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- PDB-1j7x: CRYSTAL STRUCTURE OF A FUNCTIONAL UNIT OF INTERPHOTORECEPTOR RETI... -

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Basic information

Entry
Database: PDB / ID: 1j7x
TitleCRYSTAL STRUCTURE OF A FUNCTIONAL UNIT OF INTERPHOTORECEPTOR RETINOID-BINDING PROTEIN (IRBP)
ComponentsINTERPHOTORECEPTOR RETINOID-BINDING PROTEIN
KeywordsTRANSPORT PROTEIN / beta beta alpha spiral
Function / homology
Function and homology information


interphotoreceptor matrix / retinoid binding / visual perception / serine-type peptidase activity / cytoplasm
Similarity search - Function
: / Transcription Regulator spoIIAA - #44 / tail specific protease / Tail specific protease / Peptidase family S41 / Transcription Regulator spoIIAA / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex ...: / Transcription Regulator spoIIAA - #44 / tail specific protease / Tail specific protease / Peptidase family S41 / Transcription Regulator spoIIAA / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Retinol-binding protein 3
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsLoew, A. / Gonzalez-Fernandez, F.
CitationJournal: Structure / Year: 2002
Title: Crystal structure of the functional unit of interphotoreceptor retinoid binding protein.
Authors: Loew, A. / Gonzalez-Fernandez, F.
History
DepositionMay 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INTERPHOTORECEPTOR RETINOID-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)33,5101
Polymers33,5101
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.144, 65.756, 68.174
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein INTERPHOTORECEPTOR RETINOID-BINDING PROTEIN / IRBP


Mass: 33510.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pThioHis / Production host: Escherichia coli (E. coli) / Strain (production host): TOP 10 / References: UniProt: Q7SZI7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, TRIS, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMTris-HCl1reservoirpH8.5
2200 mM1reservoirMgCl2
320 %PEG80001reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS F210.9777,0.9790,0.9793
SYNCHROTRONCHESS A120.909
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDOct 10, 2000
ADSC QUANTUM 42CCDJun 10, 2000
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED Si(111)MADMx-ray1
2Si 111Mx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97771
20.9791
30.97931
40.9091
ReflectionResolution: 1.8→19.25 Å / Num. all: 26579 / Num. obs: 26579 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 34.56 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 8.4
Reflection shellResolution: 1.8→1.846 Å / Redundancy: 2 % / Rmerge(I) obs: 0.495 / % possible all: 99.8
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 99.8 % / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
SOLVEV1.17phasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→19.25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1353 5 %RANDOM
Rwork0.205 ---
all0.2069 26579 --
obs0.2069 25564 99.99 %-
Displacement parametersBiso mean: 27.3 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 0 145 2485
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0321.777
X-RAY DIFFRACTIONp_angle_deg1.9462.899
X-RAY DIFFRACTIONp_mcangle_it2.8994.244
X-RAY DIFFRACTIONp_mcbond_it1.7775.93
LS refinement shellResolution: 1.8→1.84 Å
RfactorNum. reflection
Rfree0.345 103
Rwork0.299 -
obs-1832
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.206 / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.005
X-RAY DIFFRACTIONp_angle_deg1.234

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