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- PDB-4xu4: Crystal structure of a mycobacterial Insig homolog MvINS from Myc... -

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Basic information

Entry
Database: PDB / ID: 4xu4
TitleCrystal structure of a mycobacterial Insig homolog MvINS from Mycobacterium vanbaalenii at 1.9A resolution
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION
Function / homologylipid binding / membrane / identical protein binding / DECYLAMINE-N,N-DIMETHYL-N-OXIDE / INSIG protein homolog
Function and homology information
Biological speciesMycobacterium vanbaalenii PYR-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.901 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 1.1Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Mar 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)22,8756
Polymers21,5531
Non-polymers1,3225
Water1,76598
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,62518
Polymers64,6593
Non-polymers3,96615
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 area10460 Å2
ΔGint25 kcal/mol
Surface area23750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.498, 85.498, 125.851
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: Sugar ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-DDQ / DECYLAMINE-N,N-DIMETHYL-N-OXIDE


Mass: 201.349 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H27NO
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 4.11 Å3/Da / Density % sol: 70.05 %
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: SPring-8 / Beamline: BL41XU / Wavelength: 1.008 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: Dec 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 26815 / % possible obs: 100 % / Redundancy: 3.6 % / Net I/σ(I): 22.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.901→20.268 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 17.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2029 1350 5.03 %
Rwork0.1855 --
obs0.1863 26813 99.44 %
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.8055 Å2-0 Å2-0 Å2
2--2.8055 Å2-0 Å2
3----5.8132 Å2
Refinement stepCycle: LAST / Resolution: 1.901→20.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1368 0 77 98 1543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061489
X-RAY DIFFRACTIONf_angle_d1.032036
X-RAY DIFFRACTIONf_dihedral_angle_d13.249520
X-RAY DIFFRACTIONf_chiral_restr0.06256
X-RAY DIFFRACTIONf_plane_restr0.006244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9007-1.96860.24081370.2112536X-RAY DIFFRACTION100
1.9686-2.04740.24341320.18282555X-RAY DIFFRACTION100
2.0474-2.14040.17691340.17512566X-RAY DIFFRACTION100
2.1404-2.25320.20041350.16572560X-RAY DIFFRACTION100
2.2532-2.39410.16851380.16252566X-RAY DIFFRACTION100
2.3941-2.57860.18581520.15912556X-RAY DIFFRACTION100
2.5786-2.83750.1981350.15582550X-RAY DIFFRACTION100
2.8375-3.24670.1871460.18122562X-RAY DIFFRACTION100
3.2467-4.08490.20461220.18792577X-RAY DIFFRACTION100
4.0849-20.2690.22371190.21372435X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 71.5725 Å / Origin y: 60.9162 Å / Origin z: -11.6019 Å
111213212223313233
T0.2422 Å20.0345 Å20.0235 Å2-0.2731 Å20.0574 Å2--0.2912 Å2
L1.1933 °20.0009 °2-0.178 °2-1.2593 °20.213 °2--1.2864 °2
S0.0363 Å °-0.0406 Å °0.0785 Å °-0.0301 Å °0.0604 Å °0.189 Å °-0.0629 Å °-0.1507 Å °-0.0917 Å °
Refinement TLS groupSelection details: all

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