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- PDB-3fa8: Crystal structure of the apo R132K:Y134F:R111L:L121E mutant of ce... -

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Basic information

Entry
Database: PDB / ID: 3fa8
TitleCrystal structure of the apo R132K:Y134F:R111L:L121E mutant of cellular retinoic acid-binding protein II at 1.78 angstrom resolution
ComponentsCellular retinoic acid-binding protein 2
KeywordsTRANSPORT PROTEIN / CRABPII / retinoic acid / retinoid / 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
Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsJia, X. / Geiger, J.H.
CitationJournal: To be Published
Title: Crystal structures of apo cellular retinoic acid-binding protein II mutants: Structural integrity investigated through multiple site mutations
Authors: Jia, X. / Lee, K.S. / Vasileiou, C. / Borhan, B. / Geiger, J.H.
History
DepositionNov 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 28, 2016Group: Structure summary
Revision 1.3Oct 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 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cellular retinoic acid-binding protein 2
B: Cellular retinoic acid-binding protein 2


Theoretical massNumber of molelcules
Total (without water)31,0192
Polymers31,0192
Non-polymers00
Water4,936274
1
A: Cellular retinoic acid-binding protein 2


Theoretical massNumber of molelcules
Total (without water)15,5101
Polymers15,5101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cellular retinoic acid-binding protein 2


Theoretical massNumber of molelcules
Total (without water)15,5101
Polymers15,5101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.610, 37.169, 60.837
Angle α, β, γ (deg.)106.08, 106.47, 89.97
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 15509.708 Da / Num. of mol.: 2 / Mutation: R132K, Y134F, R111L, L121E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRABP2 / Plasmid: CRABPII-pET17b-KFLE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P29373
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M BTP, 25% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 23, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→55.81 Å / Num. obs: 23232 / % possible obs: 94.5 % / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 18.2
Reflection shellResolution: 1.78→1.89 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.181 / Mean I/σ(I) obs: 6.7 / Num. unique all: 4259 / % possible all: 95.7

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Processing

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

2g7b


Resolution: 1.78→19.42 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.566 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DATA HAS BEEN COLLECTED TO 1.5A, BUT REFINED UPTO 1.78A
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2582 10 %RANDOM
Rwork0.17873 ---
obs0.18424 23232 96.66 %-
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: 23.063 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0.15 Å2-0.25 Å2
2---0.64 Å20.22 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.78→19.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2172 0 0 274 2446
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222238
X-RAY DIFFRACTIONr_angle_refined_deg1.351.9653028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0525284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83525.91898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12915440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0341510
X-RAY DIFFRACTIONr_chiral_restr0.0940.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021626
X-RAY DIFFRACTIONr_nbd_refined0.2150.3912
X-RAY DIFFRACTIONr_nbtor_refined0.3180.51524
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.5336
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.369
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2710.541
X-RAY DIFFRACTIONr_mcbond_it1.50221441
X-RAY DIFFRACTIONr_mcangle_it2.22232258
X-RAY DIFFRACTIONr_scbond_it1.4532921
X-RAY DIFFRACTIONr_scangle_it2.2893764
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 192 -
Rwork0.182 1724 -
obs-1724 95.09 %

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