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- PDB-3tr5: Structure of a peptide chain release factor 3 (prfC) from Coxiell... -

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Basic information

Entry
Database: PDB / ID: 3tr5
TitleStructure of a peptide chain release factor 3 (prfC) from Coxiella burnetii
ComponentsPeptide chain release factor 3
KeywordsTRANSLATION / Protein synthesis
Function / homology
Function and homology information


regulation of translational termination / translation release factor activity, codon nonspecific / translation release factor activity, codon specific / translational termination / GTPase activity / GTP binding / cytosol
Similarity search - Function
Peptide chain release factor 3, domain III / Peptide chain release factor 3, C-terminal / Peptide chain release factor 3, domain III superfamily / Peptide chain release factor 3, GTP-binding domain / Class II release factor RF3, C-terminal domain / Peptide chain release factor 3 / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translational (tr)-type GTP-binding domain ...Peptide chain release factor 3, domain III / Peptide chain release factor 3, C-terminal / Peptide chain release factor 3, domain III superfamily / Peptide chain release factor 3, GTP-binding domain / Class II release factor RF3, C-terminal domain / Peptide chain release factor 3 / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Plaits / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Peptide chain release factor 3
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.11 Å
AuthorsCheung, J. / Franklin, M.C. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jan 20, 2016Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide chain release factor 3
B: Peptide chain release factor 3
C: Peptide chain release factor 3
D: Peptide chain release factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,69312
Polymers241,7604
Non-polymers1,9338
Water22,0861226
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.254, 141.429, 161.869
Angle α, β, γ (deg.)90.000, 95.620, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asym.

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Components

#1: Protein
Peptide chain release factor 3 / RF-3


Mass: 60439.910 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: CBU_0811, prfC / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83DC7
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1226 / 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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M MES pH 6.0, 0.2M calcium acetate, 20% PEG 8000 , VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 146154 / Num. obs: 143670 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.098 / Χ2: 1.166 / Net I/σ(I): 6.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.142.60.6265460.604190.8
2.14-2.182.80.55869140.627194.3
2.18-2.223.30.51871020.617198.5
2.22-2.263.80.4673850.641199.9
2.26-2.313.80.39271920.657199.9
2.31-2.373.80.35173680.656199.9
2.37-2.423.80.31872010.694199.9
2.42-2.493.80.28573200.718199.9
2.49-2.563.80.23972790.719199.8
2.56-2.653.80.20672410.786199.7
2.65-2.743.80.17772920.846199.6
2.74-2.853.80.15372710.908199.3
2.85-2.983.80.12672981.001199.2
2.98-3.143.80.10572161.089199
3.14-3.333.70.08672241.273198.8
3.33-3.593.70.07171381.486198.1
3.59-3.953.60.06672001.745198.1
3.95-4.523.50.06271052.284196.9
4.52-5.73.50.06172092.47197.6
5.7-503.50.0671693.439196.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H5E

