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- PDB-2iee: Crystal Structure of YCKB_BACSU from Bacillus subtilis. Northeast... -

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Basic information

Entry
Database: PDB / ID: 2iee
TitleCrystal Structure of YCKB_BACSU from Bacillus subtilis. Northeast Structural Genomics Consortium target SR574.
ComponentsProbable ABC transporter extracellular-binding protein yckB
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / SR574 / NESG / YCKB / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable ABC transporter extracellular-binding protein YckB
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsKuzin, A.P. / Su, M. / Jayaraman, S. / Chen, X.C. / Jang, M. / Cunningham, K. / Ma, C. / Xiao, R. / Liu, J. / Baran, M.C. ...Kuzin, A.P. / Su, M. / Jayaraman, S. / Chen, X.C. / Jang, M. / Cunningham, K. / Ma, C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of probable ABC transporter extracellular-binding protein yckB from Bacillus subtilis.
Authors: Kuzin, A.P. / Su, M. / Seetharaman, J. / Chen, X.C. / Jang, M. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionSep 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable ABC transporter extracellular-binding protein yckB
B: Probable ABC transporter extracellular-binding protein yckB


Theoretical massNumber of molelcules
Total (without water)61,0312
Polymers61,0312
Non-polymers00
Water3,423190
1
A: Probable ABC transporter extracellular-binding protein yckB


Theoretical massNumber of molelcules
Total (without water)30,5151
Polymers30,5151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable ABC transporter extracellular-binding protein yckB


Theoretical massNumber of molelcules
Total (without water)30,5151
Polymers30,5151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.284, 49.918, 106.768
Angle α, β, γ (deg.)90.00, 99.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable ABC transporter extracellular-binding protein yckB / ORF2


Mass: 30515.260 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yckB / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: P42400
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.38 Å3/Da / Density % sol: 48.29 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 34% PEG 1000, 100 mM TAPS, 100 mM Ammonium nitrate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97916, 0.97943, 0.96791
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 30, 2006 / Details: mirror
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979161
20.979431
30.967911
ReflectionResolution: 2.2→30 Å / Num. obs: 50187 / % possible obs: 88.3 % / Observed criterion σ(I): -3 / Redundancy: 17.2 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 17.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 6.8 / % possible all: 85.95

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→19.95 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 107032.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2317 4.9 %RANDOM
Rwork0.202 ---
obs0.202 47664 83.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.2004 Å2 / ksol: 0.374275 e/Å3
Displacement parametersBiso mean: 22.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å2-1.02 Å2
2---1.11 Å20 Å2
3---1.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3858 0 0 192 4050
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.72
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.267 300 4.2 %
Rwork0.199 6769 -
obs--74.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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