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- PDB-2cx7: Crystal structure of sterol carrier protein 2 -

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Basic information

Entry
Database: PDB / ID: 2cx7
TitleCrystal structure of sterol carrier protein 2
ComponentsSterol carrier protein 2
KeywordsLIPID TRANSPORT / Sterol transfer / SCP-2 / RSGI / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative
Function / homologySCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / 2-Layer Sandwich / Alpha Beta / PHOSPHATE ION / SCP2 domain-containing protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsMurayama, K. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of sterol carrier protein 2
Authors: Murayama, K. / Shirouzu, M. / Yokoyama, S.
History
DepositionJun 28, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Sterol carrier protein 2
B: Sterol carrier protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4553
Polymers28,3602
Non-polymers951
Water5,585310
1
A: Sterol carrier protein 2


Theoretical massNumber of molelcules
Total (without water)14,1801
Polymers14,1801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sterol carrier protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2752
Polymers14,1801
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.485, 64.512, 70.656
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sterol carrier protein 2


Mass: 14179.916 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SL92
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.03 Å3/Da / Density % sol: 39.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30% PEG4000, 0.2M Ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9790, 0.9793, 0.964
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 18, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97931
30.9641
ReflectionResolution: 1.75→50 Å / Num. obs: 23346 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 19.9 Å2 / Rsym value: 0.062 / Net I/σ(I): 22.8
Reflection shellResolution: 1.75→1.81 Å / Rsym value: 0.298 / % possible all: 95

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→41.08 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1293868.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1127 4.8 %RANDOM
Rwork0.213 ---
obs0.213 23313 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.3422 Å2 / ksol: 0.357631 e/Å3
Displacement parametersBiso mean: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1-7.61 Å20 Å20 Å2
2---5.33 Å20 Å2
3----2.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.75→41.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1974 0 5 310 2289
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it2.531.5
X-RAY DIFFRACTIONc_mcangle_it3.292
X-RAY DIFFRACTIONc_scbond_it4.092
X-RAY DIFFRACTIONc_scangle_it5.462.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 179 4.9 %
Rwork0.243 3486 -
obs--93.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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