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- PDB-7dzl: A69C-M71L mutant of Fabp protein -

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Basic information

Entry
Database: PDB / ID: 7dzl
TitleA69C-M71L mutant of Fabp protein
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: 1.64 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)31,8134
Polymers31,3002
Non-polymers5132
Water6,341352
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint1 kcal/mol
Surface area12020 Å2
Unit cell
Length a, b, c (Å)56.987, 66.830, 68.406
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: 15649.856 Da / Num. of mol.: 2
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.: 352 / 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: 2.02 Å3/Da / Density % sol: 39.15 %
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: BL17U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.63→47.45 Å / Num. obs: 32859 / % possible obs: 99.7 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 38.98
Reflection shellResolution: 1.63→1.72 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 10.8 / Num. unique obs: 3185 / % possible all: 98.8

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Processing

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

1lkk


Resolution: 1.64→19.85 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 21.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.215 1520 4.63 %
Rwork0.1871 31279 -
obs0.1884 32799 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.48 Å2 / Biso mean: 24.2876 Å2 / Biso min: 10.61 Å2
Refinement stepCycle: final / Resolution: 1.64→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 0 36 352 2428
Biso mean--30.16 34.11 -
Num. residues----258
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.64-1.690.25131400.21812771291199
1.69-1.750.26721390.207527882927100
1.75-1.820.20111300.201828042934100
1.82-1.90.27081340.201528432977100
1.9-20.23451420.197827992941100
2-2.130.24161360.196428202956100
2.13-2.290.24531380.204428402978100
2.29-2.520.22881360.209828362972100
2.52-2.890.2351390.200928663005100
2.89-3.630.1841420.173828933035100
3.63-19.850.18571440.162330193163100
Refinement TLS params.Method: refined / Origin x: 13.5184 Å / Origin y: -8.1344 Å / Origin z: -21.0104 Å
111213212223313233
T0.1291 Å20.008 Å2-0.0035 Å2-0.1064 Å2-0.0106 Å2--0.1015 Å2
L0.8156 °2-0.1503 °2-0.1793 °2-0.4087 °2-0.0331 °2--0.399 °2
S0.0335 Å °-0.0447 Å °0.0099 Å °0.0643 Å °-0.0034 Å °0.0041 Å °0.0064 Å °0.0251 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 150
2X-RAY DIFFRACTION1allB1 - 150
3X-RAY DIFFRACTION1allC1 - 404

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