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- PDB-7siq: Crystal structure of a peptide chain release factor 3 (prfC) from... -

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Basic information

Entry
Database: PDB / ID: 7siq
TitleCrystal structure of a peptide chain release factor 3 (prfC) from Stenotrophomonas maltophilia bound to GDP
ComponentsPeptide chain release factor 3
KeywordsHYDROLASE / NIAID / structural genomics / elongation factor G / EF-G / GTPase / GTP-dependent / GDP-dependent / aerobic / nonfermentative / Gram-negative bacterium / ribosome / peptide release / recycling / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


regulation of translational termination / translation release factor activity, codon specific / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
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 ...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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Peptide chain release factor 3
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal structure of a peptide chain release factor 3 (prfC) from Stenotrophomonas maltophilia bound to GDP
Authors: Edwards, T.E. / Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionOct 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide chain release factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4882
Polymers60,0451
Non-polymers4431
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.540, 96.540, 170.070
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 60045.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria)
Strain: K279a / Gene: prfC, Smlt3637 / Production host: Escherichia coli (E. coli) / References: UniProt: B2FR00
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.82 Å3/Da / Density % sol: 67.76 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: StmaA.18013.a.B1.PW38802 at 20.5 mg/mL with 3 mM MgCl2 and 3 mM GDP against Morpheus screen condition D5 containing 10% PEG 20,000, 20% PEG 550 MME, 0.02 mM each 1,6-hexanediol, 1-butanol, ...Details: StmaA.18013.a.B1.PW38802 at 20.5 mg/mL with 3 mM MgCl2 and 3 mM GDP against Morpheus screen condition D5 containing 10% PEG 20,000, 20% PEG 550 MME, 0.02 mM each 1,6-hexanediol, 1-butanol, 1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol, 0.1 M MOPES/Hepes pH 7.5, direct cryo, unique puck ID tja6-9, crystal tracking ID 315959d5

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Data collection

DiffractionMean temperature: 287 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.95→48.27 Å / Num. obs: 19936 / % possible obs: 99.8 % / Redundancy: 10.855 % / Biso Wilson estimate: 84.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.071 / Χ2: 0.881 / Net I/σ(I): 22.82 / Num. measured all: 216402
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.95-3.0311.1620.732416230145814540.9910.76799.7
3.03-3.1111.1320.4585.5815629140914040.9940.48199.6
3.11-3.211.2160.3956.4715366137413700.9940.41499.7
3.2-3.311.0250.3058.1714707133413340.9960.32100
3.3-3.4111.0990.21610.0214306129312890.9980.22699.7
3.41-3.5311.0780.1712.4813814124812470.9980.17899.9
3.53-3.6611.0750.14714.0213556122612240.9990.15499.8
3.66-3.8110.9910.117.7912738116111590.9990.10599.8
3.81-3.9810.9950.09121.0112567114411430.9990.09599.9
3.98-4.1710.9330.0725.5111731107310730.9990.074100
4.17-4.410.8430.06229.66111791032103110.06699.9
4.4-4.6610.8260.05235.61104809689680.9990.054100
4.66-4.9910.6840.04939.0698519229220.9990.052100
4.99-5.3910.7320.04740.7993158688680.9990.05100
5.39-5.910.5860.04940.3284377977970.9990.051100
5.9-6.610.4240.04542.2675687267260.9990.048100
6.6-7.6210.320.03849.3267496546540.9990.04100
7.62-9.3310.1410.02955.29567956056010.031100
9.33-13.199.7020.02460.4443374474470.9990.025100
13.19-48.278.1320.02754.1921632802660.9990.02995

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXdev-4274refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3tr5

3tr5


Resolution: 2.95→48.27 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 38.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2786 945 4.8 %
Rwork0.2235 18743 -
obs0.2263 19688 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 194.94 Å2 / Biso mean: 103.2994 Å2 / Biso min: 66.13 Å2
Refinement stepCycle: final / Resolution: 2.95→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3866 0 28 5 3899
Biso mean--78.05 81.52 -
Num. residues----524
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-3.110.47941170.35722609272697
3.11-3.30.36081230.30322583270697
3.3-3.550.33021290.27092669279899
3.56-3.910.28491510.25122616276799
3.91-4.480.34961230.213926942817100
4.48-5.640.21841500.194127252875100
5.64-48.270.24851520.195128472999100
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)
11.77961.02020.9924.02140.55394.20970.1476-0.00340.1603-0.0922-0.10370.05830.52470.0728-0.03070.64640.2603-0.00651.0214-0.00330.5199-43.9641-17.34239.2198
21.60131.19130.08855.921-1.09363.6655-0.13120.13010.4212-0.3021-0.15040.1455-0.89030.35420.21760.79970.15930.02021.0028-0.04550.5822-38.03126.66066.7681
34.37190.0099-0.38814.95830.48652.43330.16191.1182-0.3695-0.5456-0.2259-0.1005-0.67260.75430.07740.80020.31640.12411.03940.13170.6772-33.7261-4.41874.4863
43.99250.1323-1.48582.7897-0.86833.5979-0.14060.3922-0.2779-0.41030.0101-0.14091.36660.39320.13551.43350.4382-0.03191.1844-0.10890.6647-37.9682-33.57913.936
53.0162.23080.13654.6904-0.71984.4712-0.093-0.1509-0.3330.06670.1339-0.21961.32280.2428-0.05411.23480.38680.01561.1892-0.00230.6313-39.5564-34.235431.8196
63.55331.1407-1.02787.0930.49264.78520.181-0.6817-0.58051.1492-0.1421-0.69240.83152.2237-0.34951.07080.3115-0.19441.50460.11170.8613-25.8869-25.26732.8585
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 131 )A2 - 131
2X-RAY DIFFRACTION2chain 'A' and (resid 132 through 235 )A132 - 235
3X-RAY DIFFRACTION3chain 'A' and (resid 236 through 273 )A236 - 273
4X-RAY DIFFRACTION4chain 'A' and (resid 274 through 387 )A274 - 387
5X-RAY DIFFRACTION5chain 'A' and (resid 388 through 505 )A388 - 505
6X-RAY DIFFRACTION6chain 'A' and (resid 506 through 530 )A506 - 530

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