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- PDB-2ywi: Crystal structure of uncharacterized conserved protein from Geoba... -

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Basic information

Entry
Database: PDB / ID: 2ywi
TitleCrystal structure of uncharacterized conserved protein from Geobacillus kaustophilus
ComponentsHypothetical conserved protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Uncharacterized conserved protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


antioxidant activity / oxidoreductase activity
Similarity search - Function
: / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Hypothetical conserved protein
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsManzoku, M. / Ebihara, A. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: to be published
Title: Crystal structure of uncharacterized conserved protein from Geobacillus kaustophilus
Authors: Manzoku, M. / Ebihara, A. / Yokoyama, S. / Kuramitsu, S.
History
DepositionApr 20, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 13, 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_ref_seq_dif
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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical conserved protein
B: Hypothetical conserved protein


Theoretical massNumber of molelcules
Total (without water)44,2542
Polymers44,2542
Non-polymers00
Water7,422412
1
A: Hypothetical conserved protein


Theoretical massNumber of molelcules
Total (without water)22,1271
Polymers22,1271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical conserved protein


Theoretical massNumber of molelcules
Total (without water)22,1271
Polymers22,1271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.382, 57.223, 79.526
Angle α, β, γ (deg.)90.00, 107.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hypothetical conserved protein / uncharacterized conserved protein


Mass: 22127.162 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL-X / References: UniProt: Q5KZG6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.33 Å3/Da / Density % sol: 47.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2.4M Ammonium phosphate dibasic, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97886, 0.9000, 0.97929
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 21, 2006
RadiationMonochromator: SI Double-Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978861
20.91
30.979291
ReflectionResolution: 1.6→50 Å / Num. obs: 53368 / % possible obs: 99.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.3
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 6.19 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→38 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1130333.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.22 5154 10.1 %RANDOM
Rwork0.198 ---
obs0.198 51178 95.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.6762 Å2 / ksol: 0.387147 e/Å3
Displacement parametersBiso mean: 13.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.83 Å20 Å2-0.77 Å2
2---0.81 Å20 Å2
3----3.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.6→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2955 0 0 412 3367
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.091.5
X-RAY DIFFRACTIONc_mcangle_it1.562
X-RAY DIFFRACTIONc_scbond_it2.152
X-RAY DIFFRACTIONc_scangle_it3.12.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.246 859 10.4 %
Rwork0.23 7428 -
obs--92.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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