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- PDB-5h3i: Crystal Structure of Oryza sativa Acyl-CoA-Binding Protein 2 -

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Basic information

Entry
Database: PDB / ID: 5h3i
TitleCrystal Structure of Oryza sativa Acyl-CoA-Binding Protein 2
ComponentsPutative Acyl-CoA-binding protein
KeywordsLIPID BINDING PROTEIN / Acyl-CoA-binding domain
Function / homology
Function and homology information


fatty-acyl-CoA binding / fatty acid metabolic process / cytosol
Similarity search - Function
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
ACETATE ION / Acyl-CoA-binding domain-containing protein 2
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.302 Å
AuthorsKong, G.K.W. / Guo, Z.-H.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University of Hong Kong Hong Kong
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: The first plant acyl-CoA-binding protein structures: the close homologues OsACBP1 and OsACBP2 from rice
Authors: Guo, Z.-H. / Chan, W.H.Y. / Kong, G.K.W. / Hao, Q. / Chye, M.-L.
History
DepositionOct 24, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

Downloads & links

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Assembly

Deposited unit
A: Putative Acyl-CoA-binding protein
B: Putative Acyl-CoA-binding protein
C: Putative Acyl-CoA-binding protein
D: Putative Acyl-CoA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5289
Polymers42,9964
Non-polymers5325
Water6,161342
1
A: Putative Acyl-CoA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8672
Polymers10,7491
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5990 Å2
MethodPISA
2
B: Putative Acyl-CoA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0454
Polymers10,7491
Non-polymers2953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5980 Å2
MethodPISA
3
C: Putative Acyl-CoA-binding protein


Theoretical massNumber of molelcules
Total (without water)10,7491
Polymers10,7491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6080 Å2
MethodPISA
4
D: Putative Acyl-CoA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8672
Polymers10,7491
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-10 kcal/mol
Surface area6250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.570, 145.050, 25.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11D-243-

HOH

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Components

#1: Protein
Putative Acyl-CoA-binding protein / Acyl-CoA-Binding Protein 2 / Os06g0115300 protein / cDNA clone:001-004-B07 / full insert sequence


Mass: 10749.109 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: OSJNBa0019F11.14, P0541H01.36, Os06g0115300, OsJ_19900
Production host: Escherichia coli (E. coli) / References: UniProt: Q5VRM0
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 45.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate, 0.10 M MgCl2, 26%(w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979158 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 1, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979158 Å / Relative weight: 1
ReflectionResolution: 2.2→43.6 Å / Num. obs: 18120 / % possible obs: 89.5 % / Observed criterion σ(I): -3 / Redundancy: 6.84 % / Biso Wilson estimate: 31.53 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 9.71
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 6.76 % / Rmerge(I) obs: 1.422 / Mean I/σ(I) obs: 1.64 / % possible all: 58.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data collection
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DLN

