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- PDB-4il3: Crystal Structure of S. mikatae Ste24p -

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Basic information

Entry
Database: PDB / ID: 4il3
TitleCrystal Structure of S. mikatae Ste24p
ComponentsSte24p
KeywordsHYDROLASE / membrane protein / alpha helical / CaaX Protease / a-factor / structural genomics / MPSBC / PSI-Biology / Membrane Protein Structural Biology Consortium
Function / homology
Function and homology information


Ste24 endopeptidase / CAAX-box protein processing / metalloendopeptidase activity / membrane => GO:0016020 / endoplasmic reticulum membrane / metal ion binding
Similarity search - Function
CAAX prenyl protease 1 / CAAX prenyl protease 1, N-terminal / CAAX prenyl protease N-terminal, five membrane helices / Metalloproteases ("zincins"), catalytic domain / Peptidase M48 / Peptidase family M48 / Zincin-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CAAX prenyl protease
Similarity search - Component
Biological speciesSaccharomyces mikatae (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, MOLECULAR REPLACEMENT / SAD / molecular replacement / Resolution: 3.102 Å
AuthorsPryor Jr., E.E. / Horanyi, P.S. / Clark, K. / Fedoriw, N. / Connelly, S.M. / Koszelak-Rosenblum, M. / Zhu, G. / Malkowski, M.G. / Dumont, M.E. / Wiener, M.C. / Membrane Protein Structural Biology Consortium (MPSBC)
CitationJournal: Science / Year: 2013
Title: Structure of the integral membrane protein CAAX protease Ste24p.
Authors: Pryor, E.E. / Horanyi, P.S. / Clark, K.M. / Fedoriw, N. / Connelly, S.M. / Koszelak-Rosenblum, M. / Zhu, G. / Malkowski, M.G. / Wiener, M.C. / Dumont, M.E.
History
DepositionDec 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ste24p
B: Ste24p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8114
Polymers106,6802
Non-polymers1312
Water0
1
A: Ste24p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4052
Polymers53,3401
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ste24p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4052
Polymers53,3401
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)143.530, 143.530, 197.024
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
DetailsThe biological unit is a monomer. There are two biological units in the asymmetric unit.

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Components

#1: Protein Ste24p


Mass: 53339.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces mikatae (yeast) / Strain: IFO 1815T / Plasmid: pSGP46 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ5460 / References: UniProt: M4GGS2*PLUS, Ste24 endopeptidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 5.49 Å3/Da / Density % sol: 77.6 %
Description: MR/SAD using Zn anomalous signal and 4AW6 structure
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 7.5
Details: 10% PEG 20,000, 20% PEG 550MME, 5 mM 1,6-hexanediol, 5 mM 1-butanol, 5 mM (RS)-1,2-propanediol, 5 mM 2-propanol, 5 mM 1,4-butanediol, 5 mM 1,3-propanediol, 100 mM MOPS / Na-HEPES pH 7.5, ...Details: 10% PEG 20,000, 20% PEG 550MME, 5 mM 1,6-hexanediol, 5 mM 1-butanol, 5 mM (RS)-1,2-propanediol, 5 mM 2-propanol, 5 mM 1,4-butanediol, 5 mM 1,3-propanediol, 100 mM MOPS / Na-HEPES pH 7.5, vapor diffusion, temperature 290K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.27 Å
DetectorType: MARMOSAIC 300 / Detector: CCD / Date: Aug 19, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27 Å / Relative weight: 1
ReflectionRedundancy: 5.5 % / Av σ(I) over netI: 12.33 / Number: 148213 / Rmerge(I) obs: 0.131 / Χ2: 1.08 / D res high: 3.1 Å / D res low: 50 Å / Num. obs: 26962 / % possible obs: 64.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
8.45099.910.0521.4416.2
6.678.410010.0941.0876.4
5.836.6710010.1750.9436.5
5.35.8310010.20.9266.4
4.925.310010.1721.0376.2
4.634.9210010.1681.1366.1
4.44.6399.810.1991.1665.8
4.214.498.710.2311.1625.4
4.044.2189.810.2351.1024.8
3.914.0471.610.2361.1164.7
3.783.9156.710.2521.0454.9
3.683.7848.210.2950.9534.7
3.583.6842.410.270.9734.6
3.493.5837.110.3050.9534.6
3.413.4933.110.2880.9324.4
3.343.4128.310.3340.8194.2
3.273.342610.3490.8293.9
3.213.2723.810.340.8663.5
3.153.2120.710.3920.8443.2
3.13.1517.510.4350.922.9
ReflectionResolution: 3.1→50 Å / Num. all: 26962 / Num. obs: 26917 / % possible obs: 64.8 % / Observed criterion σ(F): 65.5 / Observed criterion σ(I): -4.1 / Redundancy: 5.5 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.131 / Χ2: 1.078 / Net I/σ(I): 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
3.1-3.152.90.4352.293620.9217.5
3.15-3.213.20.3921.864300.84420.7
3.21-3.273.50.342.144980.86623.8
3.27-3.343.90.3492.835380.82926
3.34-3.414.20.33435890.81928.3
3.41-3.494.40.2883.576840.93233.1
3.49-3.584.60.3053.577660.95337.1
3.58-3.684.60.273.888830.97342.4
3.68-3.784.70.29549970.95348.2
3.78-3.914.90.2525.1411721.04556.7
3.91-4.044.70.2365.1414761.11671.6
4.04-4.214.80.2355.2918891.10289.8
4.21-4.45.40.2317.3320231.16298.7
4.4-4.635.80.1999.1720851.16699.8
4.63-4.926.10.16811.1720871.136100
4.92-5.36.20.17211.820861.037100
5.3-5.836.40.28.620740.926100
5.83-6.676.50.17511.2520890.943100
6.67-8.46.40.09419.821081.087100
8.4-506.20.05243.321261.44199.9

