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- PDB-7dzk: Fabp protein after hv -

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Basic information

Entry
Database: PDB / ID: 7dzk
TitleFabp protein after hv
ComponentsFatty acid-binding protein, liver
KeywordsRECOMBINATION / FABP
Function / homology
Function and homology information


cellular detoxification / Heme degradation / 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 ...cellular detoxification / Heme degradation / 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 / cellular response to hydrogen peroxide / cellular response to hypoxia / chromatin binding / 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
PALMITIC ACID / Fatty acid-binding protein, liver
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsLi, H. / Yu, L.-J. / Liu, X. / Shen, J.-R. / Wang, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat.Chem. / Year: 2022
Title: Excited-state intermediates in a designer protein encoding a phototrigger caught by an X-ray free-electron laser.
Authors: Liu, X. / Liu, P. / Li, H. / Xu, Z. / Jia, L. / Xia, Y. / Yu, M. / Tang, W. / Zhu, X. / Chen, C. / Zhang, Y. / Nango, E. / Tanaka, R. / Luo, F. / Kato, K. / Nakajima, Y. / Kishi, S. / Yu, H. ...Authors: Liu, X. / Liu, P. / Li, H. / Xu, Z. / Jia, L. / Xia, Y. / Yu, M. / Tang, W. / Zhu, X. / Chen, C. / Zhang, Y. / Nango, E. / Tanaka, R. / Luo, F. / Kato, K. / Nakajima, Y. / Kishi, S. / Yu, H. / Matsubara, N. / Owada, S. / Tono, K. / Iwata, S. / Yu, L.J. / Shen, J.R. / Wang, J.
History
DepositionJan 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 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: Fatty acid-binding protein, liver
B: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7854
Polymers31,2722
Non-polymers5132
Water6,017334
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-2 kcal/mol
Surface area12030 Å2
Unit cell
Length a, b, c (Å)56.922, 66.157, 68.136
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 15635.829 Da / Num. of mol.: 2 / Mutation: C69A, L71M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP1, FABPL / Production host: Escherichia coli (E. coli) / References: UniProt: P07148
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.04 Å3/Da / Density % sol: 39.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M potassium thiocyanate, pH 7.0, 30% PEG 2000 monomethyl ether

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Aug 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.53→47.46 Å / Num. obs: 38767 / % possible obs: 99.1 % / Redundancy: 2 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.011 / Net I/σ(I): 25.3
Reflection shellResolution: 1.53→1.62 Å / Redundancy: 2 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LKK

1lkk


Resolution: 1.54→19.69 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.223 1770 4.61 %
Rwork0.191 --
obs0.192 38384 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.4 Å2
Refinement stepCycle: LAST / Resolution: 1.54→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2038 0 36 334 2408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.580.31031330.26052810X-RAY DIFFRACTION100
1.58-1.630.23191340.24322791X-RAY DIFFRACTION100
1.63-1.680.25081370.2272801X-RAY DIFFRACTION100
1.68-1.740.24821380.21152792X-RAY DIFFRACTION100
1.74-1.810.24961330.20812800X-RAY DIFFRACTION100
1.81-1.890.25761350.2082839X-RAY DIFFRACTION100
1.89-1.990.21761240.19662480X-RAY DIFFRACTION89
1.99-2.120.20771340.19952837X-RAY DIFFRACTION100
2.12-2.280.23641370.20182847X-RAY DIFFRACTION100
2.28-2.510.23841390.20572828X-RAY DIFFRACTION100
2.51-2.870.27571380.21692875X-RAY DIFFRACTION100
2.87-3.610.21451410.18162892X-RAY DIFFRACTION100
3.61-19.690.18611470.16153022X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 13.1962 Å / Origin y: -8.0686 Å / Origin z: -20.9025 Å
111213212223313233
T0.2002 Å20.0016 Å2-0.018 Å2-0.181 Å2-0.0082 Å2--0.1562 Å2
L1.5317 °2-0.3032 °2-0.423 °2-0.5833 °2-0.0189 °2--0.8963 °2
S0.0297 Å °-0.1046 Å °-0.0345 Å °0.036 Å °0.0054 Å °0.004 Å °0.0357 Å °0.1117 Å °-0.0343 Å °
Refinement TLS groupSelection details: ALL

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