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- PDB-4epu: Ang1 fibrinogen-related domain (FReD) -

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Basic information

Entry
Database: PDB / ID: 4epu
TitleAng1 fibrinogen-related domain (FReD)
ComponentsAngiopoietin-1
KeywordsSIGNALING PROTEIN / fibrinogen / signaling / Tie2/TEK / extracellular
Function / homology
Function and homology information


regulation of macrophage migration inhibitory factor signaling pathway / Tie signaling pathway / glomerulus vasculature development / positive regulation of blood-brain barrier permeability / heparin proteoglycan biosynthetic process / activation of transmembrane receptor protein tyrosine kinase activity / negative regulation of vascular endothelial growth factor signaling pathway / regulation of skeletal muscle satellite cell proliferation / positive regulation of coagulation / negative regulation of cytokine production involved in immune response ...regulation of macrophage migration inhibitory factor signaling pathway / Tie signaling pathway / glomerulus vasculature development / positive regulation of blood-brain barrier permeability / heparin proteoglycan biosynthetic process / activation of transmembrane receptor protein tyrosine kinase activity / negative regulation of vascular endothelial growth factor signaling pathway / regulation of skeletal muscle satellite cell proliferation / positive regulation of coagulation / negative regulation of cytokine production involved in immune response / regulation of tumor necrosis factor production / negative regulation of cell adhesion / negative regulation of vascular permeability / sprouting angiogenesis / regulation of canonical NF-kappaB signal transduction / protein localization to cell surface / positive regulation of peptidyl-tyrosine phosphorylation / negative regulation of protein import into nucleus / positive chemotaxis / cell-substrate adhesion / microvillus / hemopoiesis / positive regulation of receptor internalization / positive regulation of blood vessel endothelial cell migration / negative regulation of endothelial cell apoptotic process / Tie2 Signaling / positive regulation of endothelial cell migration / positive regulation of cell adhesion / positive regulation of protein ubiquitination / receptor tyrosine kinase binding / blood coagulation / RAF/MAP kinase cascade / : / angiogenesis / neuron apoptotic process / in utero embryonic development / negative regulation of neuron apoptotic process / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor ligand activity / membrane raft / positive regulation of gene expression / negative regulation of apoptotic process / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
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 alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 ...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 alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.098 Å
AuthorsYeykal, C.C. / Adams, E.J.
CitationJournal: To be Published
Title: Biochemical and structural characterization of the Ang1 fibrinogen-related domain
Authors: Yeykal, C.C. / Sundaresan, L. / Mrksich, M. / Adams, E.J.
History
DepositionApr 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Angiopoietin-1
B: Angiopoietin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6474
Polymers50,5672
Non-polymers802
Water4,179232
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.903, 80.903, 186.087
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-805-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 1:215 )A1 - 215
211chain B and (resseq 1:215 )B1 - 215

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Components

#1: Protein Angiopoietin-1 / ANG-1


Mass: 25283.457 Da / Num. of mol.: 2
Fragment: Fibrinogen C-terminal domain, UNP residues 282-497
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANGPT1, KIAA0003 / Production host: Trichopulsia ni (cabbage looper) / References: UniProt: Q15389
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.48 Å3/Da / Density % sol: 64.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M PIPES pH 6.5, 0.2M NaCl, 2M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0781 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 31, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2.098→50 Å / Num. obs: 39116 / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassificationNB
PHENIX1.7_650refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z3S

