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- PDB-2wxy: Crystal structure of mouse angiotensinogen in the reduced form -

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Basic information

Entry
Database: PDB / ID: 2wxy
TitleCrystal structure of mouse angiotensinogen in the reduced form
ComponentsANGIOTENSINOGEN
KeywordsHORMONE / GLYCOPROTEIN / HYPERTENSION / VASOCONSTRICTOR / RENIN / SERPINS / VASOACTIVE / ANGIOTENSIN
Function / homology
Function and homology information


renal response to blood flow involved in circulatory renin-angiotensin regulation of systemic arterial blood pressure / establishment of blood-nerve barrier / aldosterone secretion / smooth muscle cell proliferation / regulation of systemic arterial blood pressure by circulatory renin-angiotensin / brain renin-angiotensin system / ovarian follicle rupture / angiotensin-mediated vasodilation involved in regulation of systemic arterial blood pressure / type 2 angiotensin receptor binding / vasopressin secretion ...renal response to blood flow involved in circulatory renin-angiotensin regulation of systemic arterial blood pressure / establishment of blood-nerve barrier / aldosterone secretion / smooth muscle cell proliferation / regulation of systemic arterial blood pressure by circulatory renin-angiotensin / brain renin-angiotensin system / ovarian follicle rupture / angiotensin-mediated vasodilation involved in regulation of systemic arterial blood pressure / type 2 angiotensin receptor binding / vasopressin secretion / Metabolism of Angiotensinogen to Angiotensins / Peptide ligand-binding receptors / vascular associated smooth muscle cell proliferation / G alpha (q) signalling events / regulation of renal output by angiotensin / peristalsis / renin-angiotensin regulation of aldosterone production / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / drinking behavior / smooth muscle cell differentiation / positive regulation of organ growth / G alpha (i) signalling events / positive regulation of fatty acid biosynthetic process / type 1 angiotensin receptor binding / positive regulation of multicellular organism growth / hormone metabolic process / organ growth / branching involved in ureteric bud morphogenesis / blood vessel development / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of epithelial to mesenchymal transition / response to salt stress / extracellular matrix organization / astrocyte activation / response to cold / positive regulation of cytokine production / cell-matrix adhesion / angiotensin-activated signaling pathway / kidney development / negative regulation of smooth muscle cell proliferation / serine-type endopeptidase inhibitor activity / regulation of blood pressure / adenylate cyclase-activating G protein-coupled receptor signaling pathway / MAPK cascade / regulation of gene expression / regulation of inflammatory response / neuron apoptotic process / regulation of apoptotic process / negative regulation of neuron apoptotic process / cell population proliferation / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / receptor ligand activity / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular region
Similarity search - Function
Angiotensinogen, serpin domain / Angiotensinogen / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily ...Angiotensinogen, serpin domain / Angiotensinogen / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsZhou, A. / Wei, Z. / Carrell, R.W. / Read, R.J.
CitationJournal: Nature / Year: 2010
Title: A Redox Switch in Angiotensinogen Modulates Angiotensin Release.
Authors: Zhou, A. / Carrell, R.W. / Murphy, M.P. / Wei, Z. / Yan, Y. / Stanley, P.L. / Stein, P.E. / Pipkin, F.B. / Read, R.J.
History
DepositionNov 11, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: ANGIOTENSINOGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,00810
Polymers49,6061
Non-polymers4029
Water2,666148
1
C: ANGIOTENSINOGEN
hetero molecules

C: ANGIOTENSINOGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,01720
Polymers99,2122
Non-polymers80518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area3470 Å2
ΔGint-61.1 kcal/mol
Surface area36970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.794, 64.794, 463.197
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein ANGIOTENSINOGEN / SERPIN A8


Mass: 49606.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PSUMO3-MANGT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11859
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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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: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 4.25 / Details: 1.6-2.0M NA2HPO4, PH4.25

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 32476 / % possible obs: 91.3 % / Observed criterion σ(I): 2 / Redundancy: 17.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 27.9
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.1 / % possible all: 64.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0099refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.1→48 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.933 / SU B: 10.293 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24215 1644 5.1 %RANDOM
Rwork0.21877 ---
obs0.21996 30701 91.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.622 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20.33 Å20 Å2
2--0.67 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3256 0 24 148 3428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223366
X-RAY DIFFRACTIONr_bond_other_d0.0010.022257
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.9764578
X-RAY DIFFRACTIONr_angle_other_deg0.84835539
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1685422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45924.589146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84815551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3221517
X-RAY DIFFRACTIONr_chiral_restr0.0690.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213696
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02645
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6091.52104
X-RAY DIFFRACTIONr_mcbond_other0.1181.5839
X-RAY DIFFRACTIONr_mcangle_it1.11823412
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.47531262
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3724.51162
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 81 -
Rwork0.303 1458 -
obs--60.38 %
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)
111.0315-0.77162.00356.9467-2.794510.4752-0.301-0.11961.2489-0.19070.2228-0.3952-1.34080.26220.07830.2741-0.0007-0.0480.49970.11670.575930.8757-9.0411-15.6043
20.9834-0.14770.23181.7644-1.44441.76820.03290.075-0.0631-0.0835-0.0074-0.08760.0301-0.1483-0.02550.0540.05620.04290.24360.11740.088712.8724-23.9322-15.6663
30.85030.81880.00342.2083-1.59182.16420.03940.1136-0.242-0.1829-0.0412-0.26440.1946-0.15810.00180.17320.07110.02160.43390.15150.280716.7836-37.0724-6.3608
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C2 - 16
2X-RAY DIFFRACTION2C28 - 405
3X-RAY DIFFRACTION3C417 - 450

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