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- PDB-3d97: Crystal Structure of the R132K:R111L:L121E Mutant of Apo-Cellular... -

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Basic information

Entry
Database: PDB / ID: 3d97
TitleCrystal Structure of the R132K:R111L:L121E Mutant of Apo-Cellular Retinoic Acid Binding Protein Type II At 1.50 Angstroms Resolution
ComponentsCellular retinoic acid-binding protein 2
KeywordsTRANSPORT PROTEIN / CRABPII / RETINOIC ACID / RETINOIDS / BETA BARREL / HIGH RESOLUTION / MUTANT / Cytoplasm / Nucleus / Retinol-binding / Transport / Vitamin A
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 / 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 / Calycin beta-barrel core domain / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / 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 / molecular replacement / Resolution: 1.5 Å
AuthorsVaezeslami, S. / Geiger, J.H.
CitationJournal: Thesis
Title: Determining Crystal Structures of Proteins and Protein Complexes by X-Ray Crystallography: X-Ray Crystallographic Studies of the Mutants of Cellular Retinoic Acid Binding Protein Type II ...Title: Determining Crystal Structures of Proteins and Protein Complexes by X-Ray Crystallography: X-Ray Crystallographic Studies of the Mutants of Cellular Retinoic Acid Binding Protein Type II Toward Designing a Mimic of Rhodopsin.
Authors: Vaezeslami, S. / Jia, X. / Vasileiou, C. / Borhan, B. / Geiger, J.H.
History
DepositionMay 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity / Item: _entity.formula_weight
Revision 1.4Oct 20, 2021Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Structure summary
Category: database_2 / entity ...database_2 / entity / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3805
Polymers31,0512
Non-polymers3283
Water6,035335
1
A: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8082
Polymers15,5261
Non-polymers2821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5723
Polymers15,5261
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.553, 37.220, 61.058
Angle α, β, γ (deg.)73.400, 73.700, 89.730
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 / Retinoic acid-binding protein II / cellular


Mass: 15525.708 Da / Num. of mol.: 2 / Mutation: R111L, L121E, R132K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRABP2 / Plasmid: pET17-b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P29373
#2: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 46.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% (w/v) PEG 4000, 0.1 M Bis-TRIS Propane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→55.9 Å / Num. all: 42526 / Num. obs: 42526 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 8.3
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.2976 / Mean I/σ(I) obs: 2.4 / % possible all: 93

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FS6

2fs6


Resolution: 1.5→55.9 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.806 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.227 4167 10 %RANDOM
Rwork0.154 ---
obs0.161 41632 93.23 %-
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: 24.517 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0.25 Å20.13 Å2
2---1.26 Å2-0.11 Å2
3---1.18 Å2
Refinement stepCycle: LAST / Resolution: 1.5→55.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2163 0 23 350 2536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0222215
X-RAY DIFFRACTIONr_angle_refined_deg2.3251.9732992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4345272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71226.21195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25215420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.219158
X-RAY DIFFRACTIONr_chiral_restr0.1730.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021590
X-RAY DIFFRACTIONr_nbd_refined0.2310.2941
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21509
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2257
X-RAY DIFFRACTIONr_metal_ion_refined0.1490.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.229
X-RAY DIFFRACTIONr_mcbond_it2.6391.51365
X-RAY DIFFRACTIONr_mcangle_it3.84822223
X-RAY DIFFRACTIONr_scbond_it5.3183884
X-RAY DIFFRACTIONr_scangle_it7.6344.5769
X-RAY DIFFRACTIONr_rigid_bond_restr3.21332249
X-RAY DIFFRACTIONr_sphericity_free10.3213350
X-RAY DIFFRACTIONr_sphericity_bonded7.08532184
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 256 -
Rwork0.22 2224 -
all-2480 -
obs--75.13 %

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