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Basic information

Entry
Database: PDB / ID: 7qwa
TitleCC-Type2-(UgUe)4
ComponentsCC-Type2-(UgUe)4
KeywordsDE NOVO PROTEIN / aib / coiled coil / hexamer / 2-Aminoisobutyric acid
Function / homologyAMMONIUM ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.54 Å
AuthorsMartin, F.J.O. / Zieleniewski, F. / Dawson, W.M. / Woolfson, D.N.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
European Research Council (ERC)340764 United Kingdom
Engineering and Physical Sciences Research CouncilEP/G036764 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB R00661X 1 United Kingdom
CitationJournal: To Be Published
Title: CC-Type2-(UgUe)4
Authors: Martin, F.J.O. / Zieleniewski, F. / Dawson, W.M. / Woolfson, D.N.
History
DepositionJan 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CC-Type2-(UgUe)4
B: CC-Type2-(UgUe)4
C: CC-Type2-(UgUe)4
D: CC-Type2-(UgUe)4
E: CC-Type2-(UgUe)4
F: CC-Type2-(UgUe)4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4368
Polymers20,3226
Non-polymers1142
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9390 Å2
ΔGint-117 kcal/mol
Surface area9460 Å2
Unit cell
Length a, b, c (Å)123.965, 36.213, 45.491
Angle α, β, γ (deg.)90.000, 96.740, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-110-

HOH

21A-115-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 30
2010B1 - 30
1020A1 - 30
2020C1 - 30
1030A1 - 30
2030D1 - 30
1040A1 - 30
2040E1 - 30
1050A1 - 28
2050F1 - 28
1060B1 - 30
2060C1 - 30
1070B1 - 30
2070D1 - 30
1080B1 - 30
2080E1 - 30
1090B1 - 28
2090F1 - 28
10100C1 - 30
20100D1 - 30
10110C1 - 30
20110E1 - 30
10120C1 - 28
20120F1 - 28
10130D1 - 30
20130E1 - 30
10140D1 - 28
20140F1 - 28
10150E1 - 28
20150F1 - 28

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein/peptide
CC-Type2-(UgUe)4


Mass: 3386.947 Da / Num. of mol.: 6 / Mutation: W19BrPhe / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.49 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.5 mM pepide, 1.5 M Sodium chloride, 50 mM BIS-Tris at pH 5.5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.861 Å / Relative weight: 1
ReflectionResolution: 1.54→61.55 Å / Num. obs: 30032 / % possible obs: 99.74 % / Redundancy: 12.3 % / Biso Wilson estimate: 14.96 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.2066 / Rpim(I) all: 6156 / Rrim(I) all: 0.2158 / Net I/σ(I): 5.73
Reflection shellResolution: 1.54→1.595 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.243 / Mean I/σ(I) obs: 0.39 / Num. unique obs: 2966 / CC1/2: 0.591 / Rpim(I) all: 0.3692 / Rrim(I) all: 1.298 / % possible all: 99.66

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
Aimlessdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.54→61.55 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.888 / SU B: 4.561 / SU ML: 0.078 / SU R Cruickshank DPI: 0.0913 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2659 1532 5.1 %RANDOM
Rwork0.2265 ---
obs0.2285 28434 99.78 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 129.68 Å2 / Biso mean: 23.317 Å2 / Biso min: 5.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å2-0 Å2-0.15 Å2
2---0.02 Å20 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 1.54→61.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1383 0 6 97 1486
Biso mean--40.77 32.02 -
Num. residues----182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121387
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171570
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.6521925
X-RAY DIFFRACTIONr_angle_other_deg1.0011.583543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2995173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93328.07739
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02215280
X-RAY DIFFRACTIONr_chiral_restr0.0970.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021448
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02224
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A8310.12
12B8310.12
21A8350.15
22C8350.15
31A8260.16
32D8260.16
41A8240.13
42E8240.13
51A7790.17
52F7790.17
61B8410.14
62C8410.14
71B8230.14
72D8230.14
81B8080.15
82E8080.15
91B7970.16
92F7970.16
101C8150.18
102D8150.18
111C8080.15
112E8080.15
121C7890.17
122F7890.17
131D8030.18
132E8030.18
141D7860.17
142F7860.17
151E7750.15
152F7750.15
LS refinement shellResolution: 1.54→1.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 129 -
Rwork0.285 2099 -
all-2228 -
obs--99.91 %
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)
112.19993.00941.18792.52370.58541.6036-0.0201-0.44780.17030.1514-0.01060.01-0.01330.04730.03070.01880.01160.00040.0298-0.00310.007140.701121.9799-1.692
215.82130.50646.78351.7370.60454.56970.1289-0.0671-0.3485-0.015-0.0694-0.1320.25230.0811-0.05960.04450.00910.02120.01570.01240.028342.458814.7276-11.5488
315.29261.2377-0.62051.5210.19931.5402-0.0447-0.07090.1090.0055-0.0156-0.1016-0.1960.1320.06040.0539-0.0037-0.00790.02810.00980.014941.15427.2432-8.0337
411.6779-0.40612.63592.1142-0.33093.35630.020.4337-0.0568-0.0903-0.0925-0.12970.05020.35130.07250.0347-0.00340.00920.04460.00810.010642.29921.1855-17.2306
56.52131.59350.82173.2065-0.91792.2252-0.0293-0.27290.09650.0976-0.1812-0.07110.22250.09360.21050.04680.01050.02180.0280.01030.020941.86913.677-1.6097
66.117-1.48740.58282.885-0.54992.99430.17620.24-0.2428-0.0144-0.1639-0.2128-0.06450.3445-0.01230.0709-0.0396-0.04310.08420.02530.065945.51129.6037-17.9394
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 30
2X-RAY DIFFRACTION2B0 - 101
3X-RAY DIFFRACTION3C1 - 30
4X-RAY DIFFRACTION4D0 - 30
5X-RAY DIFFRACTION5E1 - 30
6X-RAY DIFFRACTION6F0 - 29

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