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- PDB-7g1x: Crystal Structure of apo human FABP1 - monoclinic form I -

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Basic information

Entry
Database: PDB / ID: 7g1x
TitleCrystal Structure of apo human FABP1 - monoclinic form I
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 / PPARA activates gene expression / Cytoprotection by HMOX1 / phospholipid binding / 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
Fatty acid-binding protein, liver
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 human FABP1
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


Theoretical massNumber of molelcules
Total (without water)29,0172
Polymers29,0172
Non-polymers00
Water2,666148
1
A: Fatty acid-binding protein, liver


Theoretical massNumber of molelcules
Total (without water)14,5091
Polymers14,5091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fatty acid-binding protein, liver


Theoretical massNumber of molelcules
Total (without water)14,5091
Polymers14,5091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.691, 34.929, 59.321
Angle α, β, γ (deg.)90.000, 119.210, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 1.83 Å3/Da / Density % sol: 32.75 %
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 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 1.65→34.93 Å / Num. obs: 24662 / % possible obs: 96 % / Redundancy: 3.142 % / Biso Wilson estimate: 32.297 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.055 / Χ2: 0.904 / Net I/σ(I): 13.85 / Num. measured all: 77482 / Scaling rejects: 33
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
1.65-1.691.9320.7771.172459189312730.4190.99367.2
1.69-1.743.230.5932.155708183417670.6710.70796.3
1.74-1.793.2510.4652.745624176617300.8140.55598
1.79-1.853.1890.3483.635454174217100.8740.41898.2
1.85-1.913.0410.2594.735014167016490.9170.31498.7
1.91-1.973.2180.1696.995216163616210.9720.20399.1
1.97-2.053.3650.1279.215239157015570.980.15199.2
2.05-2.133.2740.11410.634918151415020.9810.13699.2
2.13-2.233.170.08912.654603146214520.9890.10799.3
2.23-2.333.0280.0813.994109137013570.9890.09799.1
2.33-2.463.3680.06517.34493135213340.9940.07798.7
2.46-2.613.3280.05419.334053123412180.9960.06598.7
2.61-2.793.2760.04921.733849118711750.9960.05899
2.79-3.013.0180.04324.373265109910820.9960.05298.5
3.01-3.33.3120.03729.53345103010100.9970.04498.1
3.3-3.693.2520.03332.8129409259040.9970.03997.7
3.69-4.263.010.02933.3624148308020.9980.03596.6
4.26-5.223.1970.02735.821456946710.9980.03296.7
5.22-7.383.1630.02735.216865525330.9980.03296.6
7.38-34.933.010.02335.079483303150.9980.02895.5

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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: 1.65→34.93 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.147 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: yet another monoclinic crystal form result of failed soak with 6858120
RfactorNum. reflection% reflectionSelection details
Rfree0.2523 1225 5.1 %RANDOM
Rwork0.2024 ---
obs0.2051 22795 93.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80 Å2 / Biso mean: 27.266 Å2 / Biso min: 12.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å2-0.21 Å2
2--0.03 Å20 Å2
3---0.19 Å2
Refinement stepCycle: final / Resolution: 1.65→34.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1998 0 0 148 2146
Biso mean---32.72 -
Num. residues----255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192039
X-RAY DIFFRACTIONr_angle_refined_deg2.0381.9642731
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6665259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.65326.66787
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.22915427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.21154
X-RAY DIFFRACTIONr_chiral_restr0.1480.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021446
LS refinement shellResolution: 1.652→1.694 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 67 -
Rwork0.362 1042 -
all-1109 -
obs--59.12 %

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