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- PDB-3cnw: Three-dimensional structure of the protein XoxI (Q81AY6) from Bac... -

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Basic information

Entry
Database: PDB / ID: 3cnw
TitleThree-dimensional structure of the protein XoxI (Q81AY6) from Bacillus cereus. Northeast Structural Genomics Consortium target BcR196.
ComponentsProtein XoxI
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Q81AY6 / NESG / XoxI / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyPolyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / XoxI
Function and homology information
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.48 Å
AuthorsKuzin, A.P. / Abashidze, M. / Seetharaman, J. / Wang, H. / Ciccosanti, C. / Mao, L. / Xiao, R. / Nair, R. / Baran, M.C. / Acton, T.B. ...Kuzin, A.P. / Abashidze, M. / Seetharaman, J. / Wang, H. / Ciccosanti, C. / Mao, L. / Xiao, R. / Nair, R. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To Be Published
Title: Three-dimensional structure of the protein XoxI (Q81AY6) from Bacillus cereus. Northeast Structural Genomics Consortium target BcR196.
Authors: Kuzin, A.P. / Abashidze, M. / Seetharaman, J. / Wang, H. / Ciccosanti, C. / Mao, L. / Xiao, R. / Nair, R. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMar 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein XoxI
B: Protein XoxI


Theoretical massNumber of molelcules
Total (without water)34,0792
Polymers34,0792
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein XoxI


Theoretical massNumber of molelcules
Total (without water)17,0391
Polymers17,0391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Protein XoxI


Theoretical massNumber of molelcules
Total (without water)17,0391
Polymers17,0391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.758, 42.463, 201.609
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 Protein XoxI


Mass: 17039.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Species: Bacillus cereus / Strain: DSM 31 / Gene: BC_3411 / Production host: Escherichia coli (E. coli) / References: UniProt: Q81AY6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 36.32 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M Na Acetate, 30% PEG 550 MME, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 26, 2008 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.48→50 Å / Num. obs: 17694 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 18 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 20
Reflection shellResolution: 2.48→2.59 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 10.1 / % possible all: 84.3

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2.48→19.81 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 97383.19 / 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 in phasing. BULK SOLVENT MODEL WAS USED IN REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.258 821 4.9 %RANDOM
Rwork0.206 ---
obs0.206 16715 92.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.1349 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1-7.21 Å20 Å20 Å2
2---3.89 Å20 Å2
3----3.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.48→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2253 0 0 60 2313
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.85
LS refinement shellResolution: 2.48→2.55 Å / Rfactor Rfree error: 0.062 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.376 37 3.9 %
Rwork0.23 916 -
obs--28.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top

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