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- PDB-8fre: Designed loop protein RBL4 -

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Basic information

Entry
Database: PDB / ID: 8fre
TitleDesigned loop protein RBL4
ComponentsRBL4
KeywordsDE NOVO PROTEIN / designed protein / helical repeat
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJude, K.M. / Jiang, H. / Baker, D. / Garcia, K.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat.Chem.Biol. / Year: 2024
Title: De novo design of buttressed loops for sculpting protein functions.
Authors: Jiang, H. / Jude, K.M. / Wu, K. / Fallas, J. / Ueda, G. / Brunette, T.J. / Hicks, D.R. / Pyles, H. / Yang, A. / Carter, L. / Lamb, M. / Li, X. / Levine, P.M. / Stewart, L. / Garcia, K.C. / Baker, D.
History
DepositionJan 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 7, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RBL4
B: RBL4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8858
Polymers46,5132
Non-polymers3726
Water2,198122
1
A: RBL4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5055
Polymers23,2561
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RBL4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3813
Polymers23,2561
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.287, 215.442, 28.008
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-303-

EDO

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Components

#1: Protein RBL4


Mass: 23256.373 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.02 Å3/Da / Density % sol: 39.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.4 / Details: 100 mM sodium acetate, pH 4.4, 2% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.8→59.84 Å / Num. obs: 35977 / % possible obs: 98.67 % / Redundancy: 7.2 % / Biso Wilson estimate: 40.77 Å2 / CC1/2: 0.989 / CC star: 0.997 / Rpim(I) all: 0.05685 / Rrim(I) all: 0.1498 / Rsym value: 0.1381 / Net I/σ(I): 5.7
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 0.36 / Num. unique obs: 3521 / CC1/2: 0.335 / CC star: 0.708 / Rpim(I) all: 1.298 / Rrim(I) all: 3.557 / Rsym value: 3.305 / % possible all: 96.09

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Processing

Software
NameVersionClassification
autoPROCdata reduction
PHENIX1.19.1_4122refinement
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→59.84 Å / SU ML: 0.4078 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.1469
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2807 1974 5.51 %
Rwork0.2336 33829 -
obs0.2363 35803 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.05 Å2
Refinement stepCycle: LAST / Resolution: 1.8→59.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3037 0 24 122 3183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01073107
X-RAY DIFFRACTIONf_angle_d1.06034196
X-RAY DIFFRACTIONf_chiral_restr0.0575511
X-RAY DIFFRACTIONf_plane_restr0.0076565
X-RAY DIFFRACTIONf_dihedral_angle_d13.6241217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.6921380.63922325X-RAY DIFFRACTION96.82
1.85-1.890.53931360.49322323X-RAY DIFFRACTION96.7
1.89-1.950.51461370.42932335X-RAY DIFFRACTION97.48
1.95-2.010.45861380.34452368X-RAY DIFFRACTION97.7
2.01-2.090.33871380.29672364X-RAY DIFFRACTION99.72
2.09-2.170.32321380.25382391X-RAY DIFFRACTION98.44
2.17-2.270.31181410.26512410X-RAY DIFFRACTION99.92
2.27-2.390.25051400.2242410X-RAY DIFFRACTION98.99
2.39-2.540.28521430.22462439X-RAY DIFFRACTION99.61
2.54-2.730.30691400.21532403X-RAY DIFFRACTION99.07
2.73-3.010.3011400.2432419X-RAY DIFFRACTION98.73
3.01-3.440.29541450.23042491X-RAY DIFFRACTION99.96
3.44-4.340.21841450.19362497X-RAY DIFFRACTION99.85
4.34-59.840.24591550.21192654X-RAY DIFFRACTION98.49
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)
11.24628606554-1.188812699230.9805523276136.00598131202-2.331881576672.60459448575-0.1938866154970.2918173816420.2551690118850.195776294975-0.175210785032-0.662702695899-0.3241391331540.3054211767120.2715925812180.239643897324-0.0272832003527-0.01527762452760.3480300337250.01577627833180.33246510768452.216575989278.045746208217.9219461434
26.850317557831.816351132891.145337530242.74398439297-0.3616138078642.21823911519-0.4648595964130.208620490511.794335627540.506294762442-0.406781506903-0.29648792531-1.156645546740.3873456978650.5237874632880.802487974454-0.167298186779-0.1707188042870.4421303727090.1515447724320.75598953455149.2591092196103.21147656411.0736434663
38.94198112855-0.05762807774495.362512137945.457912858941.525263403059.081728950640.0560074129628-0.1278387551830.1928836482250.01469967873140.163165362574-0.2155422208010.3731918246880.307874747792-0.1595587279080.291570568341-0.04140377594890.05636437213210.224914021030.03539239220130.37673594777629.267530170357.000652617735.146422083
41.76275034413-0.4903282193470.3660578896777.46714871194-0.627813872261.78845411612-0.0415158760794-0.1046765682120.165570540743-0.1463864864150.02640861654130.537057748373-0.265997314168-0.3109527183470.01683929433870.2897063504880.0629444106463-0.001659097823010.321769199149-0.02029067300880.28100095671926.611611209682.660315860831.3198133924
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resid 1:170)AA1 - 1701 - 170
22(chain A and resid 171:205)AA171 - 205171 - 205
33(chain B and resid 1:41)BF1 - 411 - 41
44(chain B and resid 42:205)BF42 - 20542 - 205

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