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- PDB-1qw2: Crystal Structure of a Protein of Unknown Function TA1206 from Th... -

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Basic information

Entry
Database: PDB / ID: 1qw2
TitleCrystal Structure of a Protein of Unknown Function TA1206 from Thermoplasma acidophilum
Componentsconserved hypothetical protein TA1206
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Beta/Alpha / Antiparallel beta sandwich / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyHypothetical protein Ta1206 fold / Hypothetical protein YunC / Protein of unknown function DUF1805 / Hypothetical protein YunC superfamily / Domain of unknown function (DUF1805) / 2-Layer Sandwich / Alpha Beta / DUF1805 domain-containing protein
Function and homology information
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsSavchenko, A. / Evdokimova, E. / Kudrytska, M. / Edwards, A.E. / Christendat, D. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of a Hypothetical Protein "TA1206" from Thermoplasma acidophilum
Authors: Savchenko, A. / Evdokimova, E. / Kudrytska, M. / Edwards, A.E. / Christendat, D.
History
DepositionAug 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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

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Assembly

Deposited unit
A: conserved hypothetical protein TA1206


Theoretical massNumber of molelcules
Total (without water)11,3651
Polymers11,3651
Non-polymers00
Water1,22568
1
A: conserved hypothetical protein TA1206

A: conserved hypothetical protein TA1206

A: conserved hypothetical protein TA1206

A: conserved hypothetical protein TA1206


Theoretical massNumber of molelcules
Total (without water)45,4614
Polymers45,4614
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area7800 Å2
ΔGint-39 kcal/mol
Surface area16430 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)35.642, 48.060, 110.382
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein conserved hypothetical protein TA1206


Mass: 11365.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: TA1206 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q9HIX0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 40.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.2M Magnesium Nitrate, 30% PEG 3350, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Mar 6, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 24601 / % possible obs: 83.7 % / Observed criterion σ(I): 2782 / Redundancy: 7.4 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.059 / Net I/σ(I): 35.8
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 7 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 4 / Num. unique all: 2456 / Rsym value: 0.224 / % possible all: 52.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→29.22 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1183 4.8 %RANDOM
Rwork0.203 ---
obs0.203 24601 83.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.0536 Å2 / ksol: 0.412554 e/Å3
Displacement parametersBiso mean: 19.9 Å2
Baniso -1Baniso -2Baniso -3
1-8.74 Å20 Å20 Å2
2---4.37 Å20 Å2
3----4.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å-
Luzzati d res low-5 Å
Luzzati sigma a-0.09 Å
Refinement stepCycle: LAST / Resolution: 1.5→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms777 0 0 68 845
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.812
X-RAY DIFFRACTIONc_scbond_it2.72
X-RAY DIFFRACTIONc_scangle_it3.662.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.239 118 4.6 %
Rwork0.218 2456 -
obs--52.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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