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- PDB-1g2i: CRYSTAL STRUCTURE OF A NOVEL INTRACELLULAR PROTEASE FROM PYROCOCC... -

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Basic information

Entry
Database: PDB / ID: 1g2i
TitleCRYSTAL STRUCTURE OF A NOVEL INTRACELLULAR PROTEASE FROM PYROCOCCUS HORIKOSHII AT 2 A RESOLUTION
ComponentsPROTEASE I
KeywordsHYDROLASE / intracellular protease / ATP-independent intracellular protease / protease / catalytical triad / PfpI / cysteine protease / nucleophile elbow / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


protein deglycase / protein deglycase activity / peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / cytoplasm
Similarity search - Function
: / Deglycase PfpI / PfpI endopeptidase domain profile. / 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
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsDu, X. / Choi, I.-G. / Kim, R. / Jancarik, J. / Kim, S.-H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Crystal structure of an intracellular protease from Pyrococcus horikoshii at 2-A resolution.
Authors: Du, X. / Choi, I.G. / Kim, R. / Wang, W. / Jancarik, J. / Yokota, H. / Kim, S.-H.
History
DepositionOct 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 8, 2017Group: Structure summary
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: PROTEASE I
B: PROTEASE I
C: PROTEASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6104
Polymers56,5143
Non-polymers961
Water4,990277
1
A: PROTEASE I
B: PROTEASE I
C: PROTEASE I
hetero molecules

A: PROTEASE I
B: PROTEASE I
C: PROTEASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,2208
Polymers113,0286
Non-polymers1922
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)124.700, 124.700, 129.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe other three monomers of the hexameric complex may be generated by:y,x,-z-1

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Components

#1: Protein PROTEASE I


Mass: 18837.998 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH1704 / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)/SJS1244 / References: UniProt: O59413, Hydrolases; Glycosylases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.43 Å3/Da / Density % sol: 72.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Tris-HCl, EDTA, trisodium citrate dihydrate, potassium tartarate tetrahydrate, ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
220 mMTris-HCl1drop
31 mMEDTA1drop
40.1 Mtriosodium citrate dihydrate1reservoir
52.0 Mammonium sulfate1reservoir
60.2 Mpotassium tartrate tetrahydrate1reservoir
72.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 195 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97938,0.9796,0.9686
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 27, 1999
RadiationMonochromator: Double Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979381
20.97961
30.96861
ReflectionResolution: 2→20 Å / Num. all: 131170 / Num. obs: 129727 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 21.9
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 3.7 / % possible all: 95.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS0.5refinement
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3763370.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2 3333 5.1 %RANDOM
Rwork0.184 ---
all0.1848 68999 --
obs0.184 65700 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.4 Å2 / ksol: 0.393 e/Å3
Displacement parametersBiso mean: 25.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å20 Å20 Å2
2---1.78 Å20 Å2
3---3.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3942 0 5 277 4224
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.7
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.225 496 5 %
Rwork0.202 9458 -
obs--88 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7

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