2h5e


Resolution: 2.11→41.965 Å / Occupancy max: 1 / Occupancy min: 0.46 / FOM work R set: 0.8372 / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2558 7191 5.01 %RANDOM
Rwork0.2154 ---
all0.2175 154466 --
obs0.2175 143630 97.64 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.011 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso max: 224.63 Å2 / Biso mean: 40.2973 Å2 / Biso min: 4.31 Å2
Baniso -1Baniso -2Baniso -3
1-1.7587 Å2-0 Å2-1.5422 Å2
2---2.7789 Å20 Å2
3---1.0203 Å2
Refinement stepCycle: LAST / Resolution: 2.11→41.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16315 0 116 1226 17657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416775
X-RAY DIFFRACTIONf_angle_d0.76122673
X-RAY DIFFRACTIONf_chiral_restr0.0512497
X-RAY DIFFRACTIONf_plane_restr0.0032924
X-RAY DIFFRACTIONf_dihedral_angle_d12.8316335
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1096-2.13360.37021610.29973435359674
2.1336-2.15870.37032360.29234268450492
2.1587-2.1850.32142280.27044396462494
2.185-2.21260.3152240.26544489471396
2.2126-2.24180.31272370.261145874824100
2.2418-2.27250.31912480.250646604908100
2.2725-2.30490.27722390.234546464885100
2.3049-2.33930.30122170.24246284845100
2.3393-2.37590.30782300.226846864916100
2.3759-2.41480.26472600.22346154875100
2.4148-2.45650.2722420.233346604902100
2.4565-2.50110.29082550.23846474902100
2.5011-2.54920.26582320.227845894821100
2.5492-2.60120.25982470.225447174964100
2.6012-2.65780.28612420.218645584800100
2.6578-2.71960.25872410.207647244965100
2.7196-2.78760.25572550.21334544479999
2.7876-2.8630.25632250.2114676490199
2.863-2.94720.24772450.20754593483899
2.9472-3.04230.25682510.21274613486499
3.0423-3.1510.25642610.21314604486599
3.151-3.27710.25562720.21464543481599
3.2771-3.42620.23112450.20814594483998
3.4262-3.60670.2622440.20674589483398
3.6067-3.83260.24182400.20054621486198
3.8326-4.12820.22062280.19544556478497
4.1282-4.54320.21152470.18214477472497
4.5432-5.19960.21982710.18424568483997
5.1996-6.5470.27582340.23174609484398
6.547-41.9730.26082340.23484547478195
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)
10.01520.0480.00650.23150.05640.01660.03790.0516-0.01430.0053-0.0009-0.162-0.01410.0930.0020.12480.0025-0.0070.16710.00780.19015.0963-36.6403-75.3712
20.2991-0.0719-0.02780.02570.01210.0065-0.0766-0.1623-0.05690.0579-0.0402-0.19520.0340.07070.050.1629-0.023-0.03710.2530.05450.2836.7207-34.7441-65.1526
30.0399-0.0067-0.01730.20940.10130.2310.00490.099-0.00180.0127-0.0164-0.06780.0117-0.0218-0.00450.11040.00450.00640.1798-0.01590.1466-4.3101-45.9039-81.7434
40.30150.30890.07840.42740.01470.67780.06150.00670.02840.09470.0464-0.2235-0.17380.1512-0.04820.1883-0.0361-0.01770.15240.00830.25770.1288-17.6533-66.0486
50.08460.02020.22870.26120.26690.72120.0342-0.05310.11430.0555-0.17240.0421-0.0436-0.15950.05090.2007-0.02930.00990.201-0.03550.2236-13.9469-28.6941-46.7997
60.08780.09510.06230.21430.0560.21880.0959-0.17550.08130.0476-0.09330.0858-0.0101-0.09830.00580.192-0.02370.01330.2507-0.01050.2171-22.6124-32.8798-52.5421
70.14510.12630.07890.1850.02390.18430.0494-0.0417-0.02610.16370.06240.02110.0663-0.0185-0.04810.3712-0.0145-0.05160.218-0.02010.1979-8.7147-74.6394-49.1216
80.29170.0390.15810.14860.03580.09160.14710.214-0.11590.1517-0.0437-0.23040.08610.177-0.04330.35980.0097-0.10220.33250.02660.3196-3.8618-78.0651-58.3639
