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- PDB-3qsz: Crystal Structure of the STAR-related lipid transfer protein (fra... -

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Basic information

Entry
Database: PDB / ID: 3qsz
TitleCrystal Structure of the STAR-related lipid transfer protein (fragment 25-204) from Xanthomonas axonopodis at the resolution 2.4A, Northeast Structural Genomics Consortium Target XaR342
ComponentsSTAR-related lipid transfer protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / PSI-biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / STAR domain
Function / homology
Function and homology information


START domain-containing protein / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / START domain-containing protein
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.389 Å
AuthorsKuzin, A.P. / Su, M. / Vorobiev, S.M. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A.P. / Su, M. / Vorobiev, S.M. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target XaR342
Authors: Kuzin, A.P. / Su, M. / Vorobiev, S.M. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionFeb 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STAR-related lipid transfer protein
B: STAR-related lipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1076
Polymers42,7952
Non-polymers3124
Water1,27971
1
A: STAR-related lipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6554
Polymers21,3981
Non-polymers2573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: STAR-related lipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4532
Polymers21,3981
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.115, 53.885, 70.266
Angle α, β, γ (deg.)90.00, 93.44, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-26-

ASP

Detailsmonomer,15.1 kD,94.0%

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Components

#1: Protein STAR-related lipid transfer protein


Mass: 21397.596 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria)
Gene: XAC0537 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PPZ5
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.74 Å3/Da / Density % sol: 55.11 %
Crystal growTemperature: 293 K / Method: macrobatch under oik / pH: 6
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:0.1M MnSO4, 0.1M MES, 18% (w/v) PEG 4K, macrobatch under oik, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Feb 16, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.389→30 Å / Num. obs: 35747 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 18.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 2.2 / % possible all: 98.2

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.389→29.762 Å / Occupancy max: 1 / Occupancy min: 0.96 / SU ML: 0.38 / σ(F): 0 / Phase error: 32.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2644 3311 10.02 %
Rwork0.2012 --
obs0.2075 33054 91.77 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.694 Å2 / ksol: 0.28 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.4584 Å20 Å2-14.4443 Å2
2--5.9095 Å2-0 Å2
3---3.5489 Å2
Refinement stepCycle: LAST / Resolution: 2.389→29.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2799 0 14 71 2884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082882
X-RAY DIFFRACTIONf_angle_d1.1263917
X-RAY DIFFRACTIONf_dihedral_angle_d13.6271053
X-RAY DIFFRACTIONf_chiral_restr0.077421
X-RAY DIFFRACTIONf_plane_restr0.005511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3891-2.42320.41661090.2965943X-RAY DIFFRACTION69
2.4232-2.45930.37481320.29431039X-RAY DIFFRACTION80
2.4593-2.49770.3208950.28061119X-RAY DIFFRACTION82
2.4977-2.53870.289980.27741158X-RAY DIFFRACTION85
2.5387-2.58240.36581710.2751127X-RAY DIFFRACTION85
2.5824-2.62930.32241260.27921186X-RAY DIFFRACTION87
2.6293-2.67990.35311330.27131194X-RAY DIFFRACTION88
2.6799-2.73450.35181430.26491167X-RAY DIFFRACTION89
2.7345-2.7940.36491080.23841281X-RAY DIFFRACTION89
2.794-2.85890.31291380.25841226X-RAY DIFFRACTION92
2.8589-2.93030.32391380.23221264X-RAY DIFFRACTION94
2.9303-3.00950.34211610.24391241X-RAY DIFFRACTION94
3.0095-3.0980.32371450.22941284X-RAY DIFFRACTION96
3.098-3.19790.25891280.21811340X-RAY DIFFRACTION96
3.1979-3.3120.33621530.21991284X-RAY DIFFRACTION97
3.312-3.44440.24871410.20911288X-RAY DIFFRACTION96
3.4444-3.60090.26911490.20711296X-RAY DIFFRACTION96
3.6009-3.79040.28861460.21841309X-RAY DIFFRACTION97
3.7904-4.02740.27111460.17441323X-RAY DIFFRACTION97
4.0274-4.33750.19691390.15511331X-RAY DIFFRACTION99
4.3375-4.77240.20781650.12451338X-RAY DIFFRACTION100
4.7724-5.45920.19931460.15081339X-RAY DIFFRACTION100
5.4592-6.86410.22151600.18761343X-RAY DIFFRACTION99
6.8641-29.76390.1971410.17381323X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 61.3163 Å / Origin y: 18.3165 Å / Origin z: 16.9244 Å
111213212223313233
T0.1281 Å20.0284 Å2-0.0399 Å2-0.1061 Å2-0.0171 Å2--0.1566 Å2
L1.0198 °20.1933 °20.7088 °2-0.7369 °20.0594 °2--0.6898 °2
S0.0508 Å °0.0575 Å °-0.0323 Å °-0.0899 Å °-0.0105 Å °0.0176 Å °0.0467 Å °0.0754 Å °-0.029 Å °
Refinement TLS groupSelection details: all

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