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- PDB-4nkn: The Crystal Structure of the N-terminal domain of COMMD9 -

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Basic information

Entry
Database: PDB / ID: 4nkn
TitleThe Crystal Structure of the N-terminal domain of COMMD9
ComponentsCOMM domain-containing protein 9
KeywordsPROTEIN BINDING / Domain-swapped Trimer / All helical protein
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, helical N-terminal domain / COMM domain / COMM domain / COMM domain profile.
Similarity search - Domain/homology
COMM domain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.79 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
DepositionNov 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 2.0Aug 22, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_poly_seq_scheme / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.auth_seq_id / _atom_site.label_seq_id ..._atom_site.auth_seq_id / _atom_site.label_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 / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_struct_mod_residue.label_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end

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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
C: COMM domain-containing protein 9
D: COMM domain-containing protein 9
E: COMM domain-containing protein 9
F: COMM domain-containing protein 9


Theoretical massNumber of molelcules
Total (without water)81,3776
Polymers81,3776
Non-polymers00
Water1,63991
1
A: COMM domain-containing protein 9
B: COMM domain-containing protein 9
E: COMM domain-containing protein 9


Theoretical massNumber of molelcules
Total (without water)40,6893
Polymers40,6893
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9200 Å2
ΔGint-90 kcal/mol
Surface area16860 Å2
MethodPISA
2
C: COMM domain-containing protein 9
D: COMM domain-containing protein 9
F: COMM domain-containing protein 9


Theoretical massNumber of molelcules
Total (without water)40,6893
Polymers40,6893
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9720 Å2
ΔGint-90 kcal/mol
Surface area16840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.690, 79.757, 131.164
Angle α, β, γ (deg.)90.000, 90.610, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein
COMM domain-containing protein 9


Mass: 13562.909 Da / Num. of mol.: 6 / Fragment: N-terminal domain (UNP residues 1-116) / 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) / Strain (production host): BL21 / References: UniProt: Q9P000
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3 Å3/Da / Density % sol: 58.97 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 3350, 0.2M Mg Nitrate, pH 8.0, 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: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 18, 2010
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.79→39.46 Å / Num. all: 23054 / Num. obs: 23054 / % possible obs: 98.6 % / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Biso Wilson estimate: 60.38 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
2.79-2.943.70.6463.223049315891.6
8.81-39.463.80.04642.8539276699

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.1.27data scaling
PHASER2.5.3phasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→32.789 Å / FOM work R set: 0.7586 / SU ML: 0.38 / σ(F): 1.35 / Phase error: 30.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2495 1179 5.12 %
Rwork0.2097 21852 -
obs0.2117 23031 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.07 Å2 / Biso mean: 73.49 Å2 / Biso min: 20.33 Å2
Refinement stepCycle: LAST / Resolution: 2.79→32.789 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4880 0 0 91 4971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024939
X-RAY DIFFRACTIONf_angle_d0.3966695
X-RAY DIFFRACTIONf_chiral_restr0.015854
X-RAY DIFFRACTIONf_plane_restr0.001835
X-RAY DIFFRACTIONf_dihedral_angle_d11.0051706
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.79-2.91360.36871350.31572499263492
2.9136-3.06710.34061230.272527972920100
3.0671-3.25910.31361550.269227272882100
3.2591-3.51050.27681480.220627432891100
3.5105-3.86330.26911460.197627632909100
3.8633-4.42110.2271460.189827582904100
4.4211-5.56570.21791510.19527692920100
5.5657-32.79140.21551750.187827962971100

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