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- PDB-3flv: The crystal structure of human acyl-CoenzymeA binding domain cont... -

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Basic information

Entry
Database: PDB / ID: 3flv
TitleThe crystal structure of human acyl-CoenzymeA binding domain containing 5
ComponentsAcyl-CoA-binding domain-containing protein 5
KeywordsLIPID BINDING PROTEIN / acyl-coA binding / lipid binding / Structural Genomics / Structural Genomics Consortium / SGC / Lipid-binding / Membrane / Phosphoprotein / Transmembrane / Transport
Function / homology
Function and homology information


Peroxisomal lipid metabolism / Class I peroxisomal membrane protein import / fatty-acyl-CoA binding / pexophagy / peroxisomal membrane / RHOC GTPase cycle / RHOA GTPase cycle / fatty acid metabolic process / peroxisome / nucleoplasm ...Peroxisomal lipid metabolism / Class I peroxisomal membrane protein import / fatty-acyl-CoA binding / pexophagy / peroxisomal membrane / RHOC GTPase cycle / RHOA GTPase cycle / fatty acid metabolic process / peroxisome / nucleoplasm / membrane / cytosol / cytoplasm
Similarity search - Function
Acyl-CoA-binding domain-containing protein 5 / Acyl-CoA-binding protein, ACBP, conserved site / Acyl-CoA-binding (ACB) domain signature. / Acyl-CoA-binding protein, ACBP / Acyl-CoA binding protein superfamily / Acyl CoA binding protein / Acyl-CoA-binding (ACB) domain profile. / Acyl-CoA Binding Protein - #10 / Acyl-CoA Binding Protein / FERM/acyl-CoA-binding protein superfamily ...Acyl-CoA-binding domain-containing protein 5 / Acyl-CoA-binding protein, ACBP, conserved site / Acyl-CoA-binding (ACB) domain signature. / Acyl-CoA-binding protein, ACBP / Acyl-CoA binding protein superfamily / Acyl CoA binding protein / Acyl-CoA-binding (ACB) domain profile. / Acyl-CoA Binding Protein - #10 / Acyl-CoA Binding Protein / FERM/acyl-CoA-binding protein superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
COENZYME A / STEARIC ACID / Acyl-CoA-binding domain-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsUgochukwu, E. / Roos, A. / Yue, W.W. / Shafqat, N. / Salah, E. / Savitsky, P. / Muniz, J.R.C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. ...Ugochukwu, E. / Roos, A. / Yue, W.W. / Shafqat, N. / Salah, E. / Savitsky, P. / Muniz, J.R.C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The crystal structure of human acyl-Coenzyme A binding domain containing 5
Authors: Ugochukwu, E. / Roos, A. / Yue, W.W. / Shafqat, N. / Salah, E. / Savitsky, P. / Muniz, J.R.C. / von Delft, F. / Oppermann, U.
History
DepositionDec 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-CoA-binding domain-containing protein 5
B: Acyl-CoA-binding domain-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6679
Polymers27,8482
Non-polymers1,8207
Water3,045169
1
A: Acyl-CoA-binding domain-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9763
Polymers13,9241
Non-polymers1,0522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acyl-CoA-binding domain-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6916
Polymers13,9241
Non-polymers7685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)136.751, 34.064, 54.877
Angle α, β, γ (deg.)90.00, 102.16, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-IDEnd label comp-ID
11SERAA3 - 122
21SERBB3 - 122
12GLUAA30 - 849 - 27ARG
22GLUBB30 - 849 - 27ARG

NCS ensembles :
ID
1
2

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Components

#1: Protein Acyl-CoA-binding domain-containing protein 5


Mass: 13923.854 Da / Num. of mol.: 2 / Fragment: ACB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACBD5, KIAA1996 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: Q5T8D3
#2: Chemical ChemComp-STE / STEARIC ACID


