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- PDB-7g0w: Crystal Structure of apo human FABP1i monoclinic form II, twinned... -

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Basic information

Entry
Database: PDB / ID: 7g0w
TitleCrystal Structure of apo human FABP1i monoclinic form II, twinned with beta=90deg
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: 1.64 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
C: Fatty acid-binding protein, liver
D: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1906
Polymers58,0354
Non-polymers1562
Water7,999444
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
3
C: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6643
Polymers14,5091
Non-polymers1562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 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)38.947, 106.685, 56.261
Angle α, β, γ (deg.)90.000, 90.360, 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.: 4
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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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.: 444 / 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: 2.01 Å3/Da / Density % sol: 38.93 %
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: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.22
ReflectionResolution: 1.64→38.71 Å / Num. obs: 56090 / % possible obs: 99.8 % / Redundancy: 3.32 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.064 / Rsym value: 0.056 / Χ2: 0.884 / Net I/σ(I): 12.22 / Num. measured all: 184675 / Scaling rejects: 11
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
1.64-1.683.1531.0621.2113079417541480.3341.27799.4
1.68-1.733.1010.811.5712305399739680.4640.97799.3
1.73-1.782.990.6251.9811752397639300.5930.76298.8
1.78-1.833.3760.4592.9112673379237540.7250.54599
1.83-1.893.4160.3483.9712573369936810.8240.41399.5
1.89-1.963.380.2415.8112050358135650.9060.28799.6
1.96-2.033.3160.1787.4511375344034300.9430.21399.7
2.03-2.123.130.1418.9710365332933120.9520.17199.5
2.12-2.213.440.1111.7610939319131800.9740.13199.7
2.21-2.323.4870.09213.910640305830510.9820.10999.8
2.32-2.443.4570.07616.3410076291929150.9880.0999.9
2.44-2.593.3950.0619.139298274827390.9910.07299.7
2.59-2.773.1480.05121.658055256525590.9930.06199.8
2.77-2.993.5720.04127.898637242324180.9960.04899.8
2.99-3.283.4740.03432.667615219521920.9970.0499.9
3.28-3.673.3250.03136.696556199319720.9970.03898.9
3.67-4.233.1250.02937.535568179517820.9970.03499.3
4.23-5.193.4970.02641.885172149014790.9980.03199.3
5.19-7.333.2360.02639.13741116611560.9980.03199.1
7.33-38.7093.3470.02741.7222066666590.9990.03298.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_989refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.64→38.709 Å / FOM work R set: 0.7413 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.87 / Stereochemistry target values: TWIN_LSQ_F
Details: twin law -H,-K,L benzamidine at surface from crystallization conditions
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 2845 5.08 %RANDOM
Rwork0.1771 53198 --
obs0.1791 56050 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.653 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso max: 56.86 Å2 / Biso mean: 25.65 Å2 / Biso min: 13.31 Å2
Baniso -1Baniso -2Baniso -3
1--1.3499 Å2-0 Å2-0.1634 Å2
2--0.6789 Å2-0 Å2
3---0.671 Å2
Refinement stepCycle: final / Resolution: 1.64→38.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4012 0 10 444 4466
Biso mean--31.08 28.73 -
Num. residues----513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074096
X-RAY DIFFRACTIONf_angle_d1.0225485
X-RAY DIFFRACTIONf_chiral_restr0.068641
X-RAY DIFFRACTIONf_plane_restr0.003697
X-RAY DIFFRACTIONf_dihedral_angle_d16.021569
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6401-1.66830.3551600.33462671283194
1.6683-1.69870.29731350.3212666280195
1.6987-1.73130.31851250.32162615274095
1.7313-1.76670.3551430.31882674281795
1.7667-1.80510.34971320.29662665279795
1.8051-1.8470.28881410.28742649279095
1.847-1.89320.30611530.26722617277094
1.8932-1.94440.33461300.25112695282595
1.9444-2.00160.27761650.24272603276894
2.0016-2.06620.25011210.2312658277995
2.0662-2.140.25181370.21322680281795
2.14-2.22560.2361410.20652628276995
2.2256-2.32680.26131440.20172650279495
2.3268-2.44940.21581600.19532670283094
2.4494-2.60270.24751520.19152650280295
2.6027-2.80340.22361340.18082680281495
2.8034-3.0850.23221320.15972667279995
3.085-3.53040.19191420.13012678282095
3.5304-4.44380.16091530.10682658281195
4.4438-24.8850.15451370.12142724286195

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