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- PDB-5tdq: Crystal Structure of the GOLD domain of ACBD3 -

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Basic information

Entry
Database: PDB / ID: 5tdq
TitleCrystal Structure of the GOLD domain of ACBD3
ComponentsGolgi resident protein GCP60
KeywordsTRANSPORT PROTEIN / beta barrel / GOLD domain
Function / homology
Function and homology information


fatty-acyl-CoA binding / steroid biosynthetic process / Golgi Associated Vesicle Biogenesis / protein kinase A regulatory subunit binding / Golgi membrane / Golgi apparatus / mitochondrion / membrane
Similarity search - Function
: / Golgi-dynamics membrane-trafficking / Acyl-CoA-binding protein, ACBP, conserved site / GOLD domain superfamily / Acyl-CoA-binding (ACB) domain signature. / GOLD domain / GOLD domain profile. / Acyl-CoA-binding protein, ACBP / Acyl-CoA binding protein superfamily / Acyl CoA binding protein ...: / Golgi-dynamics membrane-trafficking / Acyl-CoA-binding protein, ACBP, conserved site / GOLD domain superfamily / Acyl-CoA-binding (ACB) domain signature. / GOLD domain / GOLD domain profile. / Acyl-CoA-binding protein, ACBP / Acyl-CoA binding protein superfamily / Acyl CoA binding protein / Acyl-CoA-binding (ACB) domain profile. / FERM/acyl-CoA-binding protein superfamily
Similarity search - Domain/homology
Golgi resident protein GCP60
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.493 Å
AuthorsMcPhail, J.A. / Burke, J.E.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FRN 142393 Canada
CitationJournal: Structure / Year: 2017
Title: The Molecular Basis of Aichi Virus 3A Protein Activation of Phosphatidylinositol 4 Kinase III beta , PI4KB, through ACBD3.
Authors: McPhail, J.A. / Ottosen, E.H. / Jenkins, M.L. / Burke, J.E.
History
DepositionSep 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Jan 18, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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: Golgi resident protein GCP60


Theoretical massNumber of molelcules
Total (without water)19,2141
Polymers19,2141
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.510, 55.510, 140.150
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Golgi resident protein GCP60 / Acyl-CoA-binding domain-containing protein 3 / Golgi complex-associated protein 1 / GOCAP1 / Golgi ...Acyl-CoA-binding domain-containing protein 3 / Golgi complex-associated protein 1 / GOCAP1 / Golgi phosphoprotein 1 / GOLPH1 / PBR- and PKA-associated protein 7 / Peripheral benzodiazepine receptor-associated protein PAP7


Mass: 19214.143 Da / Num. of mol.: 1 / Fragment: GOLD domain, UNP residues 367-528
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACBD3, GCP60, GOCAP1, GOLPH1 / Plasmid: pOPTH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H3P7

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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: 3.24 Å3/Da / Density % sol: 62.08 %
Preparation: The low data completeness is due to the data being severely anisotropic, and the data was processed using the diffraction anisotropy server (https://services.mbi.ucla.edu/anisoscale/). ...Preparation: The low data completeness is due to the data being severely anisotropic, and the data was processed using the diffraction anisotropy server (https://services.mbi.ucla.edu/anisoscale/). Data was truncated and scaled with dimensions a*b*c*- 3.2,3.1,2.5. This is the reason for the low completeness in the resolution shells from 3.1 to 2.5. This processing was the only way to generate maps of high enough quality for model building
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 13% PEG 4000, 200 mM Ammonium Sulfate, 100 mM HEPES, 10% 2-propanol, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9797 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.04
ReflectionResolution: 2.493→46.72 Å / Num. obs: 5907 / % possible obs: 62.9 % / Redundancy: 4.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rsym value: 0.073 / Net I/σ(I): 8.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TLG

