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- PDB-3fep: Crystal structure of the R132K:R111L:L121E:R59W-CRABPII mutant co... -

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Basic information

Entry
Database: PDB / ID: 3fep
TitleCrystal structure of the R132K:R111L:L121E:R59W-CRABPII mutant complexed with a synthetic ligand (merocyanin) at 2.60 angstrom resolution.
ComponentsCellular retinoic acid-binding protein 2
KeywordsTRANSPORT PROTEIN / merocyanin / CRABPII / retinoic acid / retinoid / PSB / protonated Schiff base / fluorescence / CRABP / Nucleus / Retinol-binding / Transport / Vitamin A
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 / cytoplasm / cytosol
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 beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-LMC / Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJia, X. / Geiger, J.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: "Turn-on" protein fluorescence: in situ formation of cyanine dyes.
Authors: Yapici, I. / Lee, K.S. / Berbasova, T. / Nosrati, M. / Jia, X. / Vasileiou, C. / Wang, W. / Santos, E.M. / Geiger, J.H. / Borhan, B.
History
DepositionNov 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 4, 2015Group: Database references
Revision 1.3Feb 11, 2015Group: Database references
Revision 1.4Dec 28, 2016Group: Structure summary
Revision 1.5Sep 9, 2020Group: Derived calculations / Structure summary / Category: struct / struct_conn / struct_site
Item: _struct.title / _struct_conn.pdbx_leaving_atom_flag ..._struct.title / _struct_conn.pdbx_leaving_atom_flag / _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_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.7Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.8Oct 16, 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)16,0173
Polymers15,5551
Non-polymers4632
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.808, 55.808, 108.177
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: 15554.726 Da / Num. of mol.: 1 / Mutation: R132K, R111L, L121E, R59W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRABP2 / Plasmid: CRABPII-pET17b-KLE-R59W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P29373
#2: Chemical ChemComp-LMC / (2E,4E,6E)-3-methyl-6-(1,3,3-trimethyl-1,3-dihydro-2H-indol-2-ylidene)hexa-2,4-dienal / (2E,4E,6Z)-3-methyl-6-(1,3,3-trimethylindolin-2-ylidene)hexa-2,4-dienal


Mass: 267.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H21NO
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.13 Å3/Da / Density % sol: 60.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 0.1M MES, 0.2M ammonium sulfate, 30% PEGMME 5000, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 26, 2007
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.6→48.34 Å / Num. obs: 5671 / % possible obs: 88.4 % / Observed criterion σ(I): 1 / Redundancy: 9.2 % / Biso Wilson estimate: 38.6 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 43.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 1.9 / Num. unique all: 265 / % possible all: 41.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2G7B

2g7b


Resolution: 2.6→44.13 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.913 / SU B: 29.52 / SU ML: 0.3 / Cross valid method: THROUGHOUT / ESU R: 0.827 / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29309 260 4.6 %RANDOM
Rwork0.23246 ---
all0.2354 ---
obs0.2354 5394 88.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.88 Å2
Baniso -1Baniso -2Baniso -3
1-3.76 Å21.88 Å20 Å2
2--3.76 Å20 Å2
3----5.65 Å2
Refinement stepCycle: LAST / Resolution: 2.6→44.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1090 0 31 39 1160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221151
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8862.0021556
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9685136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83926.04248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33915213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.159154
X-RAY DIFFRACTIONr_chiral_restr0.0440.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02828
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2740.3493
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3280.5762
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2610.566
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.325
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.360.53
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4472709
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.73931110
X-RAY DIFFRACTIONr_scbond_it0.282527
X-RAY DIFFRACTIONr_scangle_it0.4293445
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.669 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.904 6 -
Rwork0.37 172 -
obs-172 37.87 %

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