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- PDB-1ttz: X-ray structure of Northeast Structural Genomics target protein X... -

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Basic information

Entry
Database: PDB / ID: 1ttz
TitleX-ray structure of Northeast Structural Genomics target protein XcR50 from X. campestris
Componentsconserved hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyGlutaredoxin-like / Glutaredoxin-like domain (DUF836) / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta / Glutaredoxin family protein
Function and homology information
Biological speciesXanthomonas campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.11 Å
AuthorsKuzin, A.P. / Vorobiev, S.M. / Lee, I. / Acton, T.B. / Ho, C.K. / Cooper, B. / Ma, L.-C. / Xiao, R. / Montelione, G. / Tong, L. ...Kuzin, A.P. / Vorobiev, S.M. / Lee, I. / Acton, T.B. / Ho, C.K. / Cooper, B. / Ma, L.-C. / Xiao, R. / Montelione, G. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: X-ray structure of Northeast Structural Genomics target protein XcR50 from X. campestris
Authors: Kuzin, A.P. / Vorobiev, S.M. / Lee, I. / Edstrom, W. / Acton, T.B. / Ho, C.K. / Cooper, B. / Ma, L.-C. / Xiao, R. / Montelione, G. / Tong, L. / Hunt, J.F.
History
DepositionJun 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)10,0161
Polymers10,0161
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.690, 61.690, 39.043
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein conserved hypothetical protein


Mass: 10015.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris (bacteria) / Strain: ATCC33913 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8P6W3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Hepes, 0.1M NaCl, 1.6M (NH4)2SO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONNSLS X4A10.97896
ROTATING ANODEOTHER21.5418
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJun 7, 2004
RIGAKU RAXIS IV2IMAGE PLATEMay 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978961
21.54181
ReflectionResolution: 1.8→50 Å / Num. all: 37717 / Num. obs: 12147 / % possible obs: 79.8 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 14.4 Å2 / Rsym value: 0.045 / Net I/σ(I): 23.98
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 3.3 / Num. unique all: 12147 / Rsym value: 0.211 / % possible all: 31.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.11→26.71 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 202406.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 482 5.3 %RANDOM
Rwork0.189 ---
obs0.191 8998 92.9 %-
all-9688 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.3394 Å2 / ksol: 0.352024 e/Å3
Displacement parametersBiso mean: 15.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.473 Å2-1.146 Å20 Å2
2--0.473 Å20 Å2
3----0.947 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.11→26.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms589 0 0 109 698
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.5411.5
X-RAY DIFFRACTIONc_mcangle_it2.4822
X-RAY DIFFRACTIONc_scbond_it2.3072
X-RAY DIFFRACTIONc_scangle_it3.1672.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.221 93 7.5 %
Rwork0.206 1155 -
obs--78.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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