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- PDB-4qhj: Crystal structure of Methanocaldococcus jannaschii selecase mutan... -

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Basic information

Entry
Database: PDB / ID: 4qhj
TitleCrystal structure of Methanocaldococcus jannaschii selecase mutant I100F+H107F
ComponentsUncharacterized protein MJ1213
KeywordsHYDROLASE / Minigluzincin / Proteolytic enzyme
Function / homologyMetalloproteases ("zincins"), catalytic domain / Peptidase M56 / BlaR1 peptidase M56 / Zincin-like / 2-Layer Sandwich / Alpha Beta / ACETATE ION / Uncharacterized protein MJ1213
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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_ref_seq_dif / 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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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
B: Uncharacterized protein MJ1213
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,81110
Polymers26,2932
Non-polymers5188
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-103 kcal/mol
Surface area11850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.390, 49.840, 104.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein MJ1213


Mass: 13146.590 Da / Num. of mol.: 2 / Mutation: I100F, H107F
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M sodium cacodylate, 1M sodium acetate trihydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→52.4 Å / Num. all: 26633 / Num. obs: 26633 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 30.97 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 24.4
Reflection shellResolution: 1.75→52.4 Å / Rmerge(I) obs: 0.054 / Mean I/σ(I) obs: 24.4 / Num. unique all: 26633 / % possible all: 99.2

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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: 1.75→52.4 Å / Cor.coef. Fo:Fc: 0.9569 / Cor.coef. Fo:Fc free: 0.9631 / SU R Cruickshank DPI: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.196 749 2.81 %RANDOM
Rwork0.185 ---
all0.185 26632 --
obs0.185 26632 99.2 %-
Displacement parametersBiso mean: 37.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.1193 Å20 Å20 Å2
2---2.4883 Å20 Å2
3---2.6076 Å2
Refine analyzeLuzzati coordinate error obs: 0.239 Å
Refinement stepCycle: LAST / Resolution: 1.75→52.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1818 0 28 251 2097
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011920HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.032580HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d955SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes57HARMONIC2
X-RAY DIFFRACTIONt_gen_planes264HARMONIC5
X-RAY DIFFRACTIONt_it1920HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.52
X-RAY DIFFRACTIONt_other_torsion2.99
X-RAY DIFFRACTIONt_chiral_improper_torsion261SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2470SEMIHARMONIC4
LS refinement shellResolution: 1.75→1.85 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.196 749 2.74 %
Rwork0.185 2729 -
all0.2465 2806 -
obs-26632 99.2 %
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)
11.66680.12121.20850.354-0.05952.5876-0.1206-0.11580.16730.04670.00670.0626-0.2052-0.20380.11390.01640.0198-0.00570.0515-0.01690.04246.916416.5285.6956
21.223-0.09010.30943.06040.46690.72480.01350.10890.06-0.4381-0.09120.2397-0.0732-0.04350.07770.09320.015-0.0669-0.00850.0129-0.007321.852233.566619.655
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|108 A|201 - A|201 }A1 - 108
2X-RAY DIFFRACTION1{ A|1 - A|108 A|201 - A|201 }A201
3X-RAY DIFFRACTION2{ B|1 - B|108 B|201 - B|201 }B1 - 108
4X-RAY DIFFRACTION2{ B|1 - B|108 B|201 - B|201 }B201

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