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- PDB-8h55: The structure of zebrafish angiotensinogen -

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Basic information

Entry
Database: PDB / ID: 8h55
TitleThe structure of zebrafish angiotensinogen
ComponentsAngiotensinogen
KeywordsRECOMBINATION / Serpin / angiotensinogen / zebrafish
Function / homology
Function and homology information


Metabolism of Angiotensinogen to Angiotensins / Peptide ligand-binding receptors / G alpha (i) signalling events / G alpha (q) signalling events / vasoconstriction / regulation of systemic arterial blood pressure by renin-angiotensin / serine-type endopeptidase inhibitor activity / regulation of apoptotic process / extracellular space
Similarity search - Function
Angiotensinogen, serpin domain / Angiotensinogen / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors
Similarity search - Domain/homology
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsZhou, A. / Wei, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81870309 China
CitationJournal: To Be Published
Title: BIOLOGICAL IMPLICATIONS OF A 2 ANGSTROMS STRUCTURE OF DIMERIC ANGIOTENSINOGEN
Authors: Zhou, A. / Wei, H.
History
DepositionOct 12, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Angiotensinogen
B: Angiotensinogen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,78310
Polymers98,0152
Non-polymers7698
Water3,531196
1
A: Angiotensinogen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4886
Polymers49,0071
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-19 kcal/mol
Surface area19030 Å2
MethodPISA
2
B: Angiotensinogen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2964
Polymers49,0071
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-20 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.940, 88.760, 118.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Angiotensinogen / Serpin A8


Mass: 49007.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: agt, SO:0001217 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8JH29
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M Potassium Sulfate, 20% PGE 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.03→44.38 Å / Num. obs: 57090 / % possible obs: 99.41 % / Redundancy: 1.9 % / CC1/2: 0.99 / Net I/σ(I): 5.43
Reflection shellResolution: 2.03→2.103 Å / Num. unique obs: 5648 / CC1/2: 0.474

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ANT

1ant


Resolution: 2.03→44.38 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.25 2746 4.81 %
Rwork0.2186 54344 -
obs0.2202 57090 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.98 Å2 / Biso mean: 61.4488 Å2 / Biso min: 26.68 Å2
Refinement stepCycle: final / Resolution: 2.03→44.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6682 0 40 196 6918
Biso mean--79.77 51.56 -
Num. residues----861
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.03-2.060.40131250.396727102835100
2.06-2.10.42281190.37182709282899
2.1-2.140.35441380.350127392877100
2.14-2.180.33141280.31972666279499
2.18-2.230.29551370.28842703284099
2.23-2.280.29171670.30052725289299
2.28-2.340.30491460.27272644279099
2.34-2.40.28531280.266827272855100
2.4-2.480.29421390.2642705284499
2.48-2.560.26851410.25632700284199
2.56-2.650.35241380.26532676281499
2.65-2.750.26491570.24512697285499
2.75-2.880.32731020.23722757285999
2.88-3.030.25711090.227227312840100
3.03-3.220.2821200.233827482868100
3.22-3.470.27261420.221927132855100
3.47-3.820.24161520.190627452897100
3.82-4.370.20791710.170727132884100
4.37-5.50.18631480.159627442892100
5.5-44.380.21171390.19892792293199
Refinement TLS params.Method: refined / Origin x: 12.8143 Å / Origin y: -17.5035 Å / Origin z: 29.6105 Å
111213212223313233
T0.2512 Å20.093 Å2-0.0131 Å2-0.3622 Å2-0.0543 Å2--0.3574 Å2
L0.3854 °20.136 °20.0543 °2-0.8754 °20.3402 °2--1.5014 °2
S-0.0486 Å °-0.0479 Å °0.0246 Å °-0.0205 Å °-0.1063 Å °0.1375 Å °-0.0805 Å °-0.2518 Å °0.1335 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 436
2X-RAY DIFFRACTION1allB5 - 436
3X-RAY DIFFRACTION1allD1 - 8
4X-RAY DIFFRACTION1allS1 - 204

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