION100
2.41-2.450.25563300.22477092X-RAY DIFFRACTION100
2.45-2.50.2773610.22467014X-RAY DIFFRACTION99.97
2.5-2.560.25953590.22677022X-RAY DIFFRACTION100
2.56-2.620.25353510.21967050X-RAY DIFFRACTION99.99
2.62-2.680.25164050.20796976X-RAY DIFFRACTION99.99
2.68-2.760.25453930.21197033X-RAY DIFFRACTION99.99
2.76-2.840.2243690.19547041X-RAY DIFFRACTION100
2.84-2.930.21953750.18637062X-RAY DIFFRACTION100
2.93-3.030.21923730.1897061X-RAY DIFFRACTION100
3.03-3.150.21973820.18577042X-RAY DIFFRACTION100
3.15-3.30.21353640.18227075X-RAY DIFFRACTION99.99
3.3-3.470.21313510.17197100X-RAY DIFFRACTION100
3.47-3.690.18993690.1637097X-RAY DIFFRACTION100
3.69-3.970.17723730.15647144X-RAY DIFFRACTION100
3.97-4.370.17323550.14237138X-RAY DIFFRACTION100
4.37-50.15873400.1377195X-RAY DIFFRACTION100
5-6.30.18253910.16997228X-RAY DIFFRACTION99.99
6.3-49.190.19153690.16977500X-RAY DIFFRACTION99.81

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