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- PDB-6z2z: M2 mutant (R111K:Y134F:T54V:R132Q:P39Y:R59Y) of human cellular re... -

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Basic information

Entry
Database: PDB / ID: 6z2z
TitleM2 mutant (R111K:Y134F:T54V:R132Q:P39Y:R59Y) of human cellular retinoic acid binding protein II - 2a conjugate
ComponentsCellular retinoic acid-binding protein 2
KeywordsTRANSPORT PROTEIN / human cellular retinoic acid binding protein II / hCRABPII / conjugate / chromophore / M2
Function / homology
Function and homology information


positive regulation of collateral sprouting / retinoid binding / retinoic acid binding / retinal 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 / retinoic acid binding / retinal 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 / endoplasmic reticulum / signal transduction / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm
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
Similarity search - Domain/homology
Chem-Q5W / Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsTassone, G. / Pozzi, C. / Mangani, S.
CitationJournal: Chembiochem / Year: 2022
Title: Xanthopsin-Like Systems via Site-Specific Click-Functionalization of a Retinoic Acid Binding Protein.
Authors: Tassone, G. / Paolino, M. / Pozzi, C. / Reale, A. / Salvini, L. / Giorgi, G. / Orlandini, M. / Galvagni, F. / Mangani, S. / Yang, X. / Carlotti, B. / Ortica, F. / Latterini, L. / Olivucci, M. / Cappelli, A.
History
DepositionMay 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 19, 2022Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)16,2432
Polymers15,9921
Non-polymers2501
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.794, 58.794, 101.152
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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: 15992.265 Da / Num. of mol.: 1 / Mutation: R111K, Y134F, T54V, R132Q, P39Y, R59Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRABP2 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P29373
#2: Chemical ChemComp-Q5W / methyl (~{Z})-3-(6-ethynylnaphthalen-2-yl)-2-methyl-prop-2-enoate


Mass: 250.292 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.18 Å3/Da / Density % sol: 61.36 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium malonate pH 7 and 20% w/v polyethylene glycol 3,350
PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 3, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.55→101.15 Å / Num. obs: 6999 / % possible obs: 100 % / Redundancy: 7.9 % / Biso Wilson estimate: 54 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.023 / Rrim(I) all: 0.064 / Net I/σ(I): 16.6
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 8 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 986 / CC1/2: 0.948 / Rpim(I) all: 0.17 / Rrim(I) all: 0.485 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YFP

4yfp


Resolution: 2.55→50.92 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / SU B: 10.677 / SU ML: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.375 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.265 343 4.9 %RANDOM
Rwork0.2051 ---
obs0.2078 6626 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98 Å2 / Biso mean: 64.37 Å2 / Biso min: 39.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.06 Å20 Å2
2--0.13 Å2-0 Å2
3----0.41 Å2
Refine analyzeLuzzati coordinate error obs: 0.3404 Å
Refinement stepCycle: final / Resolution: 2.55→50.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1063 0 19 16 1098
Biso mean--66.71 71.2 -
Num. residues----138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121107
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.6611502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.45139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.59524.28649
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.67115191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.619154
X-RAY DIFFRACTIONr_chiral_restr0.1110.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02828
LS refinement shellResolution: 2.55→2.616 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 24 -
Rwork0.261 466 -
all-490 -
obs--99.8 %

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