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- PDB-5f4c: Crystal Structure of Ribonuclease Inhibitor Barstar from Salmonel... -

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Basic information

Entry
Database: PDB / ID: 5f4c
TitleCrystal Structure of Ribonuclease Inhibitor Barstar from Salmonella Typhimurium
ComponentsPutative cytoplasmic protein
KeywordsHYDROLASE INHIBITOR / alpha beta protein / Barstar realted / Ribonuclease Inhibitor / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyBarstar-like / Barstar-like superfamily / Barnase; Chain D / 2-Layer Sandwich / Alpha Beta / MALONATE ION / Cytoplasmic protein
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMaltseva, N. / Kim, Y. / Mulligan, R. / Stam, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal Structure of Ribonuclease Inhibitor Barstar from Salmonella Typhimurium.
Authors: Maltseva, N. / Kim, Y. / Mulligan, R. / Stam, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative cytoplasmic protein
B: Putative cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2034
Polymers21,9992
Non-polymers2042
Water3,873215
1
A: Putative cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1012
Polymers10,9991
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1012
Polymers10,9991
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.362, 52.790, 58.812
Angle α, β, γ (deg.)90.00, 93.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative cytoplasmic protein


Mass: 10999.331 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: yhcO, STM3363 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7CPM9
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.07 Å3/Da / Density % sol: 40.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4M Sodium malonate, pH 7.0 / PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 34560 / % possible obs: 97.8 % / Redundancy: 4.7 % / Rsym value: 0.047 / Net I/σ(I): 28.59
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.87 / % possible all: 80

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CX6

2cx6


Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.388 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17669 1669 4.8 %RANDOM
Rwork0.14143 ---
obs0.14321 32872 97.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.799 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å2-0.26 Å2
2---0.78 Å20 Å2
3---0.95 Å2
Refinement stepCycle: 1 / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 0 14 215 1748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191695
X-RAY DIFFRACTIONr_bond_other_d0.0020.021574
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.9722306
X-RAY DIFFRACTIONr_angle_other_deg1.02333620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5695204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.05923.73799
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9315299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.7521517
X-RAY DIFFRACTIONr_chiral_restr0.110.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021982
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02423
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_it2.0512.275786
X-RAY DIFFRACTIONr_mcbond_other2.0142.272785
X-RAY DIFFRACTIONr_mcangle_it2.5853.411000
X-RAY DIFFRACTIONr_mcangle_other2.5933.4131001
X-RAY DIFFRACTIONr_scbond_it2.7652.736909
X-RAY DIFFRACTIONr_scbond_other2.7662.737907
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6883.9591306
X-RAY DIFFRACTIONr_long_range_B_refined4.6220.5562160
X-RAY DIFFRACTIONr_long_range_B_other4.24819.5292040
X-RAY DIFFRACTIONr_rigid_bond_restr2.43233269
X-RAY DIFFRACTIONr_sphericity_free24.48544
X-RAY DIFFRACTIONr_sphericity_bonded12.33853396
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 95 -
Rwork0.259 1927 -
obs--78.31 %

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