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- PDB-4hyd: Structure of a presenilin family intramembrane aspartate protease... -

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Basic information

Entry
Database: PDB / ID: 4hyd
TitleStructure of a presenilin family intramembrane aspartate protease in C2221 space group
ComponentsPutative uncharacterized protein
KeywordsMEMBRANE PROTEIN / protease
Function / homologySignal-peptide peptidase, presenilin aspartyl protease / Signal-peptide peptidase, presenilin aspartyl protease / Presenilin/signal peptide peptidase / Presenilin, signal peptide peptidase, family / aspartic endopeptidase activity, intramembrane cleaving / endomembrane system / identical protein binding / membrane / Signal peptide peptidase
Function and homology information
Biological speciesMethanoculleus marisnigri JR1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.8 Å
AuthorsLi, X. / Dang, S. / Yan, C. / Wang, J. / Shi, Y.
CitationJournal: Nature / Year: 2013
Title: Structure of a presenilin family intramembrane aspartate protease
Authors: Li, X. / Dang, S. / Yan, C. / Gong, X. / Wang, J. / Shi, Y.
History
DepositionNov 13, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references / Structure summary
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
D: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)127,5174
Polymers127,5174
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-63 kcal/mol
Surface area51280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.077, 170.025, 181.397
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Putative uncharacterized protein


Mass: 31879.260 Da / Num. of mol.: 4 / Mutation: D40N, E42S, A147E, V148P, A229V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanoculleus marisnigri JR1 (archaea)
Strain: ATCC 35101 / DSM 1498 / JR1 / Gene: Memar_1924 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3CWV0

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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: 3.45 Å3/Da / Density % sol: 64.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.6
Details: 0.1M Glycine, 0.2M (NH4)2SO4, 20%(w/v) PEG500MME, 6%(w/v) Glycerol, 0.04%(w/v) Anapoe-C12E8, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.07171, 1.05384, 1.07206
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 12, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.071711
21.053841
31.072061
ReflectionResolution: 3.8→50 Å / Num. obs: 15330

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: MAD / Resolution: 3.8→31.577 Å / SU ML: 0.55 / σ(F): 1.34 / Phase error: 53.18 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.3081 649 4.3 %
Rwork0.3072 --
obs0.3073 15083 84.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.8→31.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7199 0 0 0 7199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017347
X-RAY DIFFRACTIONf_angle_d1.66310032
X-RAY DIFFRACTIONf_dihedral_angle_d20.844434
X-RAY DIFFRACTIONf_chiral_restr0.1041297
X-RAY DIFFRACTIONf_plane_restr0.0071196
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree: 0 / Total num. of bins used: 5

Resolution (Å)Num. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.8-4.083100.4391251872
4.0831-4.4932510.347247778
4.493-5.140700.2681270976
5.1407-6.46762450.3829325898
6.4676-31.57791530.2723347298
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.40912.0879-1.11653.8825-0.81841.1060.05081.56130.62171.09140.73640.87330.31040.04640.10881.32640.0599-1.03151.3098-0.22020.150337.959417.9252-28.7023
21.80920.6177-1.75011.7035-0.64543.2992-0.70010.28210.32140.10670.9287-0.1710.2791-0.9646-0.46370.89670.1052-0.6781.35510.50742.97031.798319.4194-10.2553
32.1295-0.03220.4293.3287-0.03982.2597-0.2325-0.74661.0898-0.46661.0741-0.0372-0.40790.0139-0.11762.00060.22180.87661.0486-0.41482.134519.587922.039625.6644
44.66370.9790.97896.33981.89375.1364-0.2592-0.3188-1.1412-0.06410.54751.9167-0.21670.2262-0.12760.43730.03130.10360.8141-0.05771.214355.7420.81057.312
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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