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- PDB-7dze: Fabp ground state captured by XFELs -

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Basic information

Entry
Database: PDB / ID: 7dze
TitleFabp ground state captured by XFELs
ComponentsFatty acid-binding protein, liver
KeywordsRECOMBINATION / FABP
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
PALMITIC ACID / Fatty acid-binding protein, liver
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.55 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
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint0 kcal/mol
Surface area12020 Å2
Unit cell
Length a, b, c (Å)57.650, 66.700, 69.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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.: 212 / 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: 2.06 Å3/Da / Density % sol: 40.32 %
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: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.24 Å
DetectorType: MPCCD / Detector: CCD / Date: Dec 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 40601 / % possible obs: 100 % / Redundancy: 207 % / CC1/2: 0.98 / Net I/σ(I): 85
Reflection shellResolution: 1.55→1.61 Å / Mean I/σ(I) obs: 4.3 / Num. unique obs: 3972 / CC1/2: 0.61 / % possible all: 100
Serial crystallography sample deliveryMethod: injection

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Processing

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

1lkk


Resolution: 1.55→19.87 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1984 1815 4.62 %
Rwork0.1769 37457 -
obs0.1779 39272 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.69 Å2 / Biso mean: 33.0856 Å2 / Biso min: 16.74 Å2
Refinement stepCycle: final / Resolution: 1.55→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2038 0 36 212 2286
Biso mean--38.9 44.54 -
Num. residues----258
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.55-1.590.31161370.299228232960
1.59-1.640.25011370.244228402977
1.64-1.690.24541370.213528422979
1.69-1.750.21151380.191228432981
1.75-1.820.23941380.207428512989
1.82-1.90.29581390.219428522991
1.91-2.010.21621380.180928653003
2.01-2.130.19981390.180228673006
2.13-2.30.21821400.178628803020
2.3-2.530.20981390.186228803019
2.53-2.890.20291410.184129153056
2.89-3.640.17741430.163529413084
3.64-19.870.16981490.15630583207
Refinement TLS params.Method: refined / Origin x: 13.8121 Å / Origin y: -7.938 Å / Origin z: -21.2236 Å
111213212223313233
T0.2096 Å2-0.0002 Å2-0.0083 Å2-0.1742 Å2-0.0053 Å2--0.1698 Å2
L1.6735 °2-0.281 °2-0.5751 °2-0.6281 °20.0407 °2--1.1188 °2
S0.0174 Å °-0.1403 Å °-0.0253 Å °0.0531 Å °0.0071 Å °0.0355 Å °-0.0045 Å °0.1172 Å °-0.021 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 266
2X-RAY DIFFRACTION1allB1 - 266

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