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Phasing

Phasing
Method
SAD
molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation11.23 Å48.45 Å
Translation11.23 Å48.45 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RESOLVEphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MAR345data collection
PHENIXphasing
RefinementMethod to determine structure: SAD, MOLECULAR REPLACEMENT
Starting model: PDB entry 4AW6

4aw6


Resolution: 3.102→48.449 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.41 / σ(F): 0 / Phase error: 37.22 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2926 1241 4.98 %Random in CCP4
Rwork0.2695 ---
obs0.2706 24941 59.95 %-
all-26182 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 242.38 Å2 / Biso mean: 90.23 Å2 / Biso min: 46.53 Å2
Refinement stepCycle: LAST / Resolution: 3.102→48.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6973 0 2 0 6975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047176
X-RAY DIFFRACTIONf_angle_d0.7789731
X-RAY DIFFRACTIONf_chiral_restr0.0411106
X-RAY DIFFRACTIONf_plane_restr0.0051189
X-RAY DIFFRACTIONf_dihedral_angle_d13.1042568
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
3.1015-3.22570.2493280.36826720.6470067215
3.2257-3.37250.4151520.33769440.6499694422
3.3725-3.55020.3359580.312612410.681299124128
3.5502-3.77260.4114890.302917040.71793170439
3.7726-4.06370.30831240.282124800.712604248057
4.0637-4.47240.29211890.279338650.74054386588
4.4724-5.1190.26962010.251442120.724413421295
5.119-6.44690.31872450.295842010.594446420196
6.4469-48.45520.25872550.240443810.734636438199
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)
11.3681-0.2405-0.03871.83330.31272.9893-0.0874-0.09460.06550.24170.18160.2095-0.7489-0.3573-0.03021.08980.04540.04530.85520.02610.378659.9165-25.292433.5634
24.16080.8899-4.71932.84931.10337.53490.11620.6697-0.1736-0.88990.06310.13740.5721-0.0279-0.12121.134-0.0015-0.11950.8797-0.0130.290665.915-31.22616.4596
30.74560.0764-0.07250.57560.11961.7082-0.047-0.08470.30680.315-0.16720.0995-0.3259-0.15730.17941.43260.0313-0.07640.5866-0.03780.309971.2589-21.218328.8759
43.0651-0.87870.1272.3932-0.04250.56890.0944-0.0225-0.1951-0.1750.0279-0.06470.20980.7461-0.11750.79260.11590.08021.0212-0.06390.3712102.5415-60.714522.1585
56.3019-4.581-3.94968.95572.42672.66190.52470.3551-0.9709-0.1493-0.81350.8039-0.32350.40240.17841.07960.04320.00631.3835-0.08360.513693.2318-63.993249.4872
62.6536-0.7958-1.14581.61930.11920.5846-0.05930.5781-0.07180.0445-0.04620.06050.07130.77380.08450.77470.02510.06050.76820.00120.38598.833-49.877127.2347
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 10:221)A10 - 221
2X-RAY DIFFRACTION2(chain A and resid 222:304)A222 - 304
3X-RAY DIFFRACTION3(chain A and resid 306:445)A306 - 445
4X-RAY DIFFRACTION4(chain B and resid 13:221)B13 - 221
5X-RAY DIFFRACTION5(chain B and resid 222:304)B222 - 304
6X-RAY DIFFRACTION6(chain B and resid 306:445)B306 - 445

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