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- PDB-8frf: Homodimeric designed loop protein RBL7_C2_3 -

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Basic information

Entry
Database: PDB / ID: 8frf
TitleHomodimeric designed loop protein RBL7_C2_3
ComponentsRBL7_C2_3
KeywordsDE NOVO PROTEIN / designed protein / helical repeat / homodimer
Function / homologyMALONATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RBL7_C2_3
B: RBL7_C2_3
C: RBL7_C2_3
D: RBL7_C2_3
E: RBL7_C2_3
F: RBL7_C2_3
G: RBL7_C2_3
H: RBL7_C2_3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,1939
Polymers187,0918
Non-polymers1021
Water68538
1
A: RBL7_C2_3
H: RBL7_C2_3


Theoretical massNumber of molelcules
Total (without water)46,7732
Polymers46,7732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RBL7_C2_3
D: RBL7_C2_3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8753
Polymers46,7732
Non-polymers1021
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: RBL7_C2_3

C: RBL7_C2_3


Theoretical massNumber of molelcules
Total (without water)46,7732
Polymers46,7732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x+1/2,-y,z+1/21
4
E: RBL7_C2_3
F: RBL7_C2_3


Theoretical massNumber of molelcules
Total (without water)46,7732
Polymers46,7732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.961, 117.644, 142.056
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 3 through 205)
d_2ens_1(chain "B" and resid 3 through 205)
d_3ens_1(chain "C" and resid 3 through 205)
d_4ens_1(chain "D" and resid 3 through 205)
d_5ens_1(chain "E" and resid 3 through 205)
d_6ens_1(chain "F" and resid 3 through 205)
d_7ens_1(chain "G" and resid 3 through 205)
d_8ens_1(chain "H" and resid 3 through 205)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1THRALAA2 - 204
d_21ens_1THRALAB2 - 204
d_31ens_1THRALAD2 - 204
d_41ens_1THRALAE1 - 203
d_51ens_1THRALAF2 - 204
d_61ens_1THRALAG2 - 204
d_71ens_1THRALAH1 - 203
d_81ens_1THRALAI1 - 203

NCS oper:
IDCodeMatrixVector
1given(0.651030175121, -0.744696842609, -0.146922849447), (-0.737745835479, -0.666328254134, 0.108340850914), (-0.178579935366, 0.0378585571728, -0.983196794306)2.84804005843, 26.1943026, -91.9317777671
2given(0.665974168716, 0.741762567972, -0.0791624870683), (0.734853400463, -0.670596920668, -0.101440868577), (-0.128331159233, 0.00938417531311, -0.991686972196)4.89161931119, -24.6140776298, -130.066319087
3given(-0.657651541411, 0.736991507706, 0.156006306441), (-0.744590052244, -0.667377031078, 0.0139123142811), (0.1143682831, -0.107011288932, 0.987658078417)53.7979298421, 22.3333348612, -20.8343016479
4given(-0.0933475208366, -0.995631812207, 0.00188012621092), (0.98722082804, -0.0928035657247, -0.129547423261), (0.129156018205, -0.0102368310375, 0.991571444855)30.5660158622, -33.3001732956, -39.3779979881
5given(-0.996415423492, 0.00314503856399, 0.0845364569852), (0.00955142113176, 0.99710116661, 0.0754853224081), (-0.084053995631, 0.0760221827963, -0.99355702078)59.8895337604, 3.91202381996, -113.190097421
6given(-0.762247827944, -0.647126807867, -0.0143228256402), (0.64313068229, -0.754666859687, -0.129849360366), (0.0732200402296, -0.108188841525, 0.991430280089)49.7889230388, -25.0465793359, 14.9469570428
7given(-0.0161400974716, 0.999100859957, 0.0392041947625), (0.997404785174, 0.0188394239839, -0.0694893561403), (-0.0701654599247, 0.0379808864737, -0.996812048731)31.1550764348, -32.0561702457, -77.8765074306

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Components

#1: Protein
RBL7_C2_3


Mass: 23386.354 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4 M sodium malonate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.99→43.97 Å / Num. obs: 38604 / % possible obs: 99.43 % / Redundancy: 6.7 % / Biso Wilson estimate: 67.39 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rpim(I) all: 0.1384 / Rrim(I) all: 0.3596 / Rsym value: 0.3313 / Net I/σ(I): 5.35
Reflection shellResolution: 2.99→3.097 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 0.66 / Num. unique obs: 3796 / CC1/2: 0.407 / CC star: 0.761 / Rpim(I) all: 1.25 / Rrim(I) all: 3.294 / Rsym value: 3.043 / % possible all: 96.63