Mass: 284.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36O2
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Mg(ac)2; 0.1M cacodylate pH 6.5; 20% PEG 8K, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99988 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 1.7→28.78 Å / Num. obs: 25392 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 1.6 / Num. unique all: 6153 / Rsym value: 0.539 / % possible all: 54.3

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.5.0055refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HBK

1hbk


Resolution: 1.7→28.78 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.277 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.117 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25926 1265 5 %RANDOM
Rwork0.21212 ---
all0.21458 24120 --
obs0.21458 24120 92.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.961 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20.23 Å2
2--1.43 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1419 0 82 169 1670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221561
X-RAY DIFFRACTIONr_bond_other_d0.0010.021068
X-RAY DIFFRACTIONr_angle_refined_deg1.5712.0052120
X-RAY DIFFRACTIONr_angle_other_deg0.9313.0062533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7735186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25423.66760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95515251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.439156
X-RAY DIFFRACTIONr_chiral_restr0.0990.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211662
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02312
X-RAY DIFFRACTIONr_mcbond_it5.3085916
X-RAY DIFFRACTIONr_mcbond_other2.8855363
X-RAY DIFFRACTIONr_mcangle_it6.88271468
X-RAY DIFFRACTIONr_scbond_it8.2719645
X-RAY DIFFRACTIONr_scangle_it10.30311648
Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNumberTypeRms dev position (Å)Weight position
1199medium positional0.230.5
22337medium positional0.210.5
1194loose positional0.775
22410loose positional0.515
1199medium thermal5.655
22337medium thermal4.435
1194loose thermal6.4110
22410loose thermal4.2310
LS refinement shellResolution: 1.7→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 46 -
Rwork0.333 947 -
obs--49.95 %
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)
13.38410.17020.28842.93080.49562.71710.037-0.0975-0.0750.06120.0032-0.00610.1504-0.1134-0.04030.08760.00130.01060.0782-0.00050.117334.15495.49189.5412
22.2589-1.31171.03951.1167-0.18240.9781-0.0183-0.2073-0.23450.16060.0086-0.10050.25010.10260.00980.1662-0.00330.00860.1712-0.00520.155841.220312.47421.1438
30.9707-0.6451-0.81461.11090.54460.93190.0014-0.12830.12540.1257-0.0140.0947-0.1009-0.12250.01260.1122-0.007-0.0040.11330.00870.121527.601921.087914.6772
46.1133-0.3173.45950.93920.00512.2509-0.0077-0.1971-0.05160.3848-0.0104-0.54360.07380.50490.01820.167-0.0010.01250.1596-0.00040.156845.101511.509211.1138
51.67970.23750.491.18490.23021.79130.0093-0.04290.02440.06430.0067-0.0697-0.02620.0475-0.01590.28920.00560.00640.29040.00640.2928-5.630931.76919.8114
61.9581-0.09090.741.6617-0.20782.6413-0.01140.20170.087-0.2371-0.02010.172-0.1088-0.18750.03160.1665-0.00380.01350.1647-0.00120.20196.904830.522417.6069
71.19490.7280.27750.44350.1690.0644-0.06510.1607-0.1013-0.10580.06250.12790.1338-0.140.00250.20670.00540.00030.20070.00110.20611.322231.311910.5382
81.82790.5017-0.87211.9808-2.17665.2889-0.023-0.2571-0.13340.24580.00790.09860.0875-0.06070.01510.30610.0003-0.00270.3081-0.00470.3133-0.335321.191624.5121
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 1822 - 37
2X-RAY DIFFRACTION2AA19 - 3438 - 53
3X-RAY DIFFRACTION3AA35 - 8154 - 100
4X-RAY DIFFRACTION4AA82 - 93101 - 112
5X-RAY DIFFRACTION5BB5 - 1924 - 38
6X-RAY DIFFRACTION6BB23 - 4742 - 66
7X-RAY DIFFRACTION7BB49 - 8368 - 102
8X-RAY DIFFRACTION8BB84 - 90103 - 109

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