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- PDB-5g5x: CBS domain tandem of site-2 protease from Archaeoglobus fulgidus ... -

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Basic information

Entry
Database: PDB / ID: 5g5x
TitleCBS domain tandem of site-2 protease from Archaeoglobus fulgidus in complex with llama Nanobody - nucleotide-bound 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
ADENOSINE MONOPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Zinc metalloprotease
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
LAMA GLAMA (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 9, 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 6, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,6424
Polymers28,7882
Non-polymers8542
Water00
1
A: SITE-2 PROTEASE
B: NANOBODY
hetero molecules

A: SITE-2 PROTEASE
B: NANOBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2848
Polymers57,5754
Non-polymers1,7094
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
MethodPISA
Unit cell
Length a, b, c (Å)70.910, 70.910, 201.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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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: DSM 4304 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, C-TERMINAL 6XHIS- TAG / 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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
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: 2.53 Å3/Da / Density % sol: 51.4 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M IMIDAZOLE PH 7.25, 0.2 M MGCL2, 12 % ETHANOL

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→61.41 Å / Num. obs: 7966 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 9.58 % / Biso Wilson estimate: 72.63 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.21
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 9.27 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.16 / % possible all: 99.3

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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 ENTRY 5G5R

5g5r


Resolution: 2.8→52.433 Å / SU ML: 0.39 / σ(F): 1.36 / Phase error: 31.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2692 399 5 %
Rwork0.2464 --
obs0.2476 7962 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.8 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 87 Å2
Refinement stepCycle: LAST / Resolution: 2.8→52.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1802 0 54 0 1856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031895
X-RAY DIFFRACTIONf_angle_d0.6752571
X-RAY DIFFRACTIONf_dihedral_angle_d16.8841124
X-RAY DIFFRACTIONf_chiral_restr0.046294
X-RAY DIFFRACTIONf_plane_restr0.003323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8004-3.20560.35211280.34272424X-RAY DIFFRACTION99
3.2056-4.03850.31311300.26432473X-RAY DIFFRACTION100
4.0385-52.44180.23171410.21782666X-RAY DIFFRACTION100

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