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- PDB-4lzk: Crystal structure of inclusion body protein (PixA pfam12306) from... -

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Basic information

Entry
Database: PDB / ID: 4lzk
TitleCrystal structure of inclusion body protein (PixA pfam12306) from Burkholderia cenocepacia J2315
ComponentsPixA inclusion body protein
KeywordsUNKNOWN FUNCTION / PixA / pfam 12306 / MCSG / PSI-Biology / Structural Genomics / Midwest Center for Structural Genomics / Inclusion body protein
Function / homologyInclusion body protein / Uncharacterised protein family PixA/AidA / PixA-like superfamily / Inclusion body protein / Immunoglobulin-like / Sandwich / Mainly Beta / Inclusion body protein
Function and homology information
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.89 Å
AuthorsNocek, B. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of inclusion body protein (PixA pfam12306) from Burkholderia cenocepacia J2315
Authors: Nocek, B. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionJul 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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

Downloads & links

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Assembly

Deposited unit
A: PixA inclusion body protein
B: PixA inclusion body protein
C: PixA inclusion body protein
D: PixA inclusion body protein
E: PixA inclusion body protein
F: PixA inclusion body protein


Theoretical massNumber of molelcules
Total (without water)119,0856
Polymers119,0856
Non-polymers00
Water11,764653
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19150 Å2
ΔGint-100 kcal/mol
Surface area34230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.852, 120.725, 125.274
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
PixA inclusion body protein


Mass: 19847.559 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / Gene: BceJ2315_48650, BCAM1413a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: B4EII9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 653 / 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 Å3/Da / Density % sol: 38.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 MgCL, 0.1 M Tris, 25% Peg 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2013 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→32.7 Å / Num. all: 76660 / Num. obs: 71601 / % possible obs: 93.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.5
Reflection shellResolution: 1.9→1.93 Å / % possible all: 95.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
DMmodel building
SHELXmodel building
ARP/wARPmodel building
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.89→32.7 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.168 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.171 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21153 3458 5 %RANDOM
Rwork0.1761 ---
all0.182 68723 --
obs0.17789 65265 89.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.484 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0 Å20 Å2
2--0.26 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.89→32.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7251 0 0 653 7904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0197444
X-RAY DIFFRACTIONr_bond_other_d0.0010.026921
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.93910148
X-RAY DIFFRACTIONr_angle_other_deg0.861315842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4215975
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.09525.148305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.143151051
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3631514
X-RAY DIFFRACTIONr_chiral_restr0.1240.21163
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218729
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021789
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.892→1.941 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 165 -
Rwork0.218 3352 -
obs--62.94 %

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