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- PDB-4qhf: Crystal structure of Methanocaldococcus jannaschii monomeric selecase -

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Basic information

Entry
Database: PDB / ID: 4qhf
TitleCrystal structure of Methanocaldococcus jannaschii monomeric selecase
ComponentsUncharacterized protein MJ1213
KeywordsHYDROLASE / Minigluzincin / Proteolytic enzyme
Function / homologyMetalloproteases ("zincins"), catalytic domain / Peptidase M56 / BlaR1 peptidase M56 / Zincin-like / 2-Layer Sandwich / Alpha Beta / NICKEL (II) ION / Uncharacterized protein MJ1213
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLopez-pelegrin, M. / Cerda-costa, N. / Cintas-pedrola, A. / Herranz-trillo, F. / Bernado, P. / Peinado, J.R. / Arolas, J.L. / Gomis-ruth, F.X.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Multiple stable conformations account for reversible concentration-dependent oligomerization and autoinhibition of a metamorphic metallopeptidase
Authors: Lopez-Pelegrin, M. / Cerda-Costa, N. / Cintas-Pedrola, A. / Herranz-Trillo, F. / Bernado, P. / Peinado, J.R. / Arolas, J.L. / Gomis-Ruth, F.X.
History
DepositionMay 28, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein MJ1213
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2543
Polymers13,1041
Non-polymers1512
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.260, 77.350, 31.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

21A-302-

HOH

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Components

#1: Protein Uncharacterized protein MJ1213


Mass: 13103.546 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: MJ1213 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58610
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl, 0.2M sodium acetate, 30%(w/v) polyethylene glycol 4,000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 19, 2013
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.1→42.7 Å / Num. all: 7658 / Num. obs: 7658 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 37.95 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.7
Reflection shellResolution: 2.1→42.7 Å / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 17.7 / Num. unique all: 7658 / % possible all: 99.9

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Processing

Software
NameVersionClassification
EDNAdata collection
PHASERphasing
BUSTER2.11.5refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Dimeric selecase

Resolution: 2.1→42.7 Å / Cor.coef. Fo:Fc: 0.9401 / Cor.coef. Fo:Fc free: 0.9134 / SU R Cruickshank DPI: 0.223 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.281 494 6.45 %RANDOM
Rwork0.208 ---
all0.208 7658 --
obs0.208 7658 99.9 %-
Displacement parametersBiso mean: 50.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.9519 Å20 Å20 Å2
2---7.1001 Å20 Å2
3---6.1482 Å2
Refine analyzeLuzzati coordinate error obs: 0.304 Å
Refinement stepCycle: LAST / Resolution: 2.1→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms914 0 7 58 979
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01933HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.011250HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d466SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes27HARMONIC2
X-RAY DIFFRACTIONt_gen_planes123HARMONIC5
X-RAY DIFFRACTIONt_it933HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion3.46
X-RAY DIFFRACTIONt_chiral_improper_torsion128SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1110SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.2 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.281 494 6.9 %
Rwork0.208 1957 -
all0.2211 2102 -
obs-7658 99.9 %
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)
19.52940.8602-2.40162.283-0.08043.4721-0.21910.4937-0.52330.00380.1172-0.04680.2232-0.00590.1019-0.0973-0.002-0.03140.014-0.0780.044736.577614.6011-0.5948
20-0.886-0.66670.9974-0.15822.93110.02940.3415-0.4341-0.0047-0.13640.09940.1984-0.38190.1069-0.0753-0.0274-0.01610.1009-0.10150.276125.33788.0858-3.3015
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|76 }A1 - 76
2X-RAY DIFFRACTION2{ A|77 - A|109 }A77 - 109

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