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- PDB-4gfq: 2.65 Angstrom Resolution Crystal Structure of Ribosome Recycling ... -

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Basic information

Entry
Database: PDB / ID: 4gfq
Title2.65 Angstrom Resolution Crystal Structure of Ribosome Recycling Factor (frr) from Bacillus anthracis
ComponentsRibosome-recycling factor
KeywordsTRANSLATION / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


translational termination / cytoplasm
Similarity search - Function
Ribosome-recycling factor / Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Gyrase A; domain 2 - #40 / Topoisomerase I; Chain A, domain 4 / Gyrase A; domain 2 / 2-Layer Sandwich / Orthogonal Bundle ...Ribosome-recycling factor / Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Gyrase A; domain 2 - #40 / Topoisomerase I; Chain A, domain 4 / Gyrase A; domain 2 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Ribosome-recycling factor
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsMinasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.65 Angstrom Resolution Crystal Structure of Ribosome Recycling Factor (frr) from Bacillus anthracis
Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosome-recycling factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9127
Polymers23,4561
Non-polymers4566
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.548, 95.548, 95.548
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ribosome-recycling factor / RRF / Ribosome-releasing factor


Mass: 23455.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAS3675, BA_3962, frr, GBAA_3962 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: Q81WL1

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Non-polymers , 5 types, 32 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.1 Å3/Da / Density % sol: 60.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: protein: 7.4 mg/mL in 0.25 M sodium cloride, 0.01 M Tris-HCl, pH 8.3, screen: Classics II (H3), 0.24 M sodium malonate, pH 7.0, 20% w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07806 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 4, 2012 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07806 Å / Relative weight: 1
ReflectionResolution: 2.65→30 Å / Num. all: 8662 / Num. obs: 8662 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 87.2 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 18
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 2.5 / Num. unique all: 430 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
BALBESphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EK8
Resolution: 2.65→28.81 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 26.974 / SU ML: 0.249
Isotropic thermal model: THERMAL FACTORS INDIVIDUALLY REFINED
Cross valid method: THROUGHOUT / ESU R: 0.563 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25452 379 4.8 %RANDOM
Rwork0.20264 ---
all0.2051 7596 --
obs0.2051 7596 91.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.329 Å2
Refinement stepCycle: LAST / Resolution: 2.65→28.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1458 0 26 26 1510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221504
X-RAY DIFFRACTIONr_bond_other_d0.0010.021062
X-RAY DIFFRACTIONr_angle_refined_deg1.4122.0032021
X-RAY DIFFRACTIONr_angle_other_deg0.74632601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.9165187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.76824.85368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.02515293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2311513
X-RAY DIFFRACTIONr_chiral_restr0.0820.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021638
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02271
X-RAY DIFFRACTIONr_mcbond_it1.0051.5933
X-RAY DIFFRACTIONr_mcbond_other0.2431.5376
X-RAY DIFFRACTIONr_mcangle_it2.00521508
X-RAY DIFFRACTIONr_scbond_it3.5173571
X-RAY DIFFRACTIONr_scangle_it5.9034.5513
LS refinement shellResolution: 2.65→2.718 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 36 -
Rwork0.299 532 -
obs-532 92.06 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
117.9567-12.5864-9.36513.05697.23936.1911-0.28130.1205-0.7760.0133-0.22590.738-0.0908-0.33370.50720.09680.0652-0.0020.09210.0150.1009-35.3301-4.3298-25.9272
25.30941.90881.0184.92190.84441.47760.01930.256-0.1387-0.19720.0129-0.20160.2240.0283-0.03220.16860.07040.04120.0690.00040.0364-24.0464-33.5691-40.042
37.0819-1.47111.63214.9359-2.132311.3832-0.08670.2278-0.36290.03440.0489-0.87780.20931.21170.03780.16410.02820.05040.1549-0.0270.392-16.3705-38.0068-40.4416
43.2554-2.7147-0.23993.89840.94881.05690.1130.25050.7833-0.25670.0372-1.0467-0.17030.0847-0.15020.16120.03250.11370.12580.04030.327-18.0256-9.7979-34.8085
511.1674-6.4997-1.399214.13863.17863.32140.15180.63030.3743-0.5075-0.2314-0.3532-0.7332-0.13590.07970.28790.124-0.12570.1249-0.04760.2483-43.461113.1633-22.9803
614.2613-11.208-6.092911.82746.16864.2459-0.8259-0.93950.96710.87090.8096-0.82590.26020.22710.01630.25160.1028-0.11710.1728-0.11940.2976-27.15371.0191-20.7186
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 28
2X-RAY DIFFRACTION2A29 - 78
3X-RAY DIFFRACTION3A79 - 97
4X-RAY DIFFRACTION4A98 - 131
5X-RAY DIFFRACTION5A132 - 149
6X-RAY DIFFRACTION6A150 - 185

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