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- PDB-5ljh: Crystal structure of human apo CRBP1/K40L mutant -

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Basic information

Entry
Database: PDB / ID: 5ljh
TitleCrystal structure of human apo CRBP1/K40L mutant
ComponentsRetinol-binding protein 1
Keywordsretinol-binding protein / Retinol / Vitamin A / RBP
Function / homology
Function and homology information


Defective visual phototransduction due to LRAT loss of function / all-trans-retinol binding / retinoic acid biosynthetic process / vitamin A metabolic process / retinoid binding / retinal binding / The canonical retinoid cycle in rods (twilight vision) / lipid homeostasis / fatty acid transport / Retinoid metabolism and transport ...Defective visual phototransduction due to LRAT loss of function / all-trans-retinol binding / retinoic acid biosynthetic process / vitamin A metabolic process / retinoid binding / retinal binding / The canonical retinoid cycle in rods (twilight vision) / lipid homeostasis / fatty acid transport / Retinoid metabolism and transport / lipid droplet / fatty acid binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Retinol-binding protein 1 / 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
Retinol-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsZanotti, G. / Vallese, F. / Berni, R. / Menozzi, I.
CitationJournal: J. Struct. Biol. / Year: 2017
Title: Structural and molecular determinants affecting the interaction of retinol with human CRBP1.
Authors: Menozzi, I. / Vallese, F. / Polverini, E. / Folli, C. / Berni, R. / Zanotti, G.
History
DepositionJul 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinol-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8782
Polymers15,8551
Non-polymers231
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-5 kcal/mol
Surface area7440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.531, 47.603, 77.944
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 Retinol-binding protein 1 / Cellular retinol-binding protein / CRBP / Cellular retinol-binding protein I / CRBP-I


Mass: 15855.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP1, CRBP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P09455
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 279 K / Method: vapor diffusion / pH: 5
Details: 0.2 M ammonium chloride, 0.1 M sodium acetate, 0.2 mM zinc chloride, pH 5,0, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.52→47.6 Å / Num. obs: 20143 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 27.2
Reflection shellResolution: 1.52→1.61 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 3.2 / % possible all: 93.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LJB

5ljb


Resolution: 1.52→40.63 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.29 / Phase error: 18.96
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1862 4.99 %Random selection
Rwork0.169 ---
obs0.171 20095 98.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.52→40.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1102 0 1 142 1245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121128
X-RAY DIFFRACTIONf_angle_d1.4211520
X-RAY DIFFRACTIONf_dihedral_angle_d15.161428
X-RAY DIFFRACTIONf_chiral_restr0.057165
X-RAY DIFFRACTIONf_plane_restr0.006195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5235-1.56470.27051220.25972385X-RAY DIFFRACTION86
1.5647-1.61080.2641450.23042729X-RAY DIFFRACTION99
1.6108-1.66280.2391480.22032775X-RAY DIFFRACTION99
1.6628-1.72220.22551530.19972771X-RAY DIFFRACTION100
1.7222-1.79120.24691460.18932731X-RAY DIFFRACTION100
1.7912-1.87270.19731410.18662763X-RAY DIFFRACTION100
1.8727-1.97140.21561470.17782760X-RAY DIFFRACTION100
1.9714-2.09490.18141460.16712770X-RAY DIFFRACTION100
2.0949-2.25670.19841430.16312772X-RAY DIFFRACTION99
2.2567-2.48370.17351460.17132747X-RAY DIFFRACTION99
2.4837-2.8430.21121390.17152762X-RAY DIFFRACTION99
2.843-3.58160.22541400.15812731X-RAY DIFFRACTION99
3.5816-40.640.1561460.15192759X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 0.8622 Å / Origin y: 0.1681 Å / Origin z: -7.1266 Å
111213212223313233
T0.1562 Å20.0015 Å20.0023 Å2-0.1539 Å2-0.0125 Å2--0.1422 Å2
L0.9053 °20.0951 °20.3098 °2-1.3764 °20.6553 °2--0.9863 °2
S0.1092 Å °0.0591 Å °-0.0368 Å °0.1801 Å °-0.0235 Å °-0.0784 Å °0.1432 Å °0.0275 Å °0.0004 Å °
Refinement TLS groupSelection details: ALL

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