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- PDB-5g5r: CBS domain tandem of site-2 protease from Archaeoglobus fulgidus ... -

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Basic information

Entry
Database: PDB / ID: 5g5r
TitleCBS domain tandem of site-2 protease from Archaeoglobus fulgidus in complex with llama Nanobody - apo form
Components
  • NANOBODY
  • SITE-2 PROTEASE
KeywordsHYDROLASE / METALLOPROTEASE / SITE-2 PROTEASE / REGULATORY DOMAIN / NUCLEOTIDE-BINDING / CBS DOMAIN / CAMELID ANTIBODY / NANOBODY
Function / homology
Function and homology information


metallopeptidase activity / proteolysis / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Uncharacterised conserved protein UCP006404, peptidase M50/CBS / Peptidase M50 / Peptidase family M50 / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Immunoglobulins / Immunoglobulin-like ...Uncharacterised conserved protein UCP006404, peptidase M50/CBS / Peptidase M50 / Peptidase family M50 / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Zinc metalloprotease
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
LAMA GLAMA (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSchacherl, M. / Baumann, U.
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: Crystallographic and biochemical characterization of the dimeric architecture of site-2 protease.
Authors: Schacherl, M. / Gompert, M. / Pardon, E. / Lamkemeyer, T. / Steyaert, J. / Baumann, U.
History
DepositionJun 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 10, 2024Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SITE-2 PROTEASE
B: NANOBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9804
Polymers28,7882
Non-polymers1922
Water55831
1
A: SITE-2 PROTEASE
B: NANOBODY
hetero molecules

A: SITE-2 PROTEASE
B: NANOBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9608
Polymers57,5754
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area5570 Å2
ΔGint-82.1 kcal/mol
Surface area22860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.440, 68.440, 196.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-2016-

HOH

21B-2014-

HOH

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Components

#1: Protein SITE-2 PROTEASE


Mass: 15469.021 Da / Num. of mol.: 1 / Fragment: REGULATORY DOMAIN, RESIDUES 236-362
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL STREPII-TAG / Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Description: DSM4304 GENOMIC DNA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: O29915, EC: 3.4.24.85
#2: Antibody NANOBODY


Mass: 13318.636 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: NB330 SELECTED FROM LLAMA GLAMA / Source: (gene. exp.) LAMA GLAMA (llama) / Plasmid: PHEN6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): WK6
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsD236-S362

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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: 2.31 Å3/Da / Density % sol: 46.7 % / Description: NONE
Crystal growpH: 6
Details: WITH 0.14 M BIS-TRIS PH 6.0, 0.28 M (NH4)2SO4 AND 19% PEG 3350

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97962
DetectorType: DECTRIS PLIATUS 2M / Detector: PIXEL / Date: Nov 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97962 Å / Relative weight: 1
ReflectionResolution: 2.4→45.18 Å / Num. obs: 11381 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 9.16 % / Biso Wilson estimate: 49.83 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.24
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 8.69 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.31 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4FHB AND 3KPB

4fhb

3kpb


Resolution: 2.4→43.979 Å / SU ML: 0.27 / σ(F): 1.36 / Phase error: 26.58 / Stereochemistry target values: ML / Details: ONE ROUND OF REFINEMENT USING BUSTER-TNT
RfactorNum. reflection% reflection
Rfree0.2498 569 5 %
Rwork0.2071 --
obs0.2093 11381 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→43.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1848 0 10 31 1889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021890
X-RAY DIFFRACTIONf_angle_d0.4432561
X-RAY DIFFRACTIONf_dihedral_angle_d12.3481124
X-RAY DIFFRACTIONf_chiral_restr0.043290
X-RAY DIFFRACTIONf_plane_restr0.003329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4002-2.64170.31551380.27682622X-RAY DIFFRACTION99
2.6417-3.02390.32041380.26172623X-RAY DIFFRACTION100
3.0239-3.80940.28411420.21582697X-RAY DIFFRACTION100
3.8094-43.9860.20411510.1782870X-RAY DIFFRACTION100
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)
12.8001-0.26230.55222.8028-0.42895.5821-0.00940.03930.00860.0750.1217-0.10220.05830.3446-0.07720.43880.0015-0.02080.34020.04110.4201-16.8453-12.9447-6.7166
22.62-3.36770.275.50261.15482.1569-0.2071.4692-0.6381-1.5791-0.5786-1.04640.77141.45390.01840.71310.02150.23290.96410.07020.6525-12.0044-18.2284-19.1484
31.27810.3689-0.34343.19384.09717.55260.1756-0.246-0.38820.35340.021-0.13571.9030.39680.17060.52650.07060.00120.54920.10580.4673-12.5022-20.49912.4403
41.93870.22483.04844.05750.04425.1972-0.0385-0.6257-0.3146-0.1483-0.19-0.133-0.03090.62350.23730.62310.0067-0.00330.47140.1060.4558-9.506-15.13437.0116
51.82840.99881.30425.46071.92253.19330.3005-0.29810.26770.181-0.521-0.8473-0.07330.20840.14850.4809-0.0966-0.03130.58820.0860.6419-9.2658-2.101911.8428
66.73255.32740.05613.79790.42216.80320.351-0.24141.099-0.6077-0.3761.5425-1.6050.1332-0.12740.71830.1303-0.00150.699-0.18290.6-38.6721-2.2273-4.4887
73.10712.4326-0.62824.2298-0.11183.7314-0.65750.6450.2416-0.2120.49520.0971-0.346-0.36660.22580.5247-0.01050.00440.4850.00580.6355-41.4142-11.7665-7.7658
89.2497-0.402-1.67935.45121.16148.80630.2337-0.7144-0.00230.4251-0.3327-0.07660.12420.11270.10630.4249-0.1269-0.0460.3259-0.03750.3567-32.6607-15.3911-2.777
93.5506-0.61340.26851.8566-1.11027.11280.19950.2029-0.02760.3069-0.4440.3110.1441-0.14410.09990.4907-0.0760.01590.369-0.03320.4765-33.9089-20.6344-9.9421
102.87372.0024-0.68893.50431.05294.35470.02550.13660.13070.3461-0.05770.2801-0.0545-0.20520.09030.5144-0.0406-00.3356-0.04270.4857-39.6341-16.1452-6.0488
115.51150.0048-3.4679.46983.14596.98760.19110.29421.08670.5125-0.1270.5489-0.3658-0.065-0.23060.4698-0.034-0.08510.2670.03780.3817-30.3242-7.6533-2.024
122.45451.2484-1.34353.8369-3.53383.01110.25530.515-0.31980.45840.01891.34010.40630.0915-0.00030.5989-0.14350.21040.5016-0.07280.8878-51.8171-23.74711.0963
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 235 THROUGH 283 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 284 THROUGH 294 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 295 THROUGH 308 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 309 THROUGH 330 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 331 THROUGH 356 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 1 THROUGH 7 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 8 THROUGH 32 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 33 THROUGH 56 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 57 THROUGH 72 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 73 THROUGH 98 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 99 THROUGH 110 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 111 THROUGH 120 )

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