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- PDB-1ukk: Structure of Osmotically Inducible Protein C from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 1ukk
TitleStructure of Osmotically Inducible Protein C from Thermus thermophilus
ComponentsOsmotically Inducible Protein C
KeywordsOXIDOREDUCTASE / peroxidase / cysteinesulfinic acid / osmotic / inducible / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


peroxidase activity / response to oxidative stress
Similarity search - Function
Peroxiredoxin OsmC / : / OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / K homology (KH) domain / GMP Synthetase; Chain A, domain 3 / K homology domain-like, alpha/beta / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Osmotically inducible protein C
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsRehse, P.H. / Kuramitsu, S. / Yokoyama, S. / Miyano, M. / Tahirov, T.H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.MOL.BIOL. / Year: 2004
Title: Crystallographic Structure and Biochemical Analysis of the Thermus thermophilus Osmotically Inducible Protein C
Authors: Rehse, P.H. / Oshima, N. / Nodaka, Y. / Tahirov, T.H.
History
DepositionAug 24, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Osmotically Inducible Protein C
B: Osmotically Inducible Protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0343
Polymers30,9122
Non-polymers1221
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-36 kcal/mol
Surface area12480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.58, 40.95, 48.14
Angle α, β, γ (deg.)76.93, 74.04, 64.05
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly corresponds to the dimer found in the assymetric unit.

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Components

#1: Protein Osmotically Inducible Protein C


Mass: 15456.159 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P84124
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 1.9 Å3/Da / Density % sol: 34.61 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: PEG 4000, Tris-HCl, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97894, 0.97910, 0.97920, 0.97500, 1.000
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 28, 2003 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978941
20.97911
30.97921
40.9751
511
ReflectionResolution: 1.6→20 Å / Num. all: 30286 / Num. obs: 30286 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.85 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 15
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.76 % / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 4.1 / % possible all: 79.3

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
d*TREKdata reduction
d*TREKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→8 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.12 / SU ML: 0.074 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.106 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23222 1535 5.1 %RANDOM
Rwork0.17798 ---
all0.18068 28490 --
obs0.18068 28490 93.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.284 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å2-0.2 Å20.26 Å2
2--0.35 Å21.8 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2132 0 8 213 2353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0212225
X-RAY DIFFRACTIONr_bond_other_d0.0030.022089
X-RAY DIFFRACTIONr_angle_refined_deg1.8991.9913012
X-RAY DIFFRACTIONr_angle_other_deg1.82834880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9995290
X-RAY DIFFRACTIONr_chiral_restr0.1240.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022488
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02432
X-RAY DIFFRACTIONr_nbd_refined0.2120.2413
X-RAY DIFFRACTIONr_nbd_other0.2670.22436
X-RAY DIFFRACTIONr_nbtor_other0.0910.21384
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2136
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2910.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.210
X-RAY DIFFRACTIONr_mcbond_it1.2981.51436
X-RAY DIFFRACTIONr_mcangle_it2.26922303
X-RAY DIFFRACTIONr_scbond_it3.5083789
X-RAY DIFFRACTIONr_scangle_it5.9154.5707
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.298 80
Rwork0.234 1718

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