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- PDB-4yd8: Bardet-Biedl Syndrome 9 Protein (aa1-407), Homo sapiens -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4yd8
TitleBardet-Biedl Syndrome 9 Protein (aa1-407), Homo sapiens
ComponentsProtein PTHB1
KeywordsPROTEIN TRANSPORT / BETA PROPELLER / STRUCTURAL PROTEIN / BBSOME / COAT COMPLEX
Function / homology
Function and homology information


BBSome / ciliary transition zone / BBSome-mediated cargo-targeting to cilium / protein localization to cilium / response to stimulus / ciliary membrane / pericentriolar material / fat cell differentiation / cilium assembly / centriolar satellite ...BBSome / ciliary transition zone / BBSome-mediated cargo-targeting to cilium / protein localization to cilium / response to stimulus / ciliary membrane / pericentriolar material / fat cell differentiation / cilium assembly / centriolar satellite / visual perception / cilium / protein transport / membrane / cytosol
Similarity search - Function
Parathyroid hormone-responsive B1 / PTHB1, N-terminal domain / PTHB1, C-terminal domain / PTHB1 N-terminus / PTHB1 C-terminus
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsKnockenhauer, K.E. / Schwartz, T.U.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM007287 United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Characterization of Bardet-Biedl Syndrome 9 Protein (BBS9).
Authors: Knockenhauer, K.E. / Schwartz, T.U.
History
DepositionFeb 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Aug 19, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein PTHB1
B: Protein PTHB1


Theoretical massNumber of molelcules
Total (without water)93,0362
Polymers93,0362
Non-polymers00
Water12,917717
1
A: Protein PTHB1


Theoretical massNumber of molelcules
Total (without water)46,5181
Polymers46,5181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein PTHB1


Theoretical massNumber of molelcules
Total (without water)46,5181
Polymers46,5181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.417, 81.878, 85.649
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-654-

HOH

21A-682-

HOH

31B-692-

HOH

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Components

#1: Protein Protein PTHB1 / Bardet-Biedl syndrome 9 protein / Parathyroid hormone-responsive B1 gene protein


Mass: 46517.836 Da / Num. of mol.: 2 / Fragment: UNP residues 1-407
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BBS9, PTHB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q3SYG4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 717 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 10% w/v PEG 4000, 0.1M tri-sodium citrate pH 6.1, and 0.15M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→44.7 Å / Num. obs: 171175 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rsym value: 0.09 / Net I/σ(I): 23.3
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.99 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIXdev_1951refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→36.936 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1997 2054 2.3 %Random Selection
Rwork0.169 ---
obs0.1697 171157 99.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→36.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5200 0 0 717 5917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085579
X-RAY DIFFRACTIONf_angle_d1.1197635
X-RAY DIFFRACTIONf_dihedral_angle_d13.182061
X-RAY DIFFRACTIONf_chiral_restr0.057882
X-RAY DIFFRACTIONf_plane_restr0.004977
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82060.33561340.29765882X-RAY DIFFRACTION97
1.8206-1.84360.27751390.35947X-RAY DIFFRACTION99
1.8436-1.86790.30131440.28156016X-RAY DIFFRACTION100
1.8679-1.89350.25271470.26285949X-RAY DIFFRACTION100
1.8935-1.92050.23571390.2526045X-RAY DIFFRACTION100
1.9205-1.94920.32241520.23845962X-RAY DIFFRACTION100
1.9492-1.97960.25561470.23475962X-RAY DIFFRACTION100
1.9796-2.01210.21121280.21696036X-RAY DIFFRACTION100
2.0121-2.04680.27881560.2055994X-RAY DIFFRACTION100
2.0468-2.0840.20891300.19716000X-RAY DIFFRACTION100
2.084-2.12410.24311560.19275935X-RAY DIFFRACTION100
2.1241-2.16740.22271350.18215987X-RAY DIFFRACTION100
2.1674-2.21460.21411300.18346012X-RAY DIFFRACTION100
2.2146-2.26610.23571430.17855986X-RAY DIFFRACTION100
2.2661-2.32270.20111530.17936015X-RAY DIFFRACTION100
2.3227-2.38550.1851430.17695950X-RAY DIFFRACTION100
2.3855-2.45570.21191410.17685986X-RAY DIFFRACTION100
2.4557-2.53490.20721430.16956018X-RAY DIFFRACTION100
2.5349-2.62550.19051420.16396021X-RAY DIFFRACTION100
2.6255-2.73060.19511420.1615993X-RAY DIFFRACTION100
2.7306-2.85480.20011390.16545982X-RAY DIFFRACTION100
2.8548-3.00530.32451400.17466002X-RAY DIFFRACTION100
3.0053-3.19350.16611480.16535986X-RAY DIFFRACTION100
3.1935-3.43990.18391370.15415912X-RAY DIFFRACTION99
3.4399-3.78580.16991320.14165897X-RAY DIFFRACTION98
3.7858-4.33280.16381440.12695961X-RAY DIFFRACTION99
4.3328-5.45610.13551290.12645879X-RAY DIFFRACTION98
5.4561-36.94420.20751280.18345901X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4567-0.53850.89332.1277-1.16943.47690.1154-0.1695-0.42180.0008-0.02350.06350.1731-0.1755-0.11050.16250.0198-0.01250.2419-0.00150.263636.741170.4489105.4835
22.9364-0.5952-0.95060.60450.021.33210.12960.4451-0.0066-0.0532-0.05260.1044-0.0199-0.1935-0.06170.22980.0917-0.0160.354-0.00820.22335.868983.680790.229
30.8004-0.15391.12941.1791-0.88232.71050.29810.93640.2724-0.5717-0.37240.3557-0.1771-0.3657-0.12590.39140.1681-0.01320.67650.09240.349546.0791.467477.622
42.78980.7048-0.87061.4622-1.06191.36770.1142-0.1336-0.19550.1047-0.1801-0.1228-0.09610.24310.04730.20840.0423-0.02570.3025-0.01390.2156.442276.1677101.4058
51.6775-0.02560.6822.3868-1.77673.4367-0.04810.1596-0.0523-0.37910.220.26540.3084-0.3212-0.14520.2776-0.0918-0.03460.21830.02160.24744.272357.983947.1116
61.43710.86790.10633.72070.15471.90650.1225-0.1524-0.30540.0901-0.0946-0.31910.19440.0372-0.07250.18060.0080.01480.1730.03960.243658.253.318865.3707
71.55630.70711.18421.80580.10661.0147-0.22620.35060.1333-0.28890.1550.0336-0.26470.30610.04190.287-0.09850.01390.30250.0150.222358.119973.644751.1529
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 84 )
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 200 )
3X-RAY DIFFRACTION3chain 'A' and (resid 201 through 236 )
4X-RAY DIFFRACTION4chain 'A' and (resid 237 through 369 )
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 84 )
6X-RAY DIFFRACTION6chain 'B' and (resid 85 through 236 )
7X-RAY DIFFRACTION7chain 'B' and (resid 237 through 369 )

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