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- PDB-9gvx: M2 mutant (R111K:Y134F:T54V:R132Q:P39Y:R59Y) of human cellular re... -

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Basic information

Entry
Database: PDB / ID: 9gvx
TitleM2 mutant (R111K:Y134F:T54V:R132Q:P39Y:R59Y) of human cellular retinoic acid binding protein II - 1e 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
: / Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTassone, G. / Pozzi, C.
Funding support Italy, 1items
OrganizationGrant numberCountry
Not funded Italy
CitationJournal: Acs Med.Chem.Lett. / Year: 2025
Title: Morita-Baylis-Hillman Adduct Chemistry as a Tool for the Design of Lysine-Targeted Covalent Ligands.
Authors: Paolino, M. / Tassone, G. / Governa, P. / Saletti, M. / Lami, M. / Carletti, R. / Sacchetta, F. / Pozzi, C. / Orlandini, M. / Manetti, F. / Olivucci, M. / Cappelli, A.
History
DepositionSep 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)16,1922
Polymers15,9921
Non-polymers2001
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-2 kcal/mol
Surface area7680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.305, 58.305, 101.735
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-367-

HOH

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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-A1IQZ / methyl (~{Z})-3-(4-ethynylphenyl)-2-methyl-prop-2-enoate


Mass: 200.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 3.22 Å3/Da / Density % sol: 61.77 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M sodium malonate pH 7 and 20% w/v polyethylene glycol 3.350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 9, 2022
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.1→101.74 Å / Num. obs: 12211 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 48.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.025 / Rrim(I) all: 0.065 / Net I/σ(I): 14.7
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.836 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1716 / CC1/2: 0.852 / Rpim(I) all: 0.341 / Rrim(I) all: 0.905 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→45.27 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.155 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25401 601 4.9 %RANDOM
Rwork0.20115 ---
obs0.20361 11576 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.545 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refine analyzeLuzzati coordinate error obs: 0.2954 Å
Refinement stepCycle: 1 / Resolution: 2.1→45.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1073 0 15 70 1158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121115
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6341.6571510
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5625139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.82723.96253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.76915197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.048155
X-RAY DIFFRACTIONr_chiral_restr0.1150.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02833
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.5825.35553
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.9797.991690
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.6235.822561
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.45172.6021649
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: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 48 -
Rwork0.324 824 -
obs--100 %

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