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- PDB-3e0h: Crystal structure of an uncharacterized protein from Chlorobium t... -

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Basic information

Entry
Database: PDB / ID: 3e0h
TitleCrystal structure of an uncharacterized protein from Chlorobium tepidum. NorthEast Structural Genomics target CtR107.
Componentsuncharacterized protein
Keywordsstructural genomics / unknown function / uncharacterized protein / Chlorobium tepidum / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Bacterial transcription activator, effector binding / Bacterial transcription activator, effector binding domain / GyrI-like small molecule binding domain / GyrI-like small molecule binding domain / Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A / Regulatory factor, effector binding domain / Regulatory factor, effector binding domain superfamily / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
AraC effector-binding domain-containing protein
Similarity search - Component
Biological speciesChlorobaculum tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.81 Å
AuthorsSeetharaman, J. / Chen, Y. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. ...Seetharaman, J. / Chen, Y. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of an uncharacterized protein from Chlorobium tepidum. NorthEast Structural Genomics target CtR107.
Authors: Seetharaman, J. / Chen, Y. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJul 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 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: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)17,3301
Polymers17,3301
Non-polymers00
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)47.508, 50.881, 55.440
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 uncharacterized protein


Mass: 17329.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobaculum tepidum (bacteria) / Gene: CT0179 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KFZ1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 1.93 Å3/Da / Density % sol: 36.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.1
Details: Sodium bromide 0.1M,MES 0.1M, PEG 20000 40%, pH 4.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 7, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 23778 / Num. obs: 23778 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.09 / Net I/σ(I): 10.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 10.2 / Num. unique all: 2380 / Rsym value: 0.318 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.81→37.49 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 175976.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2093 9.4 %RANDOM
Rwork0.21 ---
obs0.21 22371 93.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.5088 Å2 / ksol: 0.415555 e/Å3
Displacement parametersBiso mean: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---2.51 Å20 Å2
3---2.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.81→37.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1160 0 0 141 1301
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_improper_angle_d0.85
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.227 266 8.7 %
Rwork0.2 2780 -
obs--76.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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