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- PDB-9q6a: Crystal structure of octameric COMMD-like protein MBK5214510 from... -

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Basic information

Entry
Database: PDB / ID: 9q6a
TitleCrystal structure of octameric COMMD-like protein MBK5214510 from Flavobacteriaceae bacterium
ComponentsCOMMD-like protein MBK5214510
KeywordsUNKNOWN FUNCTION / COMMD / homooligomer
Biological speciesFlavobacteriaceae bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsCollins, B.M. / Healy, M.D. / Liu, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: To Be Published
Title: The prokaryotic origins of the COMMD protein family involved in eukaryotic membrane trafficking
Authors: Collins, B.M. / Healy, M.D. / Liu, M.
History
DepositionAug 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COMMD-like protein MBK5214510
B: COMMD-like protein MBK5214510


Theoretical massNumber of molelcules
Total (without water)55,5032
Polymers55,5032
Non-polymers00
Water27015
1
A: COMMD-like protein MBK5214510
B: COMMD-like protein MBK5214510

A: COMMD-like protein MBK5214510
B: COMMD-like protein MBK5214510

A: COMMD-like protein MBK5214510
B: COMMD-like protein MBK5214510

A: COMMD-like protein MBK5214510
B: COMMD-like protein MBK5214510


Theoretical massNumber of molelcules
Total (without water)222,0128
Polymers222,0128
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_755-x+2,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area36620 Å2
ΔGint-214 kcal/mol
Surface area82180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.343, 96.013, 115.614
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-305-

HOH

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Components

#1: Protein COMMD-like protein MBK5214510


Mass: 27751.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacteriaceae bacterium (bacteria) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 10% DMSO, 0.1 M sodium chloride, 25% PE5/4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.58→45.7 Å / Num. obs: 16103 / % possible obs: 98.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 57.72 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.022 / Net I/σ(I): 14.8
Reflection shellResolution: 2.58→2.66 Å / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1127 / CC1/2: 0.919 / Rpim(I) all: 0.146

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Processing

Software
NameVersionClassification
PHENIX1.21refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→45.67 Å / SU ML: 0.2868 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 30.5961
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2923 1617 10.04 %
Rwork0.2392 14486 -
obs0.2452 16103 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.23 Å2
Refinement stepCycle: LAST / Resolution: 2.58→45.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3477 0 0 15 3492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083513
X-RAY DIFFRACTIONf_angle_d1.47014705
X-RAY DIFFRACTIONf_chiral_restr0.1015537
X-RAY DIFFRACTIONf_plane_restr0.0096611
X-RAY DIFFRACTIONf_dihedral_angle_d22.7881373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.660.34091100.28811017X-RAY DIFFRACTION84.74
2.66-2.740.30311410.26381206X-RAY DIFFRACTION100
2.74-2.840.33251240.27751220X-RAY DIFFRACTION100
2.84-2.960.4481310.30921191X-RAY DIFFRACTION100
2.96-3.090.38431380.29421198X-RAY DIFFRACTION100
3.09-3.250.28551420.25811220X-RAY DIFFRACTION100
3.25-3.460.33531250.25861207X-RAY DIFFRACTION99.92
3.46-3.720.30981370.26631220X-RAY DIFFRACTION100
3.72-4.10.29691420.22081218X-RAY DIFFRACTION99.85
4.1-4.690.27561390.21451227X-RAY DIFFRACTION99.78
4.69-5.90.26811360.21791256X-RAY DIFFRACTION99.86
5.91-45.670.23581520.21651306X-RAY DIFFRACTION99.86

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