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- PDB-6r5x: 8-bladed beta-propeller formed by four 2-bladed fragments -

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Basic information

Entry
Database: PDB / ID: 6r5x
Title8-bladed beta-propeller formed by four 2-bladed fragments
ComponentsWD-40 repeat protein
KeywordsUNKNOWN FUNCTION / Repeat Protein / Fragment Amplification / Protein Evolution / Protein Design
Function / homology
Function and homology information


protein polyubiquitination / metal ion binding / membrane
Similarity search - Function
Borrelia P83100 / : / Borrelia P83/100 protein / AAA-like domain / Quinoprotein alcohol dehydrogenase-like superfamily / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. ...Borrelia P83100 / : / Borrelia P83/100 protein / AAA-like domain / Quinoprotein alcohol dehydrogenase-like superfamily / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
WD-40 repeat protein
Similarity search - Component
Biological speciesNostoc punctiforme (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMartin, J. / Lupas, A.N. / Hartmann, M.D.
Citation
Journal: Elife / Year: 2019
Title: Structural diversity of oligomeric beta-propellers with different numbers of identical blades.
Authors: Afanasieva, E. / Chaudhuri, I. / Martin, J. / Hertle, E. / Ursinus, A. / Alva, V. / Hartmann, M.D. / Lupas, A.N.
#1: Journal: Elife / Year: 2019
Title: 8-bladed beta-propeller formed by four 2-bladed fragments
Authors: Hartmann, M.D.
History
DepositionMar 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WD-40 repeat protein
B: WD-40 repeat protein
C: WD-40 repeat protein
D: WD-40 repeat protein


Theoretical massNumber of molelcules
Total (without water)36,2164
Polymers36,2164
Non-polymers00
Water5,657314
1
A: WD-40 repeat protein
B: WD-40 repeat protein

A: WD-40 repeat protein
B: WD-40 repeat protein


Theoretical massNumber of molelcules
Total (without water)36,2164
Polymers36,2164
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5570 Å2
ΔGint-49 kcal/mol
Surface area13070 Å2
MethodPISA
2
C: WD-40 repeat protein
D: WD-40 repeat protein

C: WD-40 repeat protein
D: WD-40 repeat protein


Theoretical massNumber of molelcules
Total (without water)36,2164
Polymers36,2164
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5590 Å2
ΔGint-50 kcal/mol
Surface area13010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.235, 119.673, 84.153
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-181-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA6 - 818 - 83
21LEULEUBB6 - 818 - 83
12GLYGLYAA6 - 838 - 85
22GLYGLYCC6 - 838 - 85
13LEULEUAA6 - 818 - 83
23LEULEUDD6 - 818 - 83
14LEULEUBB6 - 818 - 83
24LEULEUCC6 - 818 - 83
15THRTHRBB6 - 828 - 84
25THRTHRDD6 - 828 - 84
16LEULEUCC6 - 818 - 83
26LEULEUDD6 - 818 - 83

NCS ensembles :
ID
6
1
2
3
4
5

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Components

#1: Protein
WD-40 repeat protein / 8-bladed beta-propeller formed by four 2-bladed fragments


Mass: 9053.927 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (bacteria) / Gene: Npun_R6612 / Production host: Escherichia coli (E. coli) / References: UniProt: B2J0I0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O

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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: 1.92 Å3/Da / Density % sol: 35.94 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium acetate 0.1 M TRIS.HCl pH 8.5 30 %(w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→32.3 Å / Num. obs: 31066 / % possible obs: 99.3 % / Redundancy: 4.31 % / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Net I/σ(I): 17.8
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 4.38 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.32 / Num. unique obs: 4842 / CC1/2: 0.861 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YMU

2ymu


Resolution: 1.7→32.3 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.769 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.125 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23857 1552 5 %RANDOM
Rwork0.19778 ---
obs0.19982 29426 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.908 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2---0.1 Å2-0 Å2
3---0.1 Å2
Refinement stepCycle: 1 / Resolution: 1.7→32.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2344 0 0 314 2658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022416
X-RAY DIFFRACTIONr_bond_other_d0.0070.022246
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.9093302
X-RAY DIFFRACTIONr_angle_other_deg1.44435154
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3165314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42325.769104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.44915380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.264158
X-RAY DIFFRACTIONr_chiral_restr0.10.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022818
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02574
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7751.2481244
X-RAY DIFFRACTIONr_mcbond_other0.7751.2471243
X-RAY DIFFRACTIONr_mcangle_it1.2571.8671550
X-RAY DIFFRACTIONr_mcangle_other1.2571.8671551
X-RAY DIFFRACTIONr_scbond_it1.0221.3911172
X-RAY DIFFRACTIONr_scbond_other1.0211.3911173
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6042.0381749
X-RAY DIFFRACTIONr_long_range_B_refined6.52112.1242782
X-RAY DIFFRACTIONr_long_range_B_other6.39911.0112654
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A38690.14
12B38690.14
21A41200.09
22C41200.09
31A38670.14
32D38670.14
41B38400.14
42C38400.14
51B42780.07
52D42780.07
61C38530.14
62D38530.14
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 114 -
Rwork0.379 2129 -
obs--99.64 %
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)
14.9490.99770.84172.6895-0.4374.40870.0846-0.2681-0.15320.1987-0.12740.04510.18670.08580.04280.0899-0.0140.0380.04460.02230.100916.699819.139532.1973
24.92891.55260.36035.05330.48793.57190.0802-0.0167-0.19680.15650.04790.4310.1686-0.1679-0.1280.015-0.0055-0.00910.00910.01150.121810.577618.750322.1969
33.6320.2257-0.6193.03982.44895.7802-0.02350.0931-0.3161-0.0649-0.08710.3250.1909-0.08060.11060.04680.0014-0.03170.0094-0.01190.09815.148819.777910.6694
44.17591.3359-1.27914.95751.40214.54040.04170.28850.0556-0.3621-0.00860.0276-0.10720.1283-0.03310.08540.0205-0.01750.0482-0.00850.054725.602518.51165.6347
53.3890.0267-1.54592.667-0.54754.23140.0651-0.18330.2190.1494-0.0079-0.0085-0.1681-0.0394-0.05730.0799-0.0024-0.03030.0483-0.01890.070411.3416-11.483531.7841
65.0351.04620.71933.6191-0.0444.21330.0201-0.04520.17750.0895-0.0581-0.3957-0.22690.21090.0380.0205-0.0122-0.00020.01250.00530.077317.0994-11.0821.5559
73.6150.94360.8313.1736-1.73366.1254-0.01240.10020.2239-0.075-0.0195-0.2174-0.23310.120.03190.03690.00690.01830.01520.00680.05312.1111-12.125110.3333
83.07711.20231.07044.6194-1.83273.5052-0.01360.1808-0.0605-0.21120.06330.07170.0244-0.0398-0.04980.05680.0137-0.00160.02840.00650.01571.4263-10.92445.6891
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 42
2X-RAY DIFFRACTION2A43 - 999
3X-RAY DIFFRACTION3B-10 - 42
4X-RAY DIFFRACTION4B43 - 999
5X-RAY DIFFRACTION5C-10 - 42
6X-RAY DIFFRACTION6C43 - 999
7X-RAY DIFFRACTION7D-10 - 42
8X-RAY DIFFRACTION8D43 - 999

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