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

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Basic information

Entry
Database: PDB / ID: 4hyc
TitleStructure of a presenilin family intramembrane aspartate protease in P2 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: 3.95 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
E: Putative uncharacterized protein
F: Putative uncharacterized protein
G: Putative uncharacterized protein
H: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)255,0348
Polymers255,0348
Non-polymers00
Water00
1
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-72 kcal/mol
Surface area51110 Å2
MethodPISA
2
E: Putative uncharacterized protein
F: Putative uncharacterized protein
G: Putative uncharacterized protein
H: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)127,5174
Polymers127,5174
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-67 kcal/mol
Surface area51010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.224, 115.827, 137.173
Angle α, β, γ (deg.)90.00, 100.59, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein
Putative uncharacterized protein


Mass: 31879.260 Da / Num. of mol.: 8 / 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: 3.9 Å3/Da / Density % sol: 68.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.6
Details: 0.1 M Glycine pH 3.6, 0.2 M (NH4)2SO4, 20% (w/v) PEG500MME, 6% (w/v) Glycerol and 0.04% (w/v) Anapoe-C12E8, 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: 3.95→50 Å / Num. obs: 27265

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: MAD / Resolution: 3.95→40.161 Å / SU ML: 0.69 / σ(F): 1.34 / Phase error: 44.88 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.341 1340 4.93 %
Rwork0.3082 --
obs0.3108 27165 78.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.95→40.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14416 0 0 0 14416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814712
X-RAY DIFFRACTIONf_angle_d1.49420088
X-RAY DIFFRACTIONf_dihedral_angle_d21.2028880
X-RAY DIFFRACTIONf_chiral_restr0.1022600
X-RAY DIFFRACTIONf_plane_restr0.0072392
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.95-4.087000.3809167949
4.087-4.2504000.3597197157
4.2504-4.44370.36891710.3027200063
4.4437-4.67760.35722970.257200067
4.6776-4.9702000.2668248572
4.9702-5.3531000.2937293585
5.3531-5.89030.42355380.355275695
5.8903-6.7392000.3813340697
6.7392-8.4775000.30983501100
8.4775-40.16260.30123340.2905309296
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)
13.289-1.10880.39994.16653.03994.5875-0.24960.44210.4465-0.3547-0.47150.34210.28160.50530.76270.7788-0.0118-0.07241.13980.24831.1951-109.9337-108.95967.6464
23.7997-0.1705-0.52541.13940.1633.4372-0.0072-0.1513-0.44140.5058-0.0066-0.7406-0.23040.3757-0.05691.27370.2459-0.55471.1080.11951.4299-95.5154-72.887556.4595
33.5712-1.97730.29225.11771.2873.4403-0.1113-0.38660.7576-0.19530.5893-1.11240.1575-0.1826-0.36721.1336-0.2445-0.04821.0001-0.22141.0785-66.6738-90.721835.0313
43.52881.00580.26960.5943-0.60572.29850.2615-0.5439-0.19110.5621-0.3196-0.175-0.40810.03870.19061.7196-0.0049-0.5081.0707-0.35461.2634-81.4758-126.84445.8613
51.3993-0.95752.1954.8808-0.69144.2867-0.06260.7228-0.7227-0.78581.36970.35250.78381.3042-0.51041.2377-0.2569-0.53211.2997-0.62341.4712-94.8807-28.99740.6291
62.551.5443-0.63431.4442-0.38813.0295-0.2744-0.6750.2731.1448-0.17690.4528-1.00890.02120.32072.03930.7321-0.50661.4823-0.49721.5009-124.8643-16.028323.8025
72.84190.3571.34552.74430.3191.4528-0.0426-0.8144-0.203-0.7430.64711.231-0.4588-1.0139-0.39231.30030.131-0.21141.36690.73571.3196-135.388-54.767431.3159
81.39140.5696-0.86780.203-0.62933.44360.2591-0.6221-0.1587-0.60170.0839-0.72290.81570.8352-0.19152.14030.8167-1.04881.8064-0.62472.1212-104.8477-67.65628.576
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H

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