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- PDB-1weh: Crystal structure of the conserved hypothetical protein TT1887 fr... -

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Basic information

Entry
Database: PDB / ID: 1weh
TitleCrystal structure of the conserved hypothetical protein TT1887 from Thermus thermophilus HB8
ComponentsConserved hypothetical protein TT1887
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Rossmann fold / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


SLOG cluster4 / SLOG cluster4 family / : / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsKukimoto-Niino, M. / Murayama, K. / Idaka, M. / Terada, T. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: PROTEIN SCI. / Year: 2004
Title: Crystal structures of possible lysine decarboxylases from Thermus thermophilus HB8
Authors: Kukimoto-Niino, M. / Murayama, K. / Kato-Murayama, M. / Idaka, M. / Bessho, Y. / Tatsuguchi, A. / Ushikoshi-Nakayama, R. / Terada, T. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 25, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Oct 30, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conserved hypothetical protein TT1887
B: Conserved hypothetical protein TT1887


Theoretical massNumber of molelcules
Total (without water)37,1572
Polymers37,1572
Non-polymers00
Water7,260403
1
A: Conserved hypothetical protein TT1887


Theoretical massNumber of molelcules
Total (without water)18,5781
Polymers18,5781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Conserved hypothetical protein TT1887


Theoretical massNumber of molelcules
Total (without water)18,5781
Polymers18,5781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.663, 129.821, 119.852
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-198-

HOH

21B-321-

HOH

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Components

#1: Protein Conserved hypothetical protein TT1887 / Possible lysine decarboxylase


Mass: 18578.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SLJ9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.11 Å3/Da / Density % sol: 41.7 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9792, 0.9794, 0.9742
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 20, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97941
30.97421
ReflectionResolution: 1.8→50 Å / Num. obs: 29939 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.87354 % / Biso Wilson estimate: 10.3 Å2 / Rsym value: 0.086
Reflection shellResolution: 1.8→1.86 Å / Rsym value: 0.268 / % possible all: 99.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→14.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2374549.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2951 10 %RANDOM
Rwork0.185 ---
obs0.185 29544 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.5709 Å2 / ksol: 0.398808 e/Å3
Displacement parametersBiso mean: 15.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20 Å20 Å2
2--0.07 Å20 Å2
3----1.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.8→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2612 0 0 403 3015
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.89
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.286 475 10.1 %
Rwork0.231 4248 -
obs--96.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.top

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