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- PDB-7qwd: CC-Type2-(Ug)4 -

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Basic information

Entry
Database: PDB / ID: 7qwd
TitleCC-Type2-(Ug)4
ComponentsCC-Type2-(Ug)4
KeywordsDE NOVO PROTEIN / aib / coiled coil / pentamer / 2-Aminoisobutyric acid
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 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-(Ug)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-(Ug)4
B: CC-Type2-(Ug)4
C: CC-Type2-(Ug)4
D: CC-Type2-(Ug)4
E: CC-Type2-(Ug)4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7496
Polymers16,6545
Non-polymers951
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-91 kcal/mol
Surface area7910 Å2
Unit cell
Length a, b, c (Å)34.108, 48.994, 89.376
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

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
1050B1 - 30
2050C1 - 30
1060B1 - 30
2060D1 - 30
1070B1 - 30
2070E1 - 30
1080C1 - 30
2080D1 - 30
1090C1 - 30
2090E1 - 30
10100D1 - 30
20100E1 - 30

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

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


Mass: 3330.839 Da / Num. of mol.: 5 / Mutation: W19BrPhe / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.24 Å3/Da / Density % sol: 45.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.5 mM peptide, 50 mM SPG, 25 % w/v PEG 1500, at pH 6.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.919 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 1.35→43 Å / Num. obs: 32660 / % possible obs: 97.52 % / Redundancy: 76.4 % / Biso Wilson estimate: 17.13 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.4586 / Rpim(I) all: 0.04872 / Rrim(I) all: 0.4612 / Net I/σ(I): 11.11
Reflection shellResolution: 1.354→1.403 Å / Redundancy: 47.5 % / Mean I/σ(I) obs: 0.25 / Num. unique obs: 2788 / CC1/2: 0.357 / CC star: 0.725 / Rpim(I) all: 1.529 / Rrim(I) all: 10.61 / % possible all: 85.21

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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: 1.35→43 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.98 / SU ML: 0.079 / SU R Cruickshank DPI: 0.0726 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 1614 5 %RANDOM
Rwork0.2144 ---
obs0.2161 30975 97.55 %-
Solvent computationIon probe radii: 1.2 Å / Shrinkage radii: 1.2 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.85 Å2 / Biso mean: 23.86 Å2 / Biso min: 13.25 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å2-0 Å2-0 Å2
2---1.91 Å20 Å2
3---3.01 Å2
Refinement stepCycle: final / Resolution: 1.35→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1123 0 5 66 1194
Biso mean--49.38 31.11 -
Num. residues----152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131134
X-RAY DIFFRACTIONr_bond_other_d0.0040.0171282
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.6341529
X-RAY DIFFRACTIONr_angle_other_deg7.9121.5882919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.175141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.23228.38731
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12315234
X-RAY DIFFRACTIONr_chiral_restr0.0770.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021170
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02182
X-RAY DIFFRACTIONr_rigid_bond_restr3.11732416
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A8000.14
12B8000.14
21A7860.13
22C7860.13
31A8150.12
32D8150.12
41A8310.11
42E8310.11
51B8020.14
52C8020.14
61B8250.13
62D8250.13
71B8250.12
72E8250.12
81C7980.12
82D7980.12
91C7990.12
92E7990.12
101D8340.11
102E8340.11
LS refinement shellResolution: 1.354→1.389 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 109 -
Rwork0.379 1838 -
all-1947 -
obs--80.96 %
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)
18.6451-2.8995-6.01853.69772.06058.4657-0.33010.4007-0.2607-0.16640.0510.14960.2025-0.44550.27910.0517-0.02380.00720.0463-0.00810.01315.9987-0.37452.9002
24.46361.1633-4.71271.8082-1.735710.7787-0.0928-0.26350.2060.16130.0437-0.2810.01310.21370.04910.05380.0364-0.03890.034-0.03350.089928.43125.32564.9437
39.46112.5364-8.49832.344-2.510612.2493-0.1859-0.0342-0.20980.0294-0.0605-0.38410.30360.12790.24640.03020.0177-0.00990.01860.01220.069429.3271-2.264559.6819
42.645-0.4477-4.50392.17380.439813.442-0.0368-0.05820.24820.09390.089-0.0476-0.2363-0.1795-0.05220.02290.0251-0.01940.0298-0.01820.048920.99847.359359.6213
57.0299-0.4482-6.20652.8070.02979.9107-0.17460.0732-0.3305-0.07930.0178-0.20650.4486-0.15650.15680.03080.00020.00740.01630.0020.041521.9582-4.912356.4122
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 101
2X-RAY DIFFRACTION2B0 - 30
3X-RAY DIFFRACTION3C0 - 30
4X-RAY DIFFRACTION4D1 - 30
5X-RAY DIFFRACTION5E1 - 30

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