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- PDB-6nnx: Crystal Structure of the All-Trans Retinal-Bound R111K:Y134F:T54V... -

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Basic information

Entry
Database: PDB / ID: 6nnx
TitleCrystal Structure of the All-Trans Retinal-Bound R111K:Y134F:T54V:R132Q:P39Y:R59Y:L121M Mutant of Human Cellular Retinoic Acid Binding Protein II in the Dark at 1.87 Angstrom Resolution
ComponentsCellular retinoic acid-binding protein 2
KeywordsLIPID BINDING PROTEIN / iLBP / Rhodopsin mimic
Function / homology
Function and homology information


positive regulation of collateral sprouting / retinoid binding / retinal binding / retinoic acid binding / embryonic forelimb morphogenesis / retinoic acid metabolic process / retinol binding / Signaling by Retinoic Acid / epidermis development / fatty acid transport ...positive regulation of collateral sprouting / retinoid binding / retinal binding / retinoic acid binding / embryonic forelimb morphogenesis / retinoic acid metabolic process / retinol binding / Signaling by Retinoic Acid / epidermis development / fatty acid transport / cyclin binding / fatty acid binding / regulation of DNA-templated transcription / signal transduction / endoplasmic reticulum / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / 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
RETINAL / Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsGhanbarpour, A. / Geiger, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: To Be Published
Title: Crystal Structure of the All-Trans Retinal-Bound R111K:Y134F:T54V:R132Q:P39Y:R59Y:L121M Mutant of Human Cellular Retionic Acid Binding Protein II in the Dark at 1.87 Angstrom Resolution
Authors: Ghanbarpour, A. / Geiger, J.
History
DepositionJan 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8812
Polymers15,5971
Non-polymers2841
Water77543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cellular retinoic acid-binding protein 2
hetero molecules

A: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7634
Polymers31,1942
Non-polymers5692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area3260 Å2
ΔGint-24 kcal/mol
Surface area13210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.842, 58.842, 99.535
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Cellular retinoic acid-binding protein 2 / Cellular retinoic acid-binding protein II / CRABP-II


Mass: 15596.829 Da / Num. of mol.: 1 / Mutation: R111K, Y134F, T54V, R132Q, P39Y, R59Y, L121M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRABP2
Production host: Bacterial expression vector pBEN1-SGC (others)
References: UniProt: P29373
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.43 % / Description: Hexagonal
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Sodium Malonate / PH range: 6-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.87→45.36 Å / Num. obs: 16795 / % possible obs: 98.33 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 20.9
Reflection shellResolution: 1.87→1.937 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1647 / % possible all: 98.86

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YFP

4yfp


Resolution: 1.87→45.36 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.6
RfactorNum. reflection% reflection
Rfree0.2404 1283 7.64 %
Rwork0.2082 --
obs0.2107 16784 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.87→45.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1092 0 20 43 1155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081193
X-RAY DIFFRACTIONf_angle_d0.9691627
X-RAY DIFFRACTIONf_dihedral_angle_d10.466994
X-RAY DIFFRACTIONf_chiral_restr0.057186
X-RAY DIFFRACTIONf_plane_restr0.005207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8701-1.9450.31741430.26091705X-RAY DIFFRACTION99
1.945-2.03350.33641430.24171714X-RAY DIFFRACTION99
2.0335-2.14070.25881400.21721678X-RAY DIFFRACTION99
2.1407-2.27490.25981440.22031702X-RAY DIFFRACTION98
2.2749-2.45050.31971380.24091700X-RAY DIFFRACTION99
2.4505-2.69710.27011400.22991733X-RAY DIFFRACTION99
2.6971-3.08730.27061440.23371735X-RAY DIFFRACTION99
3.0873-3.88930.21821400.19281753X-RAY DIFFRACTION99
3.8893-45.37290.19291510.18251781X-RAY DIFFRACTION95

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