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- PDB-4oe9: The crystal structure of the n-terminal domain of COMMD9 -

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Basic information

Entry
Database: PDB / ID: 4oe9
TitleThe crystal structure of the n-terminal domain of COMMD9
ComponentsCOMM domain-containing protein 9
KeywordsPROTEIN BINDING / ALL ALPHA HELICAL
Function / homology
Function and homology information


sodium ion transport / cholesterol homeostasis / Neddylation / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / Golgi apparatus / extracellular region / nucleoplasm / cytosol
Similarity search - Function
COMM domain-containing protein 9 / : / COMMD9, N-terminal domain / COMM domain / COMM domain / COMM domain profile.
Similarity search - Domain/homology
CITRIC ACID / : / COMM domain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsHospenthal, M. / Celligoi, D. / Lott, J.S.
CitationJournal: Elife / Year: 2018
Title: Structural insights into the architecture and membrane interactions of the conserved COMMD proteins.
Authors: Healy, M.D. / Hospenthal, M.K. / Hall, R.J. / Chandra, M. / Chilton, M. / Tillu, V. / Chen, K.E. / Celligoi, D.J. / McDonald, F.J. / Cullen, P.J. / Lott, J.S. / Collins, B.M. / Ghai, R.
History
DepositionJan 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 2.0Aug 22, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_symm_contact / pdbx_validate_torsion / struct_conf / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_site_gen
Item: _atom_site.auth_seq_id / _citation.country ..._atom_site.auth_seq_id / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_site_gen.auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COMM domain-containing protein 9
B: COMM domain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7416
Polymers27,1262
Non-polymers6154
Water4,576254
1
A: COMM domain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9473
Polymers13,5631
Non-polymers3842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: COMM domain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7943
Polymers13,5631
Non-polymers2312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.490, 35.580, 54.300
Angle α, β, γ (deg.)104.03, 93.30, 91.11
Int Tables number1
Space group name H-MP1

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Components

#1: Protein COMM domain-containing protein 9


Mass: 13562.909 Da / Num. of mol.: 2 / Fragment: COMMD9, unp residues 1-117 / Mutation: L67M, I101M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COMMD9, HSPC166 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P000
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 1.96 Å3/Da / Density % sol: 37.38 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 28% mPEG 5000, 0.2M citric acid, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.979614, 0.976226
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 18, 2010
RadiationMonochromator: SILICON DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9796141
20.9762261
ReflectionRedundancy: 5.1 % / Number: 159700 / Rmerge(I) obs: 0.069 / D res high: 1.3 Å / D res low: 34.5 Å / Num. obs: 31076 / % possible obs: 61.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRedundancy
1.31.331.810.5721.8
7.1434.593.310.0515.2
ReflectionResolution: 1.55→32.74 Å / Num. all: 27029 / Num. obs: 27029 / % possible obs: 90.2 % / Observed criterion σ(I): 2
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 7.9 / Num. unique all: 3972 / % possible all: 51.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.1.27data scaling
SOLVEphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MAD / Resolution: 1.55→26.286 Å / FOM work R set: 0.907 / SU ML: 0.12 / σ(F): 1.98 / Phase error: 16.43 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1651 1367 5.06 %
Rwork0.1339 25644 -
obs0.1355 27011 90.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.29 Å2 / Biso mean: 13.11 Å2 / Biso min: 0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.55→26.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 40 254 2078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091883
X-RAY DIFFRACTIONf_angle_d1.1582559
X-RAY DIFFRACTIONf_chiral_restr0.04313
X-RAY DIFFRACTIONf_plane_restr0.005324
X-RAY DIFFRACTIONf_dihedral_angle_d18.042693
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5501-1.60550.1833780.14511566164455
1.6055-1.66970.21191060.15112098220474
1.6697-1.74570.19551480.14442700284896
1.7457-1.83770.19841530.13932721287496
1.8377-1.95280.16941300.13212764289496
1.9528-2.10350.13841520.12012754290697
2.1035-2.31510.15531510.11742772292397
2.3151-2.64990.15211570.12542747290497
2.6499-3.33750.1571340.13732782291697
3.3375-26.28950.16741580.14382740289897

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