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- PDB-1jx7: Crystal structure of ychN protein from E.coli -

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Basic information

Entry
Database: PDB / ID: 1jx7
TitleCrystal structure of ychN protein from E.coli
ComponentsHYPOTHETICAL PROTEIN YCHN
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NEW FOLD / HEXAMER / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


protein hexamerization / identical protein binding / cytosol
Similarity search - Function
Sulphur relay, DsrE/F-like / DsrE/DsrF-like family / DsrEFH-like / DsrEFH-like / Hypothetical Protein Ychn; Chain: A, / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsShin, D.H. / Yokota, H. / Kim, R. / Kim, S.-H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2002
Title: Crystal structure of a conserved hypothetical protein from Escherichia coli
Authors: Shin, D.H. / Yokota, H. / Kim, R. / Kim, S.-H.
History
DepositionSep 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN YCHN
B: HYPOTHETICAL PROTEIN YCHN
C: HYPOTHETICAL PROTEIN YCHN
D: HYPOTHETICAL PROTEIN YCHN
E: HYPOTHETICAL PROTEIN YCHN
F: HYPOTHETICAL PROTEIN YCHN


Theoretical massNumber of molelcules
Total (without water)77,0606
Polymers77,0606
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14020 Å2
ΔGint-74 kcal/mol
Surface area22760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.210, 80.460, 140.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein
HYPOTHETICAL PROTEIN YCHN


Mass: 12843.372 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0AB52
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: AMS, pH 5.5, VAPOR DIFFUSION, HANGING DROP at 295K
Crystal grow
*PLUS
Temperature: 21.5-22.5 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1250 mg/mlprotein1drop
250 mMTris-HCl1droppH7.2
3150 mM1dropNaCl
42.4 Mammonium phosphate1drop
50.1 Mcitric acid1droppH5.5
62.4 Mammonium phosphate1reservoir
70.1 Mcitric acid1reservoirpH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97949, 0.97926, 0.99999
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 9, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979491
20.979261
30.999991
ReflectionResolution: 2.8→70.1 Å / Num. all: 20429 / Num. obs: 20429 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19.5 Å2
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 35268 / Redundancy: 3.07 % / Rmerge(I) obs: 0.106
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.85 Å / % possible obs: 98.6 % / Redundancy: 2.93 % / Num. unique obs: 1756 / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 3.9

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8→19.98 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1784518.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1806 10 %RANDOM
Rwork0.229 ---
all0.208 18148 --
obs0.229 18148 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.0957 Å2 / ksol: 0.35654 e/Å3
Displacement parametersBiso mean: 27.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2--1.65 Å20 Å2
3----1.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5334 0 0 86 5420
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.951.5
X-RAY DIFFRACTIONc_mcangle_it8.012
X-RAY DIFFRACTIONc_scbond_it6.332
X-RAY DIFFRACTIONc_scangle_it9.452.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.336 302 9.9 %
Rwork0.298 2762 -
obs--97.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Rfactor all: 0.208 / Rfactor obs: 0.229 / Rfactor Rfree: 0.249 / Rfactor Rwork: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.97
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
LS refinement shell
*PLUS
Rfactor Rfree: 0.336 / Rfactor Rwork: 0.298

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