1z3s


Resolution: 2.098→46.443 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8492 / SU ML: 0.26 / σ(F): 0 / Phase error: 22.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2008 1873 5.03 %
Rwork0.1826 --
obs0.1835 37253 92.67 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.916 Å2 / ksol: 0.389 e/Å3
Displacement parametersBiso max: 147.92 Å2 / Biso mean: 37.4776 Å2 / Biso min: 14.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.899 Å2-0 Å2-0 Å2
2--0.899 Å20 Å2
3----1.7979 Å2
Refinement stepCycle: LAST / Resolution: 2.098→46.443 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3472 0 2 232 3706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073589
X-RAY DIFFRACTIONf_angle_d1.0754821
X-RAY DIFFRACTIONf_chiral_restr0.076460
X-RAY DIFFRACTIONf_plane_restr0.004629
X-RAY DIFFRACTIONf_dihedral_angle_d14.3181269
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1725X-RAY DIFFRACTIONPOSITIONAL0.015
12B1725X-RAY DIFFRACTIONPOSITIONAL0.015
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.098-2.15480.3465950.29311804189962
2.1548-2.21820.24641280.24512383251181
2.2182-2.28980.24981250.22682627275289
2.2898-2.37170.21341420.21952686282891
2.3717-2.46660.23961500.2042764291494
2.4666-2.57890.22641580.20792777293595
2.5789-2.71480.24441450.20222849299497
2.7148-2.88490.23471440.21872905304998
2.8849-3.10760.22881620.19742886304898
3.1076-3.42020.19811510.17962899305099
3.4202-3.91490.17251560.152926308299
3.9149-4.93150.14721850.129729093094100
4.9315-46.45470.19521320.18852965309799
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0030.00120.00310.0029-0.00070.0016-0.0034-0.01410.0249-0.0051-0.012-0.0218-0.01780.0144-0.01610.4432-0.31940.10680.2741-0.13710.414415.758131.2887-9.3111
20.00710.0042-0.00910.0004-0.00150.0007-0.00780.00550.0514-0.02550.00210.0021-0.05110.0358-0.04690.3668-0.46630.14110.07430.05670.117611.520621.9331-20.4854
30.01760.00010.00580.00420.00860.01970.0159-0.0520.02170.0062-0.0011-0.0131-0.05110.0756-0.0040.3341-0.30820.02670.2666-0.11250.212611.02419.3008-9.6761
40.0050.0056-0.00570.02480.01790.03090.0065-0.00010.0325-0.0040.01280.004-0.07840.1226-0.00520.2455-0.13140.01840.2158-0.03780.0674.610212.754-11.3919
50.01910.012-00.00780.00470.00130.02310.0266-0.0339-0.05130.0404-0.0221-0.04560.03090.06680.2538-0.2899-0.04030.1801-0.06550.07419.21115.1559-20.991
60.00910.0031-0.03980.001-0.01020.21720.0141-0.0189-0.00450.0199-0.01130.00950.0022-0.0014-0.00290.3246-0.17940.00760.29230.00210.172-2.30238.8284-32.459
70.01720.0048-0.01870.0103-0.00280.03030.0159-0.02740.01990.0217-0.00210.0227-0.03350.02430.00370.3802-0.16420.02380.1636-0.01480.18210.135615.4077-17.9921
80.108-0.07430.02550.0515-0.01810.0075-0.0186-0.0359-0.0255-0.00550.0067-0.0801-0.00120.0614-0.00460.1131-0.04520.05850.6003-0.13410.448934.9281-2.26121.7418
90.0095-0.0167-0.00880.03510.02550.0202-0.0197-0.0055-0.0179-0.00170.0144-0.05830.0020.0097-0.01450.09420.0466-0.00360.4846-0.05050.259726.6352-7.08377.2138
100.07830.0110.04240.0076-0.00440.03410.02160.014-0.03760.01090.0215-0.03430.00010.064-0.00530.0478-0.0867-0.07190.5793-0.0630.163323.44493.482817.0971
110.0383-0.009-0.02240.01850.00290.0076-0.00250.0028-0.0006-0.03010.0443-0.025-0.04760.0980.00960.0811-0.08920.07170.5076-0.0530.226422.2246-0.10732.2576
120.0756-0.0062-0.01690.00220.00530.0091-0.0199-0.0308-0.01380.03450.0339-0.0485-0.07550.1564-0.00640.2155-0.04790.03530.414-0.02990.215515.4249-3.6135.7849
130.00790.00740.01970.02780.04870.0991-0.01530.03220.0007-0.0344-0.01690.0044-0.07470.07280.00370.1468-0.0512-0.01150.333-0.04510.066510.565-0.75111.5467
140.04420.0188-0.01560.0169-0.00260.03220.024-0.05550.0430.01930.04020.0252-0.01720.04540.06110.0626-0.0750.04930.42050.01760.08749.06415.396613.5681
150.15390.05450.08680.04540.07890.1443-0.00730.0577-0.0027-0.01130.0056-0.0022-0.00390.01550.00550.1765-0.07220.00390.41920.01040.18556.4896-6.405625.0394
160.0737-0.00230.01390.02740.01390.0127-0.00550.0312-0.0812-0.02150.0102-0.0002-0.00090.0460.01170.10180.00860.0040.448-0.02310.19813.4091-7.587510.5754
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 283:311)A283 - 311
2X-RAY DIFFRACTION2chain 'A' and (resseq 312:358)A312 - 358
3X-RAY DIFFRACTION3chain 'A' and (resseq 359:378)A359 - 378
4X-RAY DIFFRACTION4chain 'A' and (resseq 379:415)A379 - 415
5X-RAY DIFFRACTION5chain 'A' and (resseq 416:463)A416 - 463
6X-RAY DIFFRACTION6chain 'A' and (resseq 464:473)A464 - 473
7X-RAY DIFFRACTION7chain 'A' and (resseq 474:497)A474 - 497
8X-RAY DIFFRACTION8chain 'B' and (resseq 283:311)B283 - 311
9X-RAY DIFFRACTION9chain 'B' and (resseq 312:330)B312 - 330
10X-RAY DIFFRACTION10chain 'B' and (resseq 331:358)B331 - 358
11X-RAY DIFFRACTION11chain 'B' and (resseq 359:378)B359 - 378
12X-RAY DIFFRACTION12chain 'B' and (resseq 379:399)B379 - 399
13X-RAY DIFFRACTION13chain 'B' and (resseq 400:415)B400 - 415
14X-RAY DIFFRACTION14chain 'B' and (resseq 416:463)B416 - 463
15X-RAY DIFFRACTION15chain 'B' and (resseq 464:473)B464 - 473
16X-RAY DIFFRACTION16chain 'B' and (resseq 474:497)B474 - 497

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