5dln
PDB Unreleased entry


Resolution: 2.302→41.324 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 706 5.01 %
Rwork0.2227 --
obs0.2244 14101 79.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.302→41.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2907 0 36 342 3285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023005
X-RAY DIFFRACTIONf_angle_d0.3874051
X-RAY DIFFRACTIONf_dihedral_angle_d12.2991812
X-RAY DIFFRACTIONf_chiral_restr0.03436
X-RAY DIFFRACTIONf_plane_restr0.003509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3016-2.47930.2883800.25081364X-RAY DIFFRACTION42
2.4793-2.72880.31251350.28592257X-RAY DIFFRACTION69
2.7288-3.12350.27551750.25213316X-RAY DIFFRACTION100
3.1235-3.93480.24871440.19832881X-RAY DIFFRACTION85
3.9348-41.33050.22091720.20153577X-RAY DIFFRACTION99
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)
13.3925-1.2731-1.17056.03750.60231.0540.1360.27040.3851-0.37210.2461-1.1039-0.39240.1544-0.35470.375-0.08610.04130.3851-0.12760.3021-6.32832.9710.607
23.0725-0.45510.61512.4330.15432.09430.4445-0.1746-0.13640.21950.1085-0.46820.22780.2113-0.34560.1411-0.0087-0.05720.2019-0.06820.242-11.263720.710211.4759
33.89771.0408-0.19445.5137-0.04011.9716-0.11920.0363-0.5585-0.3992-0.0002-0.64060.40730.04230.16360.2194-0.03040.06340.21260.01920.1954-19.575315.82293.7126
44.8769-0.23611.34544.2733-0.24415.8167-0.1837-0.305-0.24490.32830.1884-0.4884-0.48070.51120.07520.1642-0.0025-0.00690.1744-0.010.19-11.29828.616618.6176
50.4471-0.59630.1990.7870.86262.5157-0.16270.32930.146-0.3063-0.09591.39451.1215-1.15620.31620.03-0.02020.06860.4767-0.06970.7614-42.428-6.609-2.5284
61.73110.3003-0.00383.5870.46832.26590.16520.10810.37890.3936-0.32290.7926-0.0584-0.41680.18120.1638-0.0112-0.00380.2219-0.00130.4162-38.01178.083-0.4723
73.09580.0839-0.9565.32121.04511.29560.03590.0350.6775-1.06350.190.7879-0.12910.0256-0.11950.3507-0.0171-0.10840.2206-0.00480.2466-29.934612.0079-8.8392
86.1123-0.7626-1.18044.40910.39843.8797-0.5673-0.4869-0.09070.83860.18350.49290.7202-0.21710.33970.2256-0.01180.06760.16360.00410.2346-37.8621-0.61365.5712
93.93222.77410.22274.4851-0.53643.3157-0.0829-0.94710.71360.63660.00650.4885-0.93630.0880.06080.37890.1475-0.02450.29370.07380.2284-34.685448.556911.3405
104.2726-0.1822-0.73234.49710.10964.05230.1286-0.2276-0.2219-0.20880.04840.74140.0777-0.4606-0.19050.19820.0057-0.04640.17720.0850.2362-38.54233.240716.2575
110.7904-0.08380.2391.5853-0.35653.18670.13960.0206-0.19060.2069-0.03850.3456-0.1101-0.2454-0.12810.1810.0066-0.03070.14450.02440.206-30.739228.563423.4254
124.70631.7291-1.98665.9867-0.10662.85050.12610.71480.2762-0.5137-0.07970.68970.337-0.1209-0.08520.22270.0356-0.05370.24030.00930.1618-37.2537.83987.3273
138.79343.72231.08034.34660.72143.34440.29280.0317-0.80120.3807-0.0849-0.40340.59760.0899-0.25960.23730.088-0.01890.1855-0.04930.2156-14.8886-21.1433-1.3392
146.470.8775-0.06363.2845-0.02123.15410.0126-0.08240.2329-0.23360.035-0.6144-0.03320.4523-0.0930.16950.01510.03090.2042-0.04220.2345-10.9543-6.13373.5973
153.4851-0.8856-0.26423.48770.14772.78810.0757-0.44650.6102-0.0459-0.1867-0.46170.05590.00070.08640.1795-0.01410.00630.12150.01020.1599-19.5323-1.325911.0223
167.8241-0.3014-2.08773.61560.13224.22730.50480.7005-0.0159-0.4212-0.484-0.9247-0.47770.15570.01720.19880.03060.070.1730.00520.3243-11.0144-10.6981-5.5374
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:16 )A2 - 16
2X-RAY DIFFRACTION2( CHAIN A AND RESID 17:38 )A17 - 38
3X-RAY DIFFRACTION3( CHAIN A AND RESID 39:67 )A39 - 67
4X-RAY DIFFRACTION4( CHAIN A AND RESID 68:91 )A68 - 91
5X-RAY DIFFRACTION5( CHAIN B AND RESID 2:16 )B2 - 16
6X-RAY DIFFRACTION6( CHAIN B AND RESID 17:38 )B17 - 38
7X-RAY DIFFRACTION7( CHAIN B AND RESID 39:67 )B39 - 67
8X-RAY DIFFRACTION8( CHAIN B AND RESID 68:90 )B68 - 90
9X-RAY DIFFRACTION9( CHAIN C AND RESID -3:16 )C-3 - 16
10X-RAY DIFFRACTION10( CHAIN C AND RESID 17:38 )C17 - 38
11X-RAY DIFFRACTION11( CHAIN C AND RESID 39:67 )C39 - 67
12X-RAY DIFFRACTION12( CHAIN C AND RESID 68:88 )C68 - 88
13X-RAY DIFFRACTION13( CHAIN D AND RESID -3:16 )D-3 - 16
14X-RAY DIFFRACTION14( CHAIN D AND RESID 17:38 )D17 - 38
15X-RAY DIFFRACTION15( CHAIN D AND RESID 39:67 )D39 - 67
16X-RAY DIFFRACTION16( CHAIN D AND RESID 68:90 )D68 - 90

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