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- PDB-1ggl: HUMAN CELLULAR RETINOL BINDING PROTEIN III -

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Basic information

Entry
Database: PDB / ID: 1ggl
TitleHUMAN CELLULAR RETINOL BINDING PROTEIN III
ComponentsPROTEIN (CELLULAR RETINOL-BINDING PROTEIN III)
KeywordsTRANSPORT PROTEIN / CARRIER / RETINOL BINDING PROTEIN
Function / homology
Function and homology information


retinoid binding / retinal binding / retinol binding / fatty acid transport / fatty acid binding / extracellular exosome / nucleus / cytosol
Similarity search - Function
Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Retinol-binding protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsCalderone, V. / Zanotti, G. / Folli, C. / Ottonello, S. / Bolchi, A. / Stoppini, M. / Berni, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Identification, retinoid binding, and x-ray analysis of a human retinol-binding protein.
Authors: Folli, C. / Calderone, V. / Ottonello, S. / Bolchi, A. / Zanotti, G. / Stoppini, M. / Berni, R.
History
DepositionAug 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (CELLULAR RETINOL-BINDING PROTEIN III)
B: PROTEIN (CELLULAR RETINOL-BINDING PROTEIN III)


Theoretical massNumber of molelcules
Total (without water)31,6062
Polymers31,6062
Non-polymers00
Water2,594144
1
A: PROTEIN (CELLULAR RETINOL-BINDING PROTEIN III)


Theoretical massNumber of molelcules
Total (without water)15,8031
Polymers15,8031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (CELLULAR RETINOL-BINDING PROTEIN III)


Theoretical massNumber of molelcules
Total (without water)15,8031
Polymers15,8031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.514, 59.841, 68.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99629, -0.082064, -0.025901), (0.082064, 0.815443, 0.572991), (-0.025901, -0.572991, 0.819152)
Vector: -11.763, 19.9143, 8.5601)

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Components

#1: Protein PROTEIN (CELLULAR RETINOL-BINDING PROTEIN III)


Mass: 15802.998 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Organ: LIVER / Plasmid: PGEM / Species (production host): Escherichia coli / Culture collection (production host): ATCC 454664 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P82980
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThere are no suitable sequence database matches for this protein.

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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: 1.94 Å3/Da / Density % sol: 36.68 %
Crystal growpH: 5 / Details: pH 5.0
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
225 mMpotassium phosphate1reservoir
1PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 9874 / % possible obs: 88 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 39.6 Å2 / Rsym value: 0.127 / Net I/σ(I): 11.2
Reflection shellResolution: 2.3→2.43 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.332 / % possible all: 76.5
Reflection
*PLUS
Rmerge(I) obs: 0.127
Reflection shell
*PLUS
% possible obs: 76.5 % / Rmerge(I) obs: 0.332

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CRB

1crb


Resolution: 2.31→7.99 Å / Rfactor Rfree error: 0.01 / Data cutoff high rms absF: 1132646.83 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME USED. BULK SOLVENT MODEL USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.286 890 9.3 %RANDOM
Rwork0.229 ---
obs-9569 87 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 120.523 Å2 / ksol: 0.509829 e/Å3
Displacement parametersBiso mean: 32.9 Å2
Baniso -1Baniso -2Baniso -3
1--8.23 Å20 Å20 Å2
2---6.28 Å20 Å2
3---14.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.33 Å
Luzzati d res low-10 Å
Luzzati sigma a0.44 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.31→7.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2222 0 0 144 2366
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.33 43 3.3 %
Rwork0.329 1273 -
obs--73.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.09

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