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- PDB-1c44: STEROL CARRIER PROTEIN 2 (SCP2) FROM RABBIT -

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Basic information

Entry
Database: PDB / ID: 1c44
TitleSTEROL CARRIER PROTEIN 2 (SCP2) FROM RABBIT
ComponentsPROTEIN (STEROL CARRIER PROTEIN 2)
KeywordsLIPID BINDING PROTEIN / STEROL CARRIER PROTEIN / NON SPECIFIC LIPID TRANSFER PROTEIN / FATTY ACID BINDING / FATTY ACYL COA BINDING
Function / homology
Function and homology information


propanoyl-CoA C-acyltransferase activity / propionyl-CoA C2-trimethyltridecanoyltransferase activity / phosphatidylcholine transfer activity / acetyl-CoA C-myristoyltransferase activity / propanoyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / cholesterol transfer activity / bile acid metabolic process / lipid transport / fatty acid beta-oxidation ...propanoyl-CoA C-acyltransferase activity / propionyl-CoA C2-trimethyltridecanoyltransferase activity / phosphatidylcholine transfer activity / acetyl-CoA C-myristoyltransferase activity / propanoyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / cholesterol transfer activity / bile acid metabolic process / lipid transport / fatty acid beta-oxidation / peroxisomal matrix / peroxisome / lipid binding / mitochondrion
Similarity search - Function
SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, C-terminal ...SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Non-specific lipid-transfer protein
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.8 Å
AuthorsChoinowski, T. / Hauser, H. / Piontek, K.
Citation
Journal: Biochemistry / Year: 2000
Title: Structure of sterol carrier protein 2 at 1.8 A resolution reveals a hydrophobic tunnel suitable for lipid binding.
Authors: Choinowski, T. / Hauser, H. / Piontek, K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and initial X-ray analysis of rabbit mature sterol carrier protein 2
Authors: Choinowski, T. / Dyer, J.H. / Maderegger, B. / Winterhalter, K.P. / Hauser, H. / Piontek, K.
History
DepositionJul 2, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (STEROL CARRIER PROTEIN 2)


Theoretical massNumber of molelcules
Total (without water)13,2111
Polymers13,2111
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.486, 57.486, 86.487
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-124-

HOH

21A-125-

HOH

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Components

#1: Protein PROTEIN (STEROL CARRIER PROTEIN 2) / NON SPECIFIC LIPID BINDING PROTEIN


Mass: 13211.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Organ: LIVER / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O62742
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growpH: 6.5 / Details: AMMONIUM SULFATE, LITHIUM SULFATE, CITRATE PH=6.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
210 mMTris-HCl1drop
32.0 Mammonium sulfate1reservoir
4300 mMlithium sulfate1reservoir
5100 mMcitrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8345
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8345 Å / Relative weight: 1
ReflectionResolution: 1.8→18 Å / Num. obs: 14102 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rsym value: 4.9 / Net I/σ(I): 35.6
Reflection shellResolution: 1.8→1.82 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 5.6 / Rsym value: 36.2 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 104415 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameClassification
SOLVEphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 1.8→10 Å / σ(F): 2 / ESU R: 0.19
RfactorNum. reflection% reflectionSelection details
Rfree0.244 693 5 %RANDOM
Rwork0.175 ---
obs-13993 99.9 %-
Displacement parametersBiso mean: 30.2 Å2
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms965 0 0 140 1105
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0320.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.8682
X-RAY DIFFRACTIONp_mcangle_it4.6913
X-RAY DIFFRACTIONp_scbond_it4.432
X-RAY DIFFRACTIONp_scangle_it6.0043
X-RAY DIFFRACTIONp_plane_restr0.020.02
X-RAY DIFFRACTIONp_chiral_restr0.1460.14
X-RAY DIFFRACTIONp_singtor_nbd0.1970.3
X-RAY DIFFRACTIONp_multtor_nbd0.3010.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1990.3
X-RAY DIFFRACTIONp_planar_tor4.65
X-RAY DIFFRACTIONp_staggered_tor16.210
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor1715
X-RAY DIFFRACTIONp_special_tor

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