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- PDB-7fxo: Crystal Structure of apo human FABP1 monoclinic form III -

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Basic information

Entry
Database: PDB / ID: 7fxo
TitleCrystal Structure of apo human FABP1 monoclinic form III
ComponentsFatty acid-binding protein, liver
KeywordsLIPID BINDING PROTEIN / FATTY ACID BINDING PROTEIN / CYTOPLASM / LIPID-BINDING / TRANSPORT / PROTEIN BINDING
Function / homology
Function and homology information


response to vitamin B3 / oleic acid binding / apical cortex / positive regulation of fatty acid beta-oxidation / bile acid binding / intestinal absorption / Heme degradation / long-chain fatty acid transmembrane transporter activity / heterocyclic compound binding / Triglyceride catabolism ...response to vitamin B3 / oleic acid binding / apical cortex / positive regulation of fatty acid beta-oxidation / bile acid binding / intestinal absorption / Heme degradation / long-chain fatty acid transmembrane transporter activity / heterocyclic compound binding / Triglyceride catabolism / antioxidant activity / peroxisomal matrix / fatty acid transport / Regulation of lipid metabolism by PPARalpha / fatty acid binding / phospholipid binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PPARA activates gene expression / Cytoprotection by HMOX1 / cellular response to hydrogen peroxide / cellular response to hypoxia / chromatin binding / negative regulation of apoptotic process / protein-containing complex / extracellular exosome / nucleoplasm / nucleus / cytosol
Similarity search - Function
Lipocalin / cytosolic fatty-acid binding protein family / Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin
Similarity search - Domain/homology
BENZAMIDINE / Fatty acid-binding protein, liver
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsEhler, A. / Benz, J. / Obst, U. / Rudolph, M.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: To be published
Title: Crystal Structure of a human FABP1 complex
Authors: Obst, U. / Magnone, C. / Kuhn, B. / Rudolph, M.G.
History
DepositionApr 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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: Fatty acid-binding protein, liver
B: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2945
Polymers29,0172
Non-polymers2763
Water3,531196
1
A: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6653
Polymers14,5091
Non-polymers1562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6292
Polymers14,5091
Non-polymers1201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.941, 37.114, 60.491
Angle α, β, γ (deg.)90.000, 113.120, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fatty acid-binding protein, liver / Fatty acid-binding protein 1 / Liver-type fatty acid-binding protein / L-FABP


Mass: 14508.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP1, FABPL / Plasmid: PET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07148
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.03 Å3/Da / Density % sol: 39.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: protein in 25mM Tris/HCl pH 7.5 100mM NaCl, see also PMID 27658368

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 1.32→32.32 Å / Num. obs: 54768 / % possible obs: 99.6 % / Redundancy: 3.28 % / Biso Wilson estimate: 24.547 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.047 / Rsym value: 0.04 / Χ2: 0.892 / Net I/σ(I): 11.36 / Num. measured all: 185836 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.3-1.333.2311.1051.1113620427442160.3841.32198.6
1.33-1.373.1180.9251.3312694410940710.4831.11699.1
1.37-1.413.1070.6941.7512332401239690.6170.83898.9
1.41-1.453.3510.5352.4112896387338480.7390.63799.4
1.45-1.53.3270.4183.0312468377637470.8240.49999.2
1.5-1.553.2740.2874.3711893367136330.9020.34499
1.55-1.613.0950.1976.0210944355135360.940.23899.6
1.61-1.683.3180.1577.7111179339233690.9650.18899.3
1.68-1.753.4280.11910.0911080324632320.9810.14199.6
1.75-1.843.4050.08912.9810689315731390.9890.10699.4
1.84-1.943.3410.06417.229723293629100.9940.07699.1
1.94-2.063.0830.04921.028592282327870.9950.0698.7
2.06-2.23.4510.04325.449066266426270.9960.05198.6
2.2-2.373.40.03827.838235245324220.9970.04698.7
2.37-2.63.3320.03529.977554231022670.9970.04298.1
2.6-2.913.0080.03230.765967205019840.9980.03996.8
2.91-3.363.3280.02836.065993185418010.9980.03497.1
3.36-4.113.310.02538.525008155415130.9980.0397.4
4.11-5.813.030.02337.453587122311840.9980.02796.8
5.81-32.323.3710.02339.0223167096870.9990.02896.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.7.0018refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.3→32.32 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.419 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: best resolution for apo-structure so far, use this for modelling
RfactorNum. reflection% reflectionSelection details
Rfree0.2036 2788 5.1 %RANDOM
Rwork0.1534 ---
obs0.1559 52162 95.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.75 Å2 / Biso mean: 23.533 Å2 / Biso min: 9.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20.33 Å2
2--0.01 Å20 Å2
3---0.1 Å2
Refinement stepCycle: final / Resolution: 1.3→32.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2015 0 29 197 2241
Biso mean--26.66 32.56 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192188
X-RAY DIFFRACTIONr_bond_other_d0.0020.022261
X-RAY DIFFRACTIONr_angle_refined_deg1.8971.972952
X-RAY DIFFRACTIONr_angle_other_deg0.8663.0015163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8695292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.25826.42195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.54615458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.811156
X-RAY DIFFRACTIONr_chiral_restr0.1240.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022466
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02464
X-RAY DIFFRACTIONr_rigid_bond_restr5.13534449
X-RAY DIFFRACTIONr_sphericity_free23.505575
X-RAY DIFFRACTIONr_sphericity_bonded13.27354533
LS refinement shellResolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.451 188 -
Rwork0.346 3491 -
all-3679 -
obs--86.44 %

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