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- PDB-2yzy: Crystal structure of uncharacterized conserved protein from Therm... -

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Basic information

Entry
Database: PDB / ID: 2yzy
TitleCrystal structure of uncharacterized conserved protein from Thermus thermophilus HB8
ComponentsPutative uncharacterized protein TTHA1012
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Uncharacterized conserved protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyLipoprotein localisation LolA/LolB/LppX / outer membrane lipoprotein receptor (LolB), chain A / Clam / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsEbihara, A. / Watanabe, N. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of uncharacterized conserved protein from Thermus thermophilus HB8
Authors: Ebihara, A. / Watanabe, N. / Yokoyama, S. / Kuramitsu, S.
History
DepositionMay 6, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Putative uncharacterized protein TTHA1012
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0955
Polymers22,6221
Non-polymers4734
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.380, 58.840, 80.500
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 Putative uncharacterized protein TTHA1012 / Uncharacterized conserved protein


Mass: 22622.100 Da / Num. of mol.: 1 / Fragment: residues 15-214
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): Rosetta(DE3) / References: UniProt: Q5SJJ6
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.15M Sodium acetate, 15% PEG 4000, 29% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B211
ROTATING ANODERIGAKU FR-E+ DW22.29
Detector
TypeIDDetectorDate
RIGAKU JUPITER 2101CCDSep 28, 2005
RIGAKU RAXIS VII2IMAGE PLATEDec 19, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI Double-CrystalSINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
22.291
ReflectionResolution: 1.6→50 Å / Num. obs: 26453 / % possible obs: 99.2 % / Redundancy: 6.8 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 44.1
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.089 / Mean I/σ(I) obs: 17.7 / % possible all: 95.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.6→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1045533.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2609 9.9 %RANDOM
Rwork0.229 ---
obs0.229 26399 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.5158 Å2 / ksol: 0.373662 e/Å3
Displacement parametersBiso mean: 19.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.02 Å-0.05 Å
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1334 0 32 141 1507
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.22
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it3.082.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.25 409 9.7 %
Rwork0.217 3790 -
obs--96.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3mpd_xplor.parammpd_xplor.top

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