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- PDB-6at8: 1.1 Angstrom Resolution Structure of Human Cellular Retinol-Bindi... -

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Basic information

Entry
Database: PDB / ID: 6at8
Title1.1 Angstrom Resolution Structure of Human Cellular Retinol-Binding Protein IV
ComponentsRetinoid-binding protein 7
KeywordsLIPID BINDING PROTEIN / Retinol / Lipid transport
Function / homology
Function and homology information


retinal binding / retinol binding / fatty acid transport / fatty acid binding / nucleus / cytosol
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Retinoid-binding protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.105 Å
AuthorsSilvaroli, J.A. / Pleshinger, M.J. / Kiser, P.D. / Golczak, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY023948 United States
CitationJournal: To Be Published
Title: 1.1 Angstrom Resolution Structure of Human Cellular Retinol-Binding Protein IV
Authors: Silvaroli, J.A. / Pleshinger, M.J. / Kiser, P.D. / Golczak, M.
History
DepositionAug 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 2.0Dec 11, 2019Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.occupancy / _pdbx_audit_support.funding_organization
Revision 2.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Retinoid-binding protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0923
Polymers15,8941
Non-polymers1982
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint0 kcal/mol
Surface area7620 Å2
Unit cell
Length a, b, c (Å)34.820, 57.334, 68.115
Angle α, β, γ (deg.)90.00, 103.09, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-383-

HOH

21A-450-

HOH

31A-479-

HOH

41A-489-

HOH

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Components

#1: Protein Retinoid-binding protein 7 / Cellular retinoic acid-binding protein 4 / CRBP4 / Cellular retinoic acid-binding protein IV / CRABP-IV


Mass: 15894.110 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96R05
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.08 Å3/Da / Density % sol: 40.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2 M NaCl, 0.1 M Bis-Tris/HCl, 25% PEG3350 (w/v)

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97919 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.105→29.19 Å / Num. obs: 49226 / % possible obs: 94.4 % / Redundancy: 5.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.026 / Rrim(I) all: 0.035 / Rsym value: 0.064 / Net I/σ(I): 31.8
Reflection shellResolution: 1.105→1.16 Å / Mean I/σ(I) obs: 8.6 / Num. unique obs: 5474 / CC1/2: 0.982 / Rpim(I) all: 0.077 / Rrim(I) all: 0.09 / % possible all: 72

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LPJ

1lpj


Resolution: 1.105→29.19 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.12
RfactorNum. reflection% reflection
Rfree0.1492 2363 4.8 %
Rwork0.1255 --
obs0.1267 49226 94.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.105→29.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1083 0 13 231 1327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071243
X-RAY DIFFRACTIONf_angle_d0.9711691
X-RAY DIFFRACTIONf_dihedral_angle_d24.275509
X-RAY DIFFRACTIONf_chiral_restr0.086179
X-RAY DIFFRACTIONf_plane_restr0.005218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.105-1.12720.1468730.12811581X-RAY DIFFRACTION54
1.1272-1.15180.13281090.10892414X-RAY DIFFRACTION82
1.1518-1.17850.11941250.10342557X-RAY DIFFRACTION89
1.1785-1.2080.13151330.10592763X-RAY DIFFRACTION94
1.208-1.24070.13151280.10762807X-RAY DIFFRACTION94
1.2407-1.27720.12361440.10722768X-RAY DIFFRACTION97
1.2772-1.31840.13951570.10712819X-RAY DIFFRACTION98
1.3184-1.36550.14451770.1032858X-RAY DIFFRACTION99
1.3655-1.42020.13421530.1072887X-RAY DIFFRACTION99
1.4202-1.48480.13161340.10692901X-RAY DIFFRACTION99
1.4848-1.56310.14291390.10372930X-RAY DIFFRACTION100
1.5631-1.6610.14281370.10772939X-RAY DIFFRACTION100
1.661-1.78930.12971410.11412906X-RAY DIFFRACTION100
1.7893-1.96930.14041670.11772919X-RAY DIFFRACTION100
1.9693-2.25420.13671400.12022937X-RAY DIFFRACTION100
2.2542-2.83970.17681450.13982933X-RAY DIFFRACTION100
2.8397-29.20050.16321610.14752944X-RAY DIFFRACTION99

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