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- PDB-1a19: BARSTAR (FREE), C82A MUTANT -

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Basic information

Entry
Database: PDB / ID: 1a19
TitleBARSTAR (FREE), C82A MUTANT
ComponentsBARSTAR
KeywordsRIBONUCLEASE INHIBITOR / BARSTAR / C82A / DIMER / UNCOMPLEXED
Function / homologyBarstar-like / Barstar (barnase inhibitor) / Barstar (barnase inhibitor) / Barstar-like superfamily / Barnase; Chain D / 2-Layer Sandwich / cytoplasm / Alpha Beta / Barstar
Function and homology information
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsRatnaparkhi, G.S. / Varadarajan, R.
CitationJournal: Biochemistry / Year: 1998
Title: Discrepancies between the NMR and X-ray structures of uncomplexed barstar: analysis suggests that packing densities of protein structures determined by NMR are unreliable.
Authors: Ratnaparkhi, G.S. / Ramachandran, S. / Udgaonkar, J.B. / Varadarajan, R.
History
DepositionDec 25, 1997Processing site: BNL
Revision 1.0Apr 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BARSTAR
B: BARSTAR


Theoretical massNumber of molelcules
Total (without water)20,6412
Polymers20,6412
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.182, 104.182, 36.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein BARSTAR


Mass: 10320.674 Da / Num. of mol.: 2 / Mutation: C82A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P11540

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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: 2.4 Å3/Da / Density % sol: 49 %
Description: 1BGS & 2BRS ARE THE COMPLEX OF BARSTAR WITH BARNASE
Crystal growpH: 6.5
Details: C82A MUTANT WAS CRYSTALLIZED FROM 40-60% AMMONIUM SULFATE, 50MM PHOSPHATE, PH=6.5. PROTEIN CONC=45 MG/ML. C40A AND DTNB LABELLED CRYSTALS ALSO CRYSTALLIZED BUT DID NOT DIFFRACT TO HIGH RESOLUTION.
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
122.5 mg/mlprotein1drop
250 mMphosphate1drop
320-30 %ammonium sulfate1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1996 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.76→10 Å / Num. obs: 4796 / % possible obs: 85 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 61.2 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 33
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7 % / Rmerge(I) obs: 0.05 / % possible all: 50
Reflection
*PLUS
% possible obs: 99 % / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
MARXDSdata reduction
MARSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1BGS, 1BRS

1bgs

1brs


Resolution: 2.76→10 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
Details: MET PRESENT AT N-TERMINUS DURING EXPRESSION IS NOT INCLUDED IN THE SEQUENCE OR THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.292 618 15.1 %RANDOM
Rwork0.203 ---
obs0.203 4081 85 %-
Displacement parametersBiso mean: 48.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 2.76→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1438 0 0 0 1438
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.54
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINED, 100 KCAL/MOL WEIGHT FINAL POSITIONAL REFINEMENT USING ALL REFLECTIONS AND REMOVING NCS RESTRAINTS.
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.081 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.465 33 12.7 %
Rwork0.465 226 -
obs--55.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.54

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