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- PDB-1dc9: PROPERTIES AND CRYSTAL STRUCTURE OF A BETA-BARREL FOLDING MUTANT,... -

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Basic information

Entry
Database: PDB / ID: 1dc9
TitlePROPERTIES AND CRYSTAL STRUCTURE OF A BETA-BARREL FOLDING MUTANT, V60N INTESTINAL FATTY ACID BINDING PROTEIN (IFABP)
ComponentsINTESTINAL FATTY ACID BINDING PROTEIN
KeywordsLIPID BINDING PROTEIN / FATTY ACID BINDING PROTEIN / INTRACELLULAR LIPID BINDING PROTEIN / MUTANT / BETA- BARREL
Function / homology
Function and homology information


Triglyceride catabolism / intestinal lipid absorption / apical cortex / intestinal absorption / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / microvillus / fatty acid transport / long-chain fatty acid transport / fatty acid metabolic process ...Triglyceride catabolism / intestinal lipid absorption / apical cortex / intestinal absorption / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / microvillus / fatty acid transport / long-chain fatty acid transport / fatty acid metabolic process / fatty acid binding / nucleus / cytosol
Similarity search - Function
Fatty acid-binding protein, intestinal / Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Fatty acid-binding protein, intestinal
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsRopson, I.J. / Yowler, B.C. / Dalessio, P.M. / Banaszak, L. / Thompson, J.
CitationJournal: Biophys.J. / Year: 2000
Title: Properties and crystal structure of a beta-barrel folding mutant.
Authors: Ropson, I.J. / Yowler, B.C. / Dalessio, P.M. / Banaszak, L. / Thompson, J.
History
DepositionNov 4, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 3, 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 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTESTINAL FATTY ACID BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,0301
Polymers15,0301
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.636, 52.375, 31.594
Angle α, β, γ (deg.)90.00, 90.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein INTESTINAL FATTY ACID BINDING PROTEIN / IFABP


Mass: 15029.987 Da / Num. of mol.: 1 / Mutation: V60N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: INTESTINE / Production host: Escherichia coli (E. coli) / References: UniProt: P02693
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.3
Details: 36-38% PEG 4000, 0.1 M PIPES, 1:1 RATIO WELL AND 4.6 MG/ML PROTEIN IN WATER, pH 7.3, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14.6 mg/mlprotein1drop
236-38 %PEG40001reservoir
30.1 MPIPES1reservoirpH7.3

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Mar 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 6804 / Num. obs: 6804 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 5.7 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 23.9
Reflection shellResolution: 2.09→2.22 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.145 / % possible all: 38.2
Reflection
*PLUS
Num. measured all: 19796 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 38.2 % / Num. unique obs: 447 / Num. measured obs: 779 / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 1.4

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Processing

Software
NameClassification
CNSrefinement
X-GENdata reduction
X-GENdata scaling
CNSphasing
RefinementResolution: 2.1→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 158121.65 / Data cutoff high rms absF: 158121.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.228 502 8 %RANDOM
Rwork0.189 ---
all0.19 6804 --
obs0.189 6302 90.8 %-
Displacement parametersBiso mean: 18.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.44 Å20 Å2-0.83 Å2
2--4.02 Å20 Å2
3----7.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1058 0 0 73 1131
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.63
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it1.82
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.332.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.362 54 10.6 %
Rwork0.251 455 -
obs--44.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAM
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.63
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.362 / % reflection Rfree: 10.6 % / Rfactor Rwork: 0.251

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