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- PDB-1y71: X-ray crystal structure of kinase-associated protein B from Bacil... -

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Basic information

Entry
Database: PDB / ID: 1y71
TitleX-ray crystal structure of kinase-associated protein B from Bacillus cereus
ComponentsKinase-associated protein B
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / kinase-associated protein B / Midwest Center for Structural Genomics / MCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


Kinase associated protein B domain / Kinase associated protein B / Kinase associated protein B superfamily / Kinase associated protein B / KapB / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Kinase-associated protein B
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsOsipiuk, J. / Zhou, M. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of kinase-associated protein B from Bacillus cereus
Authors: Osipiuk, J. / Zhou, M. / Moy, S. / Collart, F. / Joachimiak, A.
History
DepositionDec 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 6, 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: Kinase-associated protein B
B: Kinase-associated protein B


Theoretical massNumber of molelcules
Total (without water)30,1152
Polymers30,1152
Non-polymers00
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.197, 99.403, 101.755
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Kinase-associated protein B


Mass: 15057.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: BC4909 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q816F1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.3 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 100 mM Sodium Acetate, 20% PEG 3350, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979456 Å
DetectorType: SBC-3 / Detector: CCD / Date: Dec 2, 2004
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979456 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. all: 20967 / Num. obs: 20380 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Rmerge(I) obs: 0.094 / Χ2: 1.126 / Net I/σ(I): 19.7
Reflection shellResolution: 1.95→2 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 1.46 / Num. unique all: 998 / Χ2: 0.694 / % possible all: 75.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.401data extraction
HKL-2000data reduction
SHELXDphasing
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→40 Å / Cor.coef. Fo:Fc: 0.938 / SU B: 5.775 / SU ML: 0.085 / SU R Cruickshank DPI: 0.164 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: All data were used in final round of refinement. R-factor-all corresponds to deposited file. R-factors, R-work and R-free, are taken from second to last round of refinement which used test data set.
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2025 -random
Rwork0.214 ---
all0.216 20319 --
obs0.216 20319 97.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.708 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20 Å20 Å2
2--0.19 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 0 108 1895
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.01618170.022
X-RAY DIFFRACTIONr_angle_refined_deg1.39624461.987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5412175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.028624.884
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.89734615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0421015
X-RAY DIFFRACTIONr_chiral_restr0.0972720.2
X-RAY DIFFRACTIONr_gen_planes_refined0.00613510.02
X-RAY DIFFRACTIONr_nbd_refined0.2137870.2
X-RAY DIFFRACTIONr_nbtor_refined0.30512400.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1281000.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.2
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.08750.2
X-RAY DIFFRACTIONr_mcbond_it1.29611551.5
X-RAY DIFFRACTIONr_mcangle_it1.7317852
X-RAY DIFFRACTIONr_scbond_it3.047723
X-RAY DIFFRACTIONr_scangle_it4.6286614.5
LS refinement shellResolution: 1.95→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 114 -
Rwork0.258 1105 -
obs-1105 75.68 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.31790.14050.21590.3721-0.03521.7066-0.0211-0.0190.0247-0.0138-0.0378-0.03910.1170.12150.0590.0011-0.0014-0.0012-0.02290.0203-0.0201-3.1703-12.157631.3438
20.443-0.4315-0.0952.0456-0.06520.65790.0013-0.0268-0.0147-0.11930.00190.10250.0063-0.0621-0.0032-0.0228-0.0169-0.0142-0.00810.0158-0.033-16.63875.282613.2654
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 4 - 127 / Label seq-ID: 7 - 130

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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