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- PDB-7kyx: Crystal structure of human CORO6 -

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Basic information

Entry
Database: PDB / ID: 7kyx
TitleCrystal structure of human CORO6
ComponentsCoronin-6
KeywordsSIGNALING PROTEIN / CORO6 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


actin filament organization / actin filament binding / cell migration
Similarity search - Function
Domain of unknown function DUF1899 / Coronin / Domain of unknown function (DUF1899) / Type of WD40 repeat / DUF1899 / DUF1900 / Anaphase-promoting complex subunit 4 WD40 domain / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. ...Domain of unknown function DUF1899 / Coronin / Domain of unknown function (DUF1899) / Type of WD40 repeat / DUF1899 / DUF1900 / Anaphase-promoting complex subunit 4 WD40 domain / WD domain, G-beta 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.63 Å
AuthorsZeng, H. / Dong, A. / Loppnau, P. / Hutchinson, A. / Seitova, A. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of human CORO6
Authors: Zeng, H. / Dong, A. / Loppnau, P. / Hutchinson, A. / Seitova, A. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L.
History
DepositionDec 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coronin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0227
Polymers45,7821
Non-polymers2406
Water4,486249
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.548, 80.764, 96.379
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Coronin-6 / Coronin-like protein E / Clipin-E


Mass: 45782.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CORO6, PP1009, PP1782, PP1881 / Plasmid: pFBOH-MHL / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6QEF8
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.15 Å3/Da / Density % sol: 42.75 % / Mosaicity: 0.521 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 30%(w/v)PEG550 MME,0.05M Magnesium Chloride, 0.1M Hepes pH7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 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: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 50011 / % possible obs: 99.5 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.032 / Rrim(I) all: 0.098 / Χ2: 1.086 / Net I/σ(I): 7.7 / Num. measured all: 454557
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.63-1.667.40.94223870.790.361.0120.56997.4
1.66-1.698.70.82424630.8670.2920.8760.56599.1
1.69-1.729.40.74924680.8980.2550.7920.57100
1.72-1.769.40.62324870.9320.2110.6590.57799.9
1.76-1.799.60.50924810.9510.1720.5380.59999.8
1.79-1.849.40.41824710.9650.1420.4430.61999.9
1.84-1.889.40.33324930.9790.1130.3530.652100
1.88-1.939.40.26624630.9840.0910.2820.701100
1.93-1.999.30.20924790.990.0720.2220.74399.8
1.99-2.059.20.17424990.9910.060.1840.78599.8
2.05-2.1390.14524900.9930.0510.1540.89199.8
2.13-2.218.80.12724820.9940.0450.1360.95499.5
2.21-2.317.80.11324620.9940.0420.1211.06498.5
2.31-2.439.30.10324960.9960.0360.1091.08799.8
2.43-2.599.90.09125010.9970.0310.0971.19199.8
2.59-2.799.80.08425300.9970.0280.0891.45599.9
2.79-3.079.60.07425180.9970.0250.0781.75199.7
3.07-3.519.20.06425710.9980.0220.0682.145100
3.51-4.428.10.05625340.9980.020.062.44398.6
4.42-5090.05127360.9980.0180.0542.21999.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.91 Å48.19 Å
Translation5.91 Å48.19 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B4E

2b4e


Resolution: 1.63→48.24 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.855 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2102 989 2 %RANDOM
Rwork0.1738 ---
obs0.1745 48957 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.62 Å2 / Biso mean: 20.465 Å2 / Biso min: 10.47 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å2-0 Å2-0 Å2
2---1.27 Å2-0 Å2
3---2.39 Å2
Refinement stepCycle: final / Resolution: 1.63→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3047 0 6 250 3303
Biso mean--29.25 31.4 -
Num. residues----397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133231
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172942
X-RAY DIFFRACTIONr_angle_refined_deg1.4491.6424428
X-RAY DIFFRACTIONr_angle_other_deg1.3441.5736836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4165418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.02822.171152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27115500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0681519
X-RAY DIFFRACTIONr_chiral_restr0.0690.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023680
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02665
LS refinement shellResolution: 1.63→1.669 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.308 65 -
Rwork0.267 3355 -
obs--93.42 %

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