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- PDB-3b4r: Site-2 Protease from Methanocaldococcus jannaschii -

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Basic information

Entry
Database: PDB / ID: 3b4r
TitleSite-2 Protease from Methanocaldococcus jannaschii
ComponentsPutative zinc metalloprotease MJ0392
KeywordsHYDROLASE / Intramembrane protease / metalloprotease / CBS domain / Metal-binding / Transmembrane / Zinc
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / membrane => GO:0016020 / 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 / CBS domain / CBS domain profile. / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Zinc metalloprotease MJ0392
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.3 Å
AuthorsJeffrey, P.D. / Feng, L. / Yan, H. / Wu, Z. / Yan, N. / Wang, Z. / Shi, Y.
CitationJournal: Science / Year: 2007
Title: Structure of a site-2 protease family intramembrane metalloprotease.
Authors: Feng, L. / Yan, H. / Wu, Z. / Yan, N. / Wang, Z. / Jeffrey, P.D. / Shi, Y.
History
DepositionOct 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative zinc metalloprotease MJ0392
B: Putative zinc metalloprotease MJ0392
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0204
Polymers49,8892
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.420, 124.420, 136.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Putative zinc metalloprotease MJ0392


Mass: 24944.367 Da / Num. of mol.: 2 / Fragment: Site-2 Protease residues 1-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3)
References: UniProt: Q57837, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#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: 2

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Sample preparation

CrystalDensity Matthews: 4.08 Å3/Da / Density % sol: 69.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 0.1 M Tris (pH 8.8), 20% (w/v) PEG400, 50 mM NaCl, 5 mM CaCl2 and 30 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11.0809
SYNCHROTRONNSLS X29A20.97909, 0.97925
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDAug 1, 2007
ADSC QUANTUM 3152CCDSep 17, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.08091
20.979091
30.979251
ReflectionResolution: 3.3→50 Å / Num. obs: 11853 / % possible obs: 99.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 96.9 Å2 / Rsym value: 0.055 / Net I/σ(I): 14
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.485 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 3.3→34.99 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1526734.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.318 570 5.1 %RANDOM
Rwork0.251 ---
obs0.251 11268 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.5494 Å2 / ksol: 0.240819 e/Å3
Displacement parametersBiso mean: 98.7 Å2
Baniso -1Baniso -2Baniso -3
1-7.43 Å224.05 Å20 Å2
2--7.43 Å20 Å2
3----14.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.63 Å0.52 Å
Luzzati d res low-5 Å
Luzzati sigma a0.95 Å0.81 Å
Refinement stepCycle: LAST / Resolution: 3.3→34.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3404 0 2 0 3406
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
X-RAY DIFFRACTIONc_improper_angle_d0
X-RAY DIFFRACTIONc_mcbond_it2.32
X-RAY DIFFRACTIONc_mcangle_it3.92.5
X-RAY DIFFRACTIONc_scbond_it2.33
X-RAY DIFFRACTIONc_scangle_it3.83.5
LS refinement shellResolution: 3.3→3.51 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.446 108 6.4 %
Rwork0.441 1592 -
obs-1592 85.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2zinc.param
X-RAY DIFFRACTION3ion.param

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