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- PDB-3mgk: CRYSTAL STRUCTURE OF PROBABLE PROTEASE/AMIDASE FROM Clostridium a... -

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Basic information

Entry
Database: PDB / ID: 3mgk
TitleCRYSTAL STRUCTURE OF PROBABLE PROTEASE/AMIDASE FROM Clostridium acetobutylicum ATCC 824
ComponentsIntracellular protease/amidase related enzyme (ThiJ family)
Keywordsstructural genomics / unknown function / AMIDOTRANFERASE-LIKE / PSI / PROTEIN STRUCTURE INITIATIVE / NYSGRC / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


peptidase activity / proteolysis
Similarity search - Function
: / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Intracellular protease/amidase related enzyme (ThiJ family)
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsPatskovsky, Y. / Toro, R. / Freeman, J. / Iizuka, M. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF PROBABLE PROTEASE/AMIDASE FROM Clostridium acetobutylicum
Authors: Patskovsky, Y. / Toro, R. / Freeman, J. / Iizuka, M. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionApr 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Intracellular protease/amidase related enzyme (ThiJ family)
B: Intracellular protease/amidase related enzyme (ThiJ family)


Theoretical massNumber of molelcules
Total (without water)47,9502
Polymers47,9502
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-19 kcal/mol
Surface area15920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.539, 70.354, 40.195
Angle α, β, γ (deg.)90.00, 101.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Intracellular protease/amidase related enzyme (ThiJ family) / PROBABLE PROTEASE/AMIDASE


Mass: 23974.822 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Gene: CA_C2826 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97FB4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.21 Å3/Da / Density % sol: 44.29 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M BIS-TRIS, PH 6.5, 25% PEG3350, 200MM AMMONIUM ACETATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2010 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 28333 / % possible obs: 99.5 % / Observed criterion σ(I): -5 / Redundancy: 3.2 % / Rsym value: 0.062 / Net I/σ(I): 9
Reflection shellResolution: 2→2.07 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.3 / Rsym value: 0.77 / % possible all: 95.8

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Processing

Software
NameVersionClassification
SHELXmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.767 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24326 901 3.2 %RANDOM
Rwork0.18643 ---
obs0.1884 27055 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 55.627 Å2
Baniso -1Baniso -2Baniso -3
1--2.86 Å20 Å22.52 Å2
2--3.69 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3198 0 0 114 3312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223342
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.954522
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8315422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.32724.731167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.76515615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.551520
X-RAY DIFFRACTIONr_chiral_restr0.0970.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022534
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.37122008
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.09133260
X-RAY DIFFRACTIONr_scbond_it7.27931334
X-RAY DIFFRACTIONr_scangle_it9.7851250
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 64 -
Rwork0.383 1910 -
obs--97.77 %

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