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- PDB-4cj6: Crystal structure of the complex of the Cellular Retinal Binding ... -

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Basic information

Entry
Database: PDB / ID: 4cj6
TitleCrystal structure of the complex of the Cellular Retinal Binding Protein Mutant R234W with 9-cis-retinal
ComponentsRETINALDEHYDE-BINDING PROTEIN 1
KeywordsISOMERASE / VISUAL CYCLE / 9-CIS-RETINAL
Function / homology
Function and homology information


The retinoid cycle in cones (daylight vision) / 11-cis retinal binding / vitamin A metabolic process / response to stimulus / phosphatidylinositol bisphosphate binding / retinol 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 / phosphatidylinositol bisphosphate binding / retinol 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 / Retinaldehyde-binding protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.896 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 19, 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)36,8282
Polymers36,5431
Non-polymers2841
Water5,549308
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.870, 57.918, 75.206
Angle α, β, γ (deg.)90.00, 122.88, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2232-

HOH

21A-2235-

HOH

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Components

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


Mass: 36543.168 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.2 Å3/Da / Density % sol: 44.26 % / 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: Nov 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→44.7 Å / Num. obs: 19606 / % possible obs: 98.4 % / Observed criterion σ(I): 3 / Redundancy: 4.6 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.48
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.12 / % possible all: 92.9

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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 3HX3

3hx3


Resolution: 1.896→44.745 Å / SU ML: 0.2 / σ(F): 2 / Phase error: 19.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1975 2502 10 %
Rwork0.1651 --
obs0.1683 25013 98.75 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.87 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso mean: 30.5 Å2
Baniso -1Baniso -2Baniso -3
1-7.6317 Å20 Å20.4498 Å2
2---2.9166 Å20 Å2
3----4.7151 Å2
Refinement stepCycle: LAST / Resolution: 1.896→44.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2047 0 21 308 2376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052115
X-RAY DIFFRACTIONf_angle_d0.8412855
X-RAY DIFFRACTIONf_dihedral_angle_d16.387795
X-RAY DIFFRACTIONf_chiral_restr0.055300
X-RAY DIFFRACTIONf_plane_restr0.003370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8958-1.93230.24721140.2381023X-RAY DIFFRACTION80
1.9323-1.97170.22031390.19721247X-RAY DIFFRACTION100
1.9717-2.01460.21071400.1831263X-RAY DIFFRACTION100
2.0146-2.06140.20871390.16921251X-RAY DIFFRACTION100
2.0614-2.1130.22561420.17231277X-RAY DIFFRACTION100
2.113-2.17010.21551390.16951252X-RAY DIFFRACTION100
2.1701-2.2340.22131380.16611241X-RAY DIFFRACTION100
2.234-2.30610.22021400.17251267X-RAY DIFFRACTION100
2.3061-2.38850.20091420.15921275X-RAY DIFFRACTION100
2.3885-2.48410.20281390.16411246X-RAY DIFFRACTION100
2.4841-2.59720.20871390.17731259X-RAY DIFFRACTION100
2.5972-2.73410.21871390.17111250X-RAY DIFFRACTION100
2.7341-2.90530.19811430.16991282X-RAY DIFFRACTION100
2.9053-3.12960.21351400.15711264X-RAY DIFFRACTION100
3.1296-3.44450.17671410.1471262X-RAY DIFFRACTION100
3.4445-3.94260.16981400.14141263X-RAY DIFFRACTION99
3.9426-4.96630.15681420.13691284X-RAY DIFFRACTION100
4.9663-44.75730.1961460.18251305X-RAY DIFFRACTION99
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)
10.28630.89360.9129-0.8070.1315.1607-0.15490.04520.3945-0.1084-0.09930.2382-0.8851-0.21170.29380.29810.1563-0.0870.1423-0.03560.2513-14.336931.94998.9848
24.3053-1.6226-0.85971.66170.17311.41950.15950.6543-0.69780.04530.03720.4534-0.2022-0.32-0.09980.0740.0922-0.00440.199-0.06520.212-17.186323.5813.8063
3-0.1262-0.30050.45070.50760.1641.27560.0261-0.0488-0.0071-0.031-0.07830.2215-0.1067-0.26870.01120.04750.00220.0270.11730.00280.0963-9.873316.429812.898
41.43530.13841.07791.1464-0.52421.99860.0902-0.0252-0.2170.21030.04690.03640.2393-0.0575-0.11830.1119-0.0340.01340.04030.0140.0915-3.4664.665520.559
50.4999-0.3420.4140.6442-0.07860.63060.02380.1314-0.00750.0678-0.0468-0.01390.02940.0910.00950.05420.00770.01210.074-0.00320.07443.30837.446415.0599
60.2191-0.19580.61171.1090.52790.3304-0.02990.03550.01730.2764-0.017-0.206-0.02320.16040.04060.0905-0.0247-0.02220.07430.01550.11189.1628.012524.3525
74.25060.0001-0.65050.665-0.64982.48570.764-0.57520.27720.2434-0.0010.146-0.2766-0.1711-0.58490.1901-0.12860.26760.14570.13190.0474-11.33593.334129.3839
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 57:85)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 86:98)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 99:143)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 144:185)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 186:255)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 256:295)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 296:306)

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