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

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Basic information

Entry
Database: PDB / ID: 4hyg
TitleStructure of a presenilin family intramembrane aspartate protease in C222 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 / identical protein binding / membrane / Signal peptide peptidase
Function and homology information
Biological speciesMethanoculleus marisnigri JR1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.32 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

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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
A: Putative uncharacterized protein
B: Putative uncharacterized protein

A: Putative uncharacterized protein
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)127,5174
Polymers127,5174
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area7320 Å2
ΔGint-73 kcal/mol
Surface area50610 Å2
MethodPISA
2
C: Putative uncharacterized protein
D: 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
crystal symmetry operation4_567x,-y+1,-z+21
Buried area7440 Å2
ΔGint-64 kcal/mol
Surface area51080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.302, 201.892, 117.534
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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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: 3.91 Å3/Da / Density % sol: 68.58 %
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: SSRF / Beamline: BL17U / Wavelength: 1.07171, 1.05384, 1.07206
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 24, 2012
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.071711
21.053841
31.072061
ReflectionResolution: 3.3→50 Å / Num. obs: 24686

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: MAD / Resolution: 3.32→49.108 Å / SU ML: 0.44 / σ(F): 1.34 / Phase error: 46.63 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.3441 1254 5.11 %
Rwork0.2984 --
obs0.3007 24554 82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.32→49.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7115 0 0 0 7115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097258
X-RAY DIFFRACTIONf_angle_d1.6259913
X-RAY DIFFRACTIONf_dihedral_angle_d22.2364364
X-RAY DIFFRACTIONf_chiral_restr0.0991288
X-RAY DIFFRACTIONf_plane_restr0.0091174
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.32-3.45330.3542530.339588028
3.4533-3.61040.392700.3316166653
3.6104-3.80070.4191280.3378226973
3.8007-4.03870.40371700.3006285792
4.0387-4.35030.36991590.2728309399
4.3503-4.78780.27791800.2384310799
4.7878-5.47980.32161670.2668314599
5.4798-6.90090.43351610.3868318699
6.9009-49.11370.31821660.2961309793
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)
11.7725-0.32651.54734.5529-0.09211.34740.06850.11990.3836-0.1387-0.01380.1271-0.1148-0.7082-0.09280.62020.0610.18531.4569-0.09560.5313104.428692.004231.5485
22.86940.5877-0.21052.14530.35754.7280.06470.1715-0.30670.0987-0.3518-0.42480.64050.17210.1650.68780.08130.06040.69090.32340.3154105.176174.317268.0436
32.4262-1.3434-1.05963.87210.11423.8001-0.4226-1.10071.34080.3151-0.3006-0.4199-0.5788-0.130.50840.75940.1691-0.5461.7046-0.18541.1492147.8776126.5346104.3957
41.7876-0.6331-1.68331.93420.79112.0709-0.0969-0.59820.1106-0.0993-0.59170.7988-0.6388-0.42680.3460.8557-0.0356-0.16882.7742-0.88531.4006148.1751112.8445143.3328
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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