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- PDB-6u73: Human Angiopoietin-Like 4 C-Terminal Domain (cANGPTL4) with Myris... -

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Basic information

Entry
Database: PDB / ID: 6u73
TitleHuman Angiopoietin-Like 4 C-Terminal Domain (cANGPTL4) with Myristic Acid
ComponentsAngiopoietin-related protein 4
KeywordsSIGNALING PROTEIN / Fibrinogen-like domain / Angiogenesis / Cancer cells / Metastasis
Function / homology
Function and homology information


negative regulation of lipoprotein lipase activity / Assembly of active LPL and LIPC lipase complexes / Regulation of CDH11 function / endothelial cell apoptotic process / triglyceride homeostasis / enzyme inhibitor activity / protein unfolding / negative regulation of endothelial cell apoptotic process / lipid metabolic process / PPARA activates gene expression ...negative regulation of lipoprotein lipase activity / Assembly of active LPL and LIPC lipase complexes / Regulation of CDH11 function / endothelial cell apoptotic process / triglyceride homeostasis / enzyme inhibitor activity / protein unfolding / negative regulation of endothelial cell apoptotic process / lipid metabolic process / PPARA activates gene expression / Transcriptional regulation of white adipocyte differentiation / positive regulation of angiogenesis / angiogenesis / collagen-containing extracellular matrix / blood microparticle / response to hypoxia / negative regulation of apoptotic process / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain ...Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
MYRISTIC ACID / Angiopoietin-related protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsTarver, C.L. / Yuan, Q. / Singhal, A.J. / Ramaker, R. / Cooper, S. / Pusey, M.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)5R42GM116283-03 United States
CitationJournal: To Be Published
Title: Crystal Structures of Angiopoietin-Like 4s C-Terminal Domain (cANGPTL4) Reveal a Binding Site for Various Ligands
Authors: Tarver, C.L. / Yuan, Q. / Singhal, A.J. / Ramaker, R. / Cooper, S. / Pusey, M.L.
History
DepositionAug 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Angiopoietin-related protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6872
Polymers24,4581
Non-polymers2281
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)132.496, 135.632, 39.596
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Angiopoietin-related protein 4 / Angiopoietin-like protein 4 / Hepatic fibrinogen/angiopoietin-related protein / HFARP


Mass: 24458.404 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ANGPTL4, ARP4, HFARP, PGAR, PP1158, PSEC0166, UNQ171/PRO197
Plasmid: pET3a / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): T7 Shuffle Cells / References: UniProt: Q9BY76
#2: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.64 Å3/Da / Density % sol: 66.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES 7.5, 0.1M Sodium chloride, 1.6M Ammonium sulfate, Myristic acid
PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.34→42.79 Å / Num. obs: 14821 / % possible obs: 96.39 % / Redundancy: 6.3 % / Biso Wilson estimate: 38.32 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.039 / Net I/σ(I): 17.2
Reflection shellResolution: 2.34→2.47 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.408 / Num. unique obs: 712 / CC1/2: 0.937 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-30001.16_3549data reduction
HKL-30001.16_3549data scaling
AutoSolphasing
PHENIXmodel building
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EUB

6eub


Resolution: 2.38→42.79 Å / SU ML: 0.2509 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.2553
RfactorNum. reflection% reflection
Rfree0.2398 1453 9.95 %
Rwork0.1944 --
obs0.1989 14610 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41.1 Å2
Refinement stepCycle: LAST / Resolution: 2.38→42.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 0 16 42 1784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091793
X-RAY DIFFRACTIONf_angle_d1.10412426
X-RAY DIFFRACTIONf_chiral_restr0.065241
X-RAY DIFFRACTIONf_plane_restr0.0066318
X-RAY DIFFRACTIONf_dihedral_angle_d19.2764663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.460.25391390.18391242X-RAY DIFFRACTION94.98
2.46-2.560.22751390.18861271X-RAY DIFFRACTION97.11
2.56-2.670.28991420.20031283X-RAY DIFFRACTION97.54
2.67-2.820.25421380.19811300X-RAY DIFFRACTION96.7
2.82-2.990.26551470.20231273X-RAY DIFFRACTION97.66
2.99-3.220.26731430.20351321X-RAY DIFFRACTION99.19
3.22-3.550.24881490.20531341X-RAY DIFFRACTION99.73
3.55-4.060.22161440.18941332X-RAY DIFFRACTION99.26
4.06-5.110.21241530.171359X-RAY DIFFRACTION99.28
5.11-6.460.23961590.21061435X-RAY DIFFRACTION99.31

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