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.99→43.97 Å / SU ML: 0.4817 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.4431
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2587 1988 5.17 %
Rwork0.2096 36436 -
obs0.2122 38424 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.82 Å2
Refinement stepCycle: LAST / Resolution: 2.99→43.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12331 0 7 38 12376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003712406
X-RAY DIFFRACTIONf_angle_d0.691916820
X-RAY DIFFRACTIONf_chiral_restr0.03982082
X-RAY DIFFRACTIONf_plane_restr0.00472262
X-RAY DIFFRACTIONf_dihedral_angle_d15.26284811
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.946387931626
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.827148479423
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.977297908246
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.893693113606
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.8498286582
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS0.685090368938
ens_1d_8AX-RAY DIFFRACTIONTorsion NCS0.902278231349
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.060.41481290.34612317X-RAY DIFFRACTION89.73
3.06-3.140.35591450.3252569X-RAY DIFFRACTION99.41
3.14-3.240.39451320.30622600X-RAY DIFFRACTION99.71
3.24-3.340.36831480.26692577X-RAY DIFFRACTION99.89
3.34-3.460.33381450.25032593X-RAY DIFFRACTION99.82
3.46-3.60.27981290.23072604X-RAY DIFFRACTION99.85
3.6-3.760.29731430.2232606X-RAY DIFFRACTION100
3.76-3.960.2571460.19132603X-RAY DIFFRACTION99.96
3.96-4.210.2341410.17342624X-RAY DIFFRACTION99.96
4.21-4.530.23381410.15312616X-RAY DIFFRACTION100
4.53-4.990.19991410.15882631X-RAY DIFFRACTION100
4.99-5.710.24811430.21062647X-RAY DIFFRACTION99.79
5.71-7.190.29541520.23672679X-RAY DIFFRACTION99.89
7.19-43.970.17961530.1812770X-RAY DIFFRACTION98.68
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)
13.45460243105-0.2796682760380.9292676127251.64832511617-0.4162330913741.093983633490.07694584838080.166577725190.000276085444854-0.4294911845990.05013103203820.4256291792140.0385408372904-0.0749470452029-0.1115223344910.507567264183-0.0249158928195-0.06918732295480.354503131767-0.0091728662710.3848011971221.87138147139-3.67734367868-47.8678286682
23.88736163829-1.99243319252-0.5991532610792.162833663090.612910468871.44851116903-0.2511813628450.1752910474260.08151622862480.23895372060.09459386514510.144060212634-0.03748672322440.1711217286660.1765119776740.442019128889-0.075215083373-0.04074671195090.3508975468980.05243926421740.3751345308913.827907480122.0861461238-45.3328649818
34.013122617680.448381644937-0.04041928143385.03681208577-1.223788263071.95979872573-0.06671375345-0.344695491102-0.495839355790.4164694653370.1969752036180.660252859070.102776881519-0.316405697371-0.1079426007990.3957390593260.03892118244570.05954822772640.523700021510.06228901605470.4141064683267.11221369749-15.7776867205-82.8914510793
42.480896497780.716244174985-0.854140994042.96639064885-1.278630035291.94937441209-0.1831974641870.1003816940330.153467389297-0.2966224009910.252125666654-0.370725395922-0.5344147155040.0147516713456-0.03336102316840.858044762720.04625468526890.02959285881830.565166653666-0.1044706267440.44955790653942.220388733622.7057913371-67.4133845901
51.730263249480.381490951958-0.2174158216615.156661798870.9866523844171.45425640109-0.01706372442110.0154813173201-0.249965733826-0.0924921898293-0.1527419445040.1007653159550.04487136133220.02468853643640.190268836130.354990933324-0.0164003352666-0.001275391926910.4043340357260.02323450310410.34874895778334.1618249585-24.7499165317-86.5435893639
64.384844934320.826210152520.9707245915933.917022728980.2622770951042.635423241660.152930598616-0.265730393182-0.1918408378110.4945264956410.17101730001-0.8661103456570.06598627409210.304172113282-0.2568057123080.5140133019620.0341235809107-0.07249482150880.506967952018-0.08699448651360.46858113522153.967817007-3.40822834454-66.0828991435
73.43364929643-0.798799917493-1.2634014513.52273598721-0.04655996175681.83965455058-0.0733174831817-0.211483530778-0.414892172031-0.1895495967160.0210940663748-0.4024795116010.1210859922720.4381145911640.03753861720440.309602377965-0.0544786264708-0.07998227304520.651838541033-0.01082449616970.45861819765251.4231661952-14.5144489116-31.8637754268
82.9195995383-0.4296361742360.4548094614514.29834624507-0.393110385011.655755061160.0534264231199-0.211382598335-0.647150012640.03378012508860.1299004886-0.1548240898380.2781166564560.139024161113-0.1650440420370.3579808043040.00192806276336-0.0463744069690.3594996644350.006124247368950.34971193239424.5375199281-26.394300234-30.7104233142
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 2 through 205)AA2 - 2051 - 204
22(chain 'B' and resid 2 through 205)BB2 - 2051 - 204
33(chain 'C' and resid 2 through 207)CD2 - 2071 - 206
44(chain 'D' and resid 3 through 206)DE3 - 2061 - 204
55(chain 'E' and resid 2 through 208)EF2 - 2081 - 207
66(chain 'F' and resid 2 through 206)FG2 - 2061 - 205
77(chain 'G' and resid 3 through 208)GH3 - 2081 - 206
88(chain 'H' and resid 3 through 214)HI3 - 2141 - 212

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