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- PDB-4xu5: Crystal structure of MvINS bound to a bromine-derived 14C Diacylg... -

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Basic information

Entry
Database: PDB / ID: 4xu5
TitleCrystal structure of MvINS bound to a bromine-derived 14C Diacylglycerol (DAG) at 2.1A resolution
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION
Function / homologylipid binding / identical protein binding / membrane / DECANE / Chem-LBR / INSIG protein homolog
Function and homology information
Biological speciesMycobacterium vanbaalenii PYR-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsRen, R.B. / Wu, J.P. / Yan, C.Y. / He, Y. / Yan, N.
CitationJournal: Science / Year: 2015
Title: PROTEIN STRUCTURE. Crystal structure of a mycobacterial Insig homolog provides insight into how these sensors monitor sterol levels
Authors: Ren, R. / Zhou, X. / He, Y. / Ke, M. / Wu, J. / Liu, X. / Yan, C. / Wu, Y. / Gong, X. / Lei, X. / Yan, S.F. / Radhakrishnan, A. / Yan, N.
History
DepositionJan 25, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1358
Polymers21,5531
Non-polymers1,5817
Water73941
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,40424
Polymers64,6593
Non-polymers4,74421
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
Buried area3960 Å2
ΔGint-42 kcal/mol
Surface area24000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.393, 83.393, 124.885
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Uncharacterized protein


Mass: 21553.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium vanbaalenii PYR-1 (bacteria)
Strain: PYR-1 / Gene: Mvan_1475 / Production host: Escherichia coli (E. coli) / References: UniProt: A1T557
#2: Chemical ChemComp-LBR / (2S)-1-[(13-bromotridecanoyl)oxy]-3-hydroxypropan-2-yl tetradecanoate


Mass: 577.675 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H57BrO5
#3: Chemical
ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H22
#4: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 3.88 Å3/Da / Density % sol: 68.28 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9185 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9185 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 37844 / % possible obs: 99.9 % / Redundancy: 4.1 % / Net I/σ(I): 20

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.1→34.689 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.59 / Phase error: 19.76 / Stereochemistry target values: ML
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2251 1947 5.21 %
Rwork0.1996 --
obs0.2008 37346 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→34.689 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1369 0 106 41 1516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141507
X-RAY DIFFRACTIONf_angle_d1.6772043
X-RAY DIFFRACTIONf_dihedral_angle_d15.321524
X-RAY DIFFRACTIONf_chiral_restr0.335249
X-RAY DIFFRACTIONf_plane_restr0.006244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0985-2.1510.22351730.24462451X-RAY DIFFRACTION97
2.151-2.20910.28781320.22632496X-RAY DIFFRACTION97
2.2091-2.27410.21281740.22412545X-RAY DIFFRACTION98
2.2741-2.34750.22551150.20742551X-RAY DIFFRACTION99
2.3475-2.43140.20471400.20622481X-RAY DIFFRACTION99
2.4314-2.52870.26871390.18852610X-RAY DIFFRACTION99
2.5287-2.64380.19391460.1812444X-RAY DIFFRACTION99
2.6438-2.78310.18151620.17382590X-RAY DIFFRACTION99
2.7831-2.95740.24081460.17722505X-RAY DIFFRACTION99
2.9574-3.18560.19391280.19582592X-RAY DIFFRACTION99
3.1856-3.50590.24491310.18642534X-RAY DIFFRACTION99
3.5059-4.01260.2111380.19192541X-RAY DIFFRACTION99
4.0126-5.05290.25231230.20532517X-RAY DIFFRACTION99
5.0529-34.69390.2251000.21452542X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 80.7332 Å / Origin y: 30.5871 Å / Origin z: -8.9642 Å
111213212223313233
T0.3109 Å2-0.0064 Å2-0.0625 Å2-0.2356 Å20.0011 Å2--0.2774 Å2
L1.2852 °20.1773 °2-0.1795 °2-1.0789 °2-0.1515 °2--0.76 °2
S0.0277 Å °0.0047 Å °-0.1456 Å °0.0317 Å °0.0464 Å °-0.029 Å °0.1609 Å °0.0424 Å °-0.071 Å °
Refinement TLS groupSelection details: all

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