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- PDB-4ciz: Crystal structure of the complex of the Cellular Retinal Binding ... -

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Basic information

Entry
Database: PDB / ID: 4ciz
TitleCrystal structure of the complex of the Cellular Retinal Binding Protein with 9-cis-retinal
ComponentsRETINALDEHYDE-BINDING PROTEIN 1
KeywordsISOMERASE / RETINALDEHYDE BINDING PROTEIN / VISUAL CYCLE / 9-CIS-RETINAL / CELLULAR RETINAL BINDING PROTEIN
Function / homology
Function and homology information


The retinoid cycle in cones (daylight vision) / 11-cis retinal binding / vitamin A metabolic process / response to stimulus / retinol binding / phosphatidylinositol bisphosphate binding / Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / visual perception / cell body ...The retinoid cycle in cones (daylight vision) / 11-cis retinal binding / vitamin A metabolic process / response to stimulus / retinol binding / phosphatidylinositol bisphosphate binding / Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / visual perception / cell body / centrosome / nucleoplasm / cytosol
Similarity search - Function
N-terminal domain of phosphatidylinositol transfer protein sec14p / Phosphatidylinositol Transfer Protein Sec14p / CRAL-TRIO lipid binding domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) ...N-terminal domain of phosphatidylinositol transfer protein sec14p / Phosphatidylinositol Transfer Protein Sec14p / CRAL-TRIO lipid binding domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RETINAL / L(+)-TARTARIC ACID / Retinaldehyde-binding protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.403 Å
AuthorsBolze, C.S. / Helbling, R.E. / Owen, R.L. / Pearson, A.R. / Pompidor, G. / Dworkowski, F. / Fuchs, M.R. / Furrer, J. / Golczak, M. / Palczewski, K. ...Bolze, C.S. / Helbling, R.E. / Owen, R.L. / Pearson, A.R. / Pompidor, G. / Dworkowski, F. / Fuchs, M.R. / Furrer, J. / Golczak, M. / Palczewski, K. / Cascella, M. / Stocker, A.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Human Cellular Retinaldehyde-Binding Protein Has Secondary Thermal 9-Cis-Retinal Isomerase Activity.
Authors: Bolze, C.S. / Helbling, R.E. / Owen, R.L. / Pearson, A.R. / Pompidor, G. / Dworkowski, F. / Fuchs, M.R. / Furrer, J. / Golczak, M. / Palczewski, K. / Cascella, M. / Stocker, A.
History
DepositionDec 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: RETINALDEHYDE-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9493
Polymers36,5141
Non-polymers4352
Water724
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.556, 70.556, 299.747
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein RETINALDEHYDE-BINDING PROTEIN 1 / CELLULAR RETINALDEHYDE-BINDING PROTEIN / CELLULAR RETINALDEHYDE BINDING PROTEIN


Mass: 36514.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P12271
#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsRETINAL (RET): 9-CIS-RETINAL

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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: 2.95 Å3/Da / Density % sol: 58.29 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 14, 2011 / Details: M1
RadiationMonochromator: DCCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→47.36 Å / Num. obs: 6770 / % possible obs: 99.6 % / Observed criterion σ(I): 2.74 / Redundancy: 13 % / Biso Wilson estimate: 115.51 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 22.68
Reflection shellResolution: 3.4→3.61 Å / Redundancy: 12.7 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 2.74 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HY5
Resolution: 3.403→47.356 Å / SU ML: 0.55 / σ(F): 1.99 / Phase error: 30.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2649 576 5 %
Rwork0.234 --
obs0.2356 6704 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 126.805 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso mean: 102.69 Å2
Baniso -1Baniso -2Baniso -3
1-8.8611 Å20 Å20 Å2
2--8.8611 Å20 Å2
3----17.7223 Å2
Refinement stepCycle: LAST / Resolution: 3.403→47.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2317 0 24 4 2345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032391
X-RAY DIFFRACTIONf_angle_d0.5673227
X-RAY DIFFRACTIONf_dihedral_angle_d10.84923
X-RAY DIFFRACTIONf_chiral_restr0.042340
X-RAY DIFFRACTIONf_plane_restr0.003422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4026-3.74490.44241420.35282694X-RAY DIFFRACTION99
3.7449-4.28640.24241430.2732696X-RAY DIFFRACTION100
4.2864-5.39930.23211480.20872739X-RAY DIFFRACTION100
5.3993-47.36040.25091430.20552718X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
17.8860.9865-0.55614.59011.52539.62210.3-0.31770.05680.8084-0.1019-0.4012-0.8162-0.9783-0.24582.1994-0.4736-0.04111.9958-0.55621.4079-5.591837.601727.3286
22.0519-3.47123.11376.97285.57382.0071.5039-1.24441.46861.26910.8299-0.9692-1.32340.0174-2.28952.9085-0.45930.16051.9403-0.32181.6348-11.841530.791136.6263
38.34-4.271.32939.6397-2.87572.18930.8681-2.2281-0.8490.6311-1.38260.43180.02170.91340.53861.3719-0.657-0.2953.06480.35081.622-0.118911.713542.8589
42.93721.298-1.28299.46535.89437.75460.033-0.2465-0.0152-0.38990.2387-1.0539-0.41961.4365-0.46231.5295-1.0821-0.32772.61470.36131.6536.567916.80436.9401
51.23141.7657-0.63644.6137-0.48755.18210.4016-1.319-1.12-0.0972-1.2266-1.6078-1.37171.70760.72751.4786-0.5713-0.32211.64640.19941.67753.560214.780525.7713
64.8858-1.4558-0.999110.01851.5019.261-0.2844-0.13940.5531-1.0291-1.0833-0.9428-1.7491.17071.19571.547-0.6263-0.28591.36850.02451.3942.158423.410413.0419
73.254-0.0841-1.1448.26161.34765.73620.2582-0.1726-0.3769-1.4528-1.2033-0.7484-1.31961.2170.581.8375-0.7763-0.18631.1086-0.07051.1457-5.078618.198412.8337
82.89042.9399-0.4119.8943-2.82372.6632-0.0025-0.12890.76310.2197-0.32070.6423-1.5326-0.23290.27592.0082-0.3464-0.29660.9124-0.16831.4094-10.764927.553711.1747
92.70050.7439-0.37944.78880.714.1568-0.9161-0.1066-0.2602-0.0904-0.9511-0.63080.14891.08751.07443.3329-2.85540.29411.1558-0.20761.962410.097932.340315.3244
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 23:41)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 42:55)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 56:85)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 86:98)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 99:143)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 144:185)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 186:255)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 256:295)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 296:306)

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