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- PDB-2cwq: Crystal structure of conserved protein TTHA0727 from Thermus ther... -

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Basic information

Entry
Database: PDB / ID: 2cwq
TitleCrystal structure of conserved protein TTHA0727 from Thermus thermophilus HB8
Componentshypothetical protein TTHA0727
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Conserved Hypothetical Protein / All Alpha / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyAhpD-like / Carboxymuconolactone decarboxylase-like / AhpD-like / Carboxymuconolactone decarboxylase family / AhpD-like / peroxiredoxin activity / Up-down Bundle / Mainly Alpha / Carboxymuconolactone decarboxylase-like domain-containing protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsIto, K. / Arai, R. / Fusatomi, E. / Kamo-Uchikubo, T. / Kawaguchi, S. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Protein Sci. / Year: 2006
Title: Crystal structure of the conserved protein TTHA0727 from Thermus thermophilus HB8 at 1.9 A resolution: A CMD family member distinct from carboxymuconolactone decarboxylase (CMD) and AhpD
Authors: Ito, K. / Arai, R. / Fusatomi, E. / Kamo-Uchikubo, T. / Kawaguchi, S. / Akasaka, R. / Terada, T. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S.
History
DepositionJun 23, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 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 / 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

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein TTHA0727
B: hypothetical protein TTHA0727
C: hypothetical protein TTHA0727


Theoretical massNumber of molelcules
Total (without water)45,0173
Polymers45,0173
Non-polymers00
Water4,720262
1
A: hypothetical protein TTHA0727
B: hypothetical protein TTHA0727
C: hypothetical protein TTHA0727

A: hypothetical protein TTHA0727
B: hypothetical protein TTHA0727
C: hypothetical protein TTHA0727


Theoretical massNumber of molelcules
Total (without water)90,0346
Polymers90,0346
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area24570 Å2
ΔGint-198 kcal/mol
Surface area25750 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)107.102, 107.102, 55.455
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a hexamer consist of A, B, C and A', B', C' generated by the operation: y, x, -z.

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Components

#1: Protein hypothetical protein TTHA0727


Mass: 15005.659 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0727 / Plasmid: pHCEH / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SMF5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.08 Å3/Da / Density % sol: 40.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M potassium formate, 21% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97919, 0.97953, 0.96000
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 15, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979191
20.979531
30.961
ReflectionResolution: 1.9→50 Å / Num. obs: 29204 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 20.6 Å2 / Rsym value: 0.103 / Net I/σ(I): 17.54
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 8.8 / Num. unique all: 2883 / Rsym value: 0.293 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→47.6 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1815174.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2893 10 %RANDOM
Rwork0.165 ---
obs-29021 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.719 Å2 / ksol: 0.323284 e/Å3
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1--1.37 Å20.16 Å20 Å2
2---1.37 Å20 Å2
3---2.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.9→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2725 0 0 262 2987
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it3.261.5
X-RAY DIFFRACTIONc_mcangle_it3.782
X-RAY DIFFRACTIONc_scbond_it4.882
X-RAY DIFFRACTIONc_scangle_it6.362.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.258 452 9.6 %
Rwork0.188 4280 -
obs-4732 98.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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