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- PDB-3cew: Crystal structure of a cupin protein (BF4112) from Bacteroides fr... -

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Basic information

Entry
Database: PDB / ID: 3cew
TitleCrystal structure of a cupin protein (BF4112) from Bacteroides fragilis. Northeast Structural Genomics Consortium target BfR205
ComponentsUncharacterized cupin protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / all beta-protein / jelly-roll (cupin-2) / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cupin / Cupin_2 domain-containing protein
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.31 Å
AuthorsForouhar, F. / Chen, Y. / Seetharaman, J. / Mao, L. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Maglaqui, M. / Wang, H. / Baran, M.C. ...Forouhar, F. / Chen, Y. / Seetharaman, J. / Mao, L. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Maglaqui, M. / Wang, H. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of a cupin protein (BF4112) from Bacteroides fragilis. Northeast Structural Genomics Consortium target BfR205.
Authors: Forouhar, F. / Chen, Y. / Seetharaman, J. / Mao, L. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Maglaqui, M. / Wang, H. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionFeb 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized cupin protein
B: Uncharacterized cupin protein
C: Uncharacterized cupin protein
D: Uncharacterized cupin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3188
Polymers55,0564
Non-polymers2624
Water5,639313
1
A: Uncharacterized cupin protein
B: Uncharacterized cupin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6594
Polymers27,5282
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-18.7 kcal/mol
Surface area11160 Å2
MethodPISA
2
C: Uncharacterized cupin protein
D: Uncharacterized cupin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6594
Polymers27,5282
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-18.7 kcal/mol
Surface area11060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.140, 87.834, 128.032
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 cupin protein


Mass: 13764.029 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF4112 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q5L811, UniProt: A0A380YRY7*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.51 Å3/Da / Density % sol: 50.98 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 6
Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM Sodium chloride, 5 mM DTT. Precipitant solution: 100 mM MES pH 6.0, 20% PEG 4000, 100 mM Magnesium chloride, MICROBATCH UNDER OIL, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 26, 2008 / Details: Mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 43936 / Num. obs: 43936 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.073 / Net I/σ(I): 30.36
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.134 / Mean I/σ(I) obs: 13.38 / Num. unique all: 4634 / Rsym value: 0.124 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.31→19.81 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 529681.23 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.246 4094 9.8 %RANDOM
Rwork0.217 ---
all0.218 43936 --
obs0.217 41989 89.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.8914 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 21.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20 Å20 Å2
2---1.01 Å20 Å2
3----0.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2.31→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3552 0 4 313 3869
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d0.71
LS refinement shellResolution: 2.31→2.38 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.298 301 9.2 %
Rwork0.216 2979 -
obs-2979 69.3 %

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