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- PDB-2wq9: Crystal Structure of RBP4 bound to Oleic Acid -

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Basic information

Entry
Database: PDB / ID: 2wq9
TitleCrystal Structure of RBP4 bound to Oleic Acid
ComponentsRETINOL-BINDING PROTEIN 4
KeywordsSIGNALING PROTEIN / DISEASE MUTATION / SENSORY TRANSDUCTION / RETINOL-BINDING / VISION / VITAMIN A
Function / homology
Function and homology information


Retinoid metabolism disease events / urinary bladder development / embryonic retina morphogenesis in camera-type eye / retinol transport / female genitalia morphogenesis / retinol transmembrane transporter activity / embryonic organ morphogenesis / maintenance of gastrointestinal epithelium / embryonic skeletal system development / negative regulation of cardiac muscle cell proliferation ...Retinoid metabolism disease events / urinary bladder development / embryonic retina morphogenesis in camera-type eye / retinol transport / female genitalia morphogenesis / retinol transmembrane transporter activity / embryonic organ morphogenesis / maintenance of gastrointestinal epithelium / embryonic skeletal system development / negative regulation of cardiac muscle cell proliferation / eye development / heart trabecula formation / retinal binding / cardiac muscle tissue development / retinol metabolic process / retinol binding / positive regulation of immunoglobulin production / Defective visual phototransduction due to STRA6 loss of function / The canonical retinoid cycle in rods (twilight vision) / uterus development / vagina development / response to retinoic acid / Retinoid metabolism and transport / visual perception / gluconeogenesis / lung development / positive regulation of insulin secretion / glucose homeostasis / heart development / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Retinol binding protein/Purpurin / Lipocalin, ApoD type / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
OLEIC ACID / Retinol-binding protein 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsNanao, M. / Mercer, D. / Nguyen, L. / Buckley, D. / Stout, T.J.
CitationJournal: To be Published
Title: Crystal Structure of Rbp4 Bound to Oleic Acid
Authors: Nanao, M. / Stout, T.J.
History
DepositionAug 14, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.5Dec 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
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE ... THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RETINOL-BINDING PROTEIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,79010
Polymers20,0541
Non-polymers7369
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.060, 103.060, 72.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-2143-

HOH

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Components

#1: Protein RETINOL-BINDING PROTEIN 4 / PLASMA RETINOL-BINDING PROTEIN / PRBP / RBP / RBP4


Mass: 20054.467 Da / Num. of mol.: 1 / Fragment: RESIDUES 19-192
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P02753
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.13 % / Description: NONE
Crystal growDetails: 3.5 TO 4.2 M NACL, 1M HEPES PH 7.2

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.541
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 34250 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.96
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.82 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QAB

1qab


Resolution: 1.65→56.34 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.035 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21919 1727 5 %RANDOM
Rwork0.18769 ---
obs0.18924 32522 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.401 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.06 Å20 Å2
2--0.13 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.65→56.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1399 0 43 233 1675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221504
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.9522028
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0745181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.69723.5881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37215251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4941514
X-RAY DIFFRACTIONr_chiral_restr0.0720.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021156
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.2726
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21029
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2197
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5011.5888
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.80621407
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5073693
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3744.5616
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 138 -
Rwork0.29 2415 -
obs--99.69 %
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)
13.0142.54991.46198.90022.75852.24520.1280.1950.3605-0.2909-0.24860.514-0.2482-0.10320.1206-0.04640.01840.0418-0.0412-0.0049-0.0899-30.687913.212415.9501
22.84030.1503-0.42893.53360.00621.67730.0925-0.06910.15640.3759-0.0552-0.2141-0.12150.2737-0.0373-0.0632-0.04440.0068-0.0523-0.0422-0.1103-18.178710.381528.8855
332.137231.15077.494595.917445.144125.7439-0.5371.91270.0301-6.76342.8597-1.4416-3.2591.1552-2.32270.362-0.07350.24670.0875-0.00330.2379-13.202526.656412.8032
42.5457-3.96224.90839.3942-10.269318.8027-0.1241-0.06390.18980.14720.1599-0.5122-0.08910.3343-0.0357-0.0485-0.06430.0480.0429-0.02140.0482-12.565515.182124.7232
531.9878-17.282610.679769.8613-32.960341.6675-0.1817-1.7443-2.17380.44060.1668-1.43342.8820.61060.01490.40550.1224-0.11220.31180.00360.3548-8.2804-1.028833.5673
68.8447-1.84745.95992.0367-0.97647.25680.10620.30210.171-0.1608-0.0418-0.2907-0.11920.3739-0.0644-0.0565-0.07870.0874-0.016-0.0057-0.0273-14.865712.982318.5912
72.7353-0.42070.26682.8905-0.08631.90970.07920.3350.0738-0.0339-0.0656-0.3025-0.07380.326-0.0136-0.0804-0.0440.0573-0.0343-0.0199-0.0764-16.663811.48619.353
80.42010.69040.61121.2990.59391.91580.14240.19130.0008-0.09360.043-0.0446-0.01050.1567-0.1855-0.0911-0.00090.0092-0.0761-0.0636-0.1046-25.98592.53317.4424
91.8097-0.7995-0.38123.39750.2841.27880.0919-0.15590.19510.32150.0249-0.1509-0.18980.1219-0.1169-0.0375-0.04620.0488-0.1137-0.0534-0.1125-24.602614.504930.1878
102.24860.4308-0.81233.66291.48733.71310.0647-0.06430.03480.26770.04810.1588-0.10180.1205-0.1128-0.0475-0.03050.0761-0.1047-0.0251-0.1345-29.32919.105130.6579
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 21
2X-RAY DIFFRACTION2A22 - 46
3X-RAY DIFFRACTION3A47 - 51
4X-RAY DIFFRACTION4A52 - 60
5X-RAY DIFFRACTION5A61 - 67
6X-RAY DIFFRACTION6A68 - 84
7X-RAY DIFFRACTION7A85 - 113
8X-RAY DIFFRACTION8A114 - 131
9X-RAY DIFFRACTION9A132 - 145
10X-RAY DIFFRACTION10A146 - 174

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