90.0417-0.0012-0.03090.03150.01180.0370.0266-0.0764-0.04190.1399-0.04810.0312-0.19850.0947-0.02410.3934-0.0793-0.08180.10290.0554-0.0995-14.033-59.97-49.4827
100.07910.0129-0.06950.0176-0.00980.06020.0461-0.06740.06970.1479-0.0265-0.017-0.08130.0022-0.01380.5113-0.0898-0.00970.33890.00410.2393-18.5354-53.3136-37.3613
110.12120.16270.08980.20860.06550.13680.1888-0.093-0.2940.24070.0251-0.11170.302-0.01220.01880.4652-0.0271-0.14210.13990.01130.3062-16.6451-85.0121-55.3119
120.27460.17490.10430.16250.09290.0780.04910.0791-0.19780.07310.0277-0.09540.2882-0.0685-0.05840.2825-0.025-0.04720.174-0.02790.2708-18.4479-82.9951-76.6202
130.19480.0643-0.02470.25160.12780.13940.08830.0594-0.13870.0673-0.1310.13830.0161-0.02030.01030.16260.0359-0.03470.1727-0.05050.2362-23.114-70.1094-81.9527
140.28240.1013-0.15090.0522-0.02340.2336-0.03370.02540.1468-0.17290.01780.0687-0.1090.00020.00560.4219-0.0862-0.04970.24410.06880.263711.0007-112.6946-31.395
150.2498-0.0815-0.11720.04480.04330.0469-0.0389-0.06870.2177-0.28020.0466-0.0063-0.10150.14490.00190.4372-0.11070.04340.24920.07650.320717.6648-110.0519-22.2633
160.30730.0417-0.17570.127-0.04970.3048-0.0280.16690.3561-0.67220.20.1563-0.09020.01680.09840.6138-0.1027-0.11210.07030.2283-0.16256.5403-117.0204-30.346
170.5801-0.0542-0.05570.48140.32330.4413-0.0434-0.04830.1126-0.03620.06220.3747-0.0936-0.0411-0.02830.18260.00850.0310.16960.01150.3572-1.6598-112.1331-1.1402
180.2053-0.0480.01150.21170.07280.34150.0810.076-0.25960.08110.01380.1467-0.0119-0.09420.06360.12570.04020.02420.21860.0090.2744-26.429-77.8513.4676
190.4924-0.06950.01770.3518-0.06380.3433-0.04670.0887-0.1142-0.01910.07470.1506-0.27010.0130.01460.2185-0.0072-0.01950.18430.02930.1619-18.2775-67.76820.522
200.3185-0.03880.05980.2669-0.00540.2292-0.0104-0.0008-0.28360.00360.09680.20970.0477-0.03230.0380.13520.01520.02640.1540.04040.3292-18.2475-90.614810.4068
210.80850.1294-0.21790.1337-0.16190.2693-0.0866-0.0855-0.26020.07410.0006-0.065-0.0948-0.06380.03130.15580.0202-0.00820.23170.06530.2197-1.2487-83.672527.5467
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 3:44)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 45:84)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 85:291)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 292:385)A0
5X-RAY DIFFRACTION5chain 'A' and (resseq 386:438)A0
6X-RAY DIFFRACTION6chain 'A' and (resseq 439:525)A0
7X-RAY DIFFRACTION7chain 'B' and (resseq 3:44)B0
8X-RAY DIFFRACTION8chain 'B' and (resseq 45:84)B0
9X-RAY DIFFRACTION9chain 'B' and (resseq 85:209)B0
10X-RAY DIFFRACTION10chain 'B' and (resseq 210:246)B0
11X-RAY DIFFRACTION11chain 'B' and (resseq 247:365)B0
12X-RAY DIFFRACTION12chain 'B' and (resseq 366:417)B0
13X-RAY DIFFRACTION13chain 'B' and (resseq 418:525)B0
14X-RAY DIFFRACTION14chain 'C' and (resseq 3:34)C0
15X-RAY DIFFRACTION15chain 'C' and (resseq 35:93)C0
16X-RAY DIFFRACTION16chain 'C' and (resseq 94:365)C0
17X-RAY DIFFRACTION17chain 'C' and (resseq 366:525)C0
18X-RAY DIFFRACTION18chain 'D' and (resseq 3:52)D0
19X-RAY DIFFRACTION19chain 'D' and (resseq 53:233)D0
20X-RAY DIFFRACTION20chain 'D' and (resseq 234:417)D0
21X-RAY DIFFRACTION21chain 'D' and (resseq 418:525)D0

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