4tlg


Resolution: 2.493→46.717 Å / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.7
RfactorNum. reflection% reflection
Rfree0.2617 324 5.56 %
Rwork0.2383 --
obs0.2398 5830 62.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 116.67 Å2 / Biso mean: 49.2406 Å2 / Biso min: 11.71 Å2
Refinement stepCycle: final / Resolution: 2.493→46.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1028 0 0 0 1028
Num. residues----123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091059
X-RAY DIFFRACTIONf_angle_d1.1511438
X-RAY DIFFRACTIONf_chiral_restr0.048149
X-RAY DIFFRACTIONf_plane_restr0.004179
X-RAY DIFFRACTIONf_dihedral_angle_d15.372373
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4993-3.14820.3507640.31211140120425
3.1482-28.31680.25242550.234367462293
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)
10.0366-0.027-0.01210.0286-0.01180.04590.0107-0.03620.05820.0054-0.0070.0042-0.05690.05440.05060.1733-0.12280.00130.0837-0.05650.2427-26.97855.6276-15.2482
20.0088-0.0090.00620.0097-0.00590.00390.01480.0029-0.0139-0.0204-0.0038-0.00850.0149-0.00290.0250.3179-0.054-0.00160.0507-0.00630.3327-28.1416-12.2998-22.1607
30.0153-0.02520.00130.03530.00240.11010.0266-0.0078-0.03240.0126-0.02050.01880.0340.00620.0750.2628-0.01150.00570.04290.07910.2731-23.0494-15.4558-8.2851
40.0024-0.01520.00110.1178-0.02010.003-0.019-0.0122-0.0534-0.0093-0.0273-0.0743-0.05320.09010.04680.1615-0.1398-0.09320.17810.11750.2278-17.17570.4082-13.7859
50.1610.13720.10240.43240.0670.0684-0.1348-0.0484-0.16230.05470.02770.0805-0.03950.0722-0.12960.3965-0.2445-0.00160.27010.10140.2848-25.4786-4.2467-6.6439
60.1069-0.09470.07130.1346-0.00920.1021-0.0417-0.0496-0.0090.0037-0.0378-0.0284-0.09340.0385-0.17010.2423-0.0251-0.12740.31120.16970.3225-11.1944-0.164-5.3143
70.0002-0.0009-0.00090.00280.00350.004-0.0285-0.0041-0.019-0.0008-0.02730.0175-0.0690.0147-0.04420.35-0.0175-0.08350.05930.00740.3101-27.2142.9287-4.06
80.0097-0.00730.04340.006-0.03080.2179-0.04750.0403-0.13350.0298-0.02090.0597-0.08710.0487-0.23250.1367-0.18650.00130.15930.01460.2108-23.00210.6525-11.237
90.0150.0013-0.00470-0.00020.00170.00110.0132-0.0438-0.00930.0168-0.01450.0138-0.00210.00690.4117-0.11440.01960.12670.01220.4215-30.6438-14.28231.1412
100.0047-0.0040.01560.14150.04120.0772-0.11560.0469-0.07040.0698-0.0066-0.03390.14810.02080.02180.19010.02580.11470.24950.13650.3975-21.6263-6.937-16.0535
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 367 through 379 )A367 - 379
2X-RAY DIFFRACTION2chain 'A' and (resid 380 through 387 )A380 - 387
3X-RAY DIFFRACTION3chain 'A' and (resid 388 through 401 )A388 - 401
4X-RAY DIFFRACTION4chain 'A' and (resid 402 through 422 )A402 - 422
5X-RAY DIFFRACTION5chain 'A' and (resid 423 through 434 )A423 - 434
6X-RAY DIFFRACTION6chain 'A' and (resid 435 through 476 )A435 - 476
7X-RAY DIFFRACTION7chain 'A' and (resid 477 through 485 )A477 - 485
8X-RAY DIFFRACTION8chain 'A' and (resid 486 through 509 )A486 - 509
9X-RAY DIFFRACTION9chain 'A' and (resid 510 through 517 )A510 - 517
10X-RAY DIFFRACTION10chain 'A' and (resid 518 through 526 )A518 - 526

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