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- PDB-5h3g: Crystal Structure of Oryza sativa Acyl-CoA-Binding Protein 1 -

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Basic information

Entry
Database: PDB / ID: 5h3g
TitleCrystal Structure of Oryza sativa Acyl-CoA-Binding Protein 1
ComponentsPutative Acyl-CoA binding protein (ACBP)
KeywordsLIPID BINDING PROTEIN / Acyl-CoA-binding domain / Rice / Oryza sativa / ACB
Function / homology
Function and homology information


fatty-acyl-CoA binding / fatty acid metabolic process / cytosol
Similarity search - Function
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
Acyl-CoA-binding domain-containing protein 1
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsKong, G.K.W. / Chan, W.H.Y.
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

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Assembly

Deposited unit
A: Putative Acyl-CoA binding protein (ACBP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9618
Polymers10,4871
Non-polymers4757
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-7 kcal/mol
Surface area6060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.680, 59.680, 60.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-267-

HOH

21A-306-

HOH

31A-338-

HOH

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Components

#1: Protein Putative Acyl-CoA binding protein (ACBP) / Acyl-CoA-Binding Protein 1 / Os08g0162800 protein / cDNA clone:001-027-C02 / full insert sequence / ...Acyl-CoA-Binding Protein 1 / Os08g0162800 protein / cDNA clone:001-027-C02 / full insert sequence / cDNA clone:J033115J15


Mass: 10486.702 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: P0577B11.140, OJ9990_A01.106, Os08g0162800, OsJ_26146 / Production host: Escherichia coli (E. coli) / References: UniProt: Q84SC3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.98 Å3/Da / Density % sol: 58.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 3.8 / Details: 0.1M Citric acid, 2.6M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.5→39.4 Å / Num. obs: 20012 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 21.678 % / Biso Wilson estimate: 22.66 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.094 / Χ2: 0.966 / Net I/σ(I): 20.32 / Num. measured all: 429466
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.5-1.60.8862.6422.172449353733422.70494.5
1.6-1.70.961.63.3359782278427311.63898.1
1.7-1.80.9840.8395.7946446216421260.85998.2
1.8-1.90.9940.4838.9737837176817410.49598.5
1.9-20.9970.29612.8630622142614170.30399.4
2-2.50.9990.11127.6890646421341810.11499.2
2.5-30.9990.06444.7939606188018740.06599.7
3-40.9990.05456.1631685152215070.05599
4-50.9970.05457.99105765535290.05695.7
5-60.9990.05557.0148422492440.05798
6-100.9960.05651.0142242792560.05891.8
10-39.40.9960.05738.7475186640.0674.4

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Phasing

PhasingMethod: molecular replacement

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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: 2FJ9

2fj9


Resolution: 1.6→39.357 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2335 790 5.06 %
Rwork0.1906 --
obs0.1927 15626 92.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→39.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms724 0 27 139 890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005793
X-RAY DIFFRACTIONf_angle_d0.7711069
X-RAY DIFFRACTIONf_dihedral_angle_d14.078498
X-RAY DIFFRACTIONf_chiral_restr0.041115
X-RAY DIFFRACTIONf_plane_restr0.004136
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6003-1.70060.29081040.25381590X-RAY DIFFRACTION61
1.7006-1.83190.30121360.24362580X-RAY DIFFRACTION98
1.8319-2.01630.22191260.22362637X-RAY DIFFRACTION99
2.0163-2.3080.22971530.19062626X-RAY DIFFRACTION99
2.308-2.90770.23431340.18922677X-RAY DIFFRACTION100
2.9077-39.36910.21571370.16512726X-RAY DIFFRACTION97
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)
14.0419-1.69643.43342.7744-1.89885.4044-0.05530.39830.2046-0.067-0.0083-0.1945-0.41880.20720.00230.1518-0.04790.00020.26960.0080.125524.125623.71970.947
21.6680.25950.69711.0730.18632.04850.04880.055-0.07220.0573-0.0772-0.08940.1833-0.0830.03670.0206-0.00940.00730.255-0.03860.118724.09489.90366.0037
31.2835-0.99610.31313.4104-1.00930.97860.11410.2116-0.1028-0.5477-0.19810.24340.30590.00150.02840.1286-0.0007-0.03110.32-0.05240.130920.3983.901-0.583
41.43990.19470.69731.1144-0.29210.47890.12690.2812-0.02460.1603-0.03680.1535-0.0704-0.41980.0201-0.00170.01260.01210.3427-0.02370.146318.599418.60727.9084
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND (RESID -1:16 OR RESID 102:102 OR RESID 105:106) )A-1 - 16
2X-RAY DIFFRACTION1(CHAIN A AND (RESID -1:16 OR RESID 102:102 OR RESID 105:106) )A102
3X-RAY DIFFRACTION1(CHAIN A AND (RESID -1:16 OR RESID 102:102 OR RESID 105:106) )A105 - 106
4X-RAY DIFFRACTION2(CHAIN A AND (RESID 17:38 OR RESID 319:338) )A17 - 38
5X-RAY DIFFRACTION2(CHAIN A AND (RESID 17:38 OR RESID 319:338) )A319 - 338
6X-RAY DIFFRACTION3(CHAIN A AND (RESID 39:67 OR RESID 202:318) )A39 - 67
7X-RAY DIFFRACTION3(CHAIN A AND (RESID 39:67 OR RESID 202:318) )A202 - 318
8X-RAY DIFFRACTION4(CHAIN A AND (RESID 68:91 OR RESID 107:107) )A68 - 91
9X-RAY DIFFRACTION4(CHAIN A AND (RESID 68:91 OR RESID 107:107) )A107

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