[English] 日本語
Yorodumi
- PDB-5inw: Structure of reaction loop cleaved lamprey angiotensinogen -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5inw
TitleStructure of reaction loop cleaved lamprey angiotensinogen
Components
  • C-terminal peptide of Putative angiotensinogen
  • Putative angiotensinogen
KeywordsHORMONE / Angiotensinogen / Serpin / Heparin binding
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / regulation of apoptotic process / extracellular space
Similarity search - Function
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / 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 / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Putative angiotensinogen / Putative angiotensinogen
Similarity search - Component
Biological speciesLampetra fluviatilis (European river lamprey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWei, H. / Zhou, A.
Funding support China, 4items
OrganizationGrant numberCountry
National Basic Research Program of China2014CB910304 China
National Natural Science Foundation of China31370727 China
National Natural Science Foundation of China31170724 China
Program for Professor of Special Appointment (Eastern Scholar) at Shanghai Institutions of Higher Learning, Shanghai PuJiang Program, and Innovation Program of Shanghai Municipal Education Commission12ZZ113 China
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Heparin Binds Lamprey Angiotensinogen and Promotes Thrombin Inhibition through a Template Mechanism
Authors: Wei, H. / Cai, H. / Wu, J. / Wei, Z. / Zhang, F. / Huang, X. / Ma, L. / Feng, L. / Zhang, R. / Wang, Y. / Ragg, H. / Zheng, Y. / Zhou, A.
History
DepositionMar 8, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Dec 7, 2016Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative angiotensinogen
B: Putative angiotensinogen
C: C-terminal peptide of Putative angiotensinogen
D: C-terminal peptide of Putative angiotensinogen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4565
Polymers101,3604
Non-polymers961
Water362
1
A: Putative angiotensinogen
C: C-terminal peptide of Putative angiotensinogen


Theoretical massNumber of molelcules
Total (without water)50,6802
Polymers50,6802
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-35 kcal/mol
Surface area16370 Å2
MethodPISA
2
B: Putative angiotensinogen
D: C-terminal peptide of Putative angiotensinogen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7763
Polymers50,6802
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-33 kcal/mol
Surface area16030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.400, 119.360, 141.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A75 - 417
2010B75 - 417
1020C422 - 451
2020D422 - 451

NCS ensembles :
ID
1
2

-
Components

#1: Protein Putative angiotensinogen


Mass: 46697.180 Da / Num. of mol.: 2 / Fragment: UNP residues 26-443 / Mutation: INSERTION OF TWO ALA BETWEEN 416 AND 417, I418R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lampetra fluviatilis (European river lamprey)
Gene: agt / Production host: Escherichia coli (E. coli) / References: UniProt: C0MNC6
#2: Protein/peptide C-terminal peptide of Putative angiotensinogen


Mass: 3982.689 Da / Num. of mol.: 2 / Fragment: UNP residues 444-478
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lampetra fluviatilis (European river lamprey)
Gene: agt / Production host: Escherichia coli (E. coli) / References: UniProt: C0MNC7, UniProt: C0MNC6*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.77 Å3/Da / Density % sol: 30.41 %
Crystal growTemperature: 295 K / Method: liquid diffusion / pH: 4.6
Details: 25% PEG 4000, 0.1M Na acetate pH4.6, 0.2M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.7→91.26 Å / Num. obs: 18674 / % possible obs: 90.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 12.3
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.065 / Mean I/σ(I) obs: 1.7 / % possible all: 84.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NDD

3ndd


Resolution: 2.7→91.26 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.905 / SU B: 41.066 / SU ML: 0.36 / Cross valid method: THROUGHOUT / ESU R Free: 0.446 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27698 930 5 %RANDOM
Rwork0.20426 ---
obs0.20774 17694 90.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.062 Å2
Baniso -1Baniso -2Baniso -3
1-3.24 Å20 Å2-0 Å2
2---1.85 Å20 Å2
3----1.39 Å2
Refinement stepCycle: LAST / Resolution: 2.7→91.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5697 0 5 2 5704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195815
X-RAY DIFFRACTIONr_bond_other_d0.0060.025683
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.9627847
X-RAY DIFFRACTIONr_angle_other_deg1.208313075
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1615723
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.49623.433233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.525151043
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0391534
X-RAY DIFFRACTIONr_chiral_restr0.0930.2892
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026437
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021317
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_it2.9525.2482910
X-RAY DIFFRACTIONr_mcbond_other2.9515.2472909
X-RAY DIFFRACTIONr_mcangle_it4.797.8653627
X-RAY DIFFRACTIONr_mcangle_other4.7897.8663628
X-RAY DIFFRACTIONr_scbond_it2.9865.6512905
X-RAY DIFFRACTIONr_scbond_other2.9855.6512906
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9628.334221
X-RAY DIFFRACTIONr_long_range_B_refined7.61341.7756187
X-RAY DIFFRACTIONr_long_range_B_other7.61341.786188
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A389460.06
12B389460.06
21C29280.04
22D29280.04
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 66 -
Rwork0.325 1197 -
obs--85.11 %
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)
11.2999-0.2159-0.53081.56960.40292.3127-0.03310.1078-0.06170.01750.0242-0.11820.21590.10360.00890.0761-0.0325-0.02320.0560.00240.069823.8284375.76615.3301
21.8089-1.4937-0.41773.27950.46152.20790.0441-0.13360.06-0.07380.09470.0347-0.0611-0.1561-0.13880.0803-0-0.04380.05960.05120.13.8336374.45348.7057
31.50440.201-0.56920.89670.07234.6448-0.09420.0038-0.34780.3122-0.1104-0.12010.65660.23390.20450.25020.01480.04370.04940.00970.162225.4171362.892612.3228
42.9711-2.5477-1.09994.73220.78681.23260.0707-0.23330.638-0.208-0.084-0.5306-0.396-0.17240.01330.2390.1445-0.09170.1798-0.07930.30181.3339387.692951.9035
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A73 - 416
2X-RAY DIFFRACTION2B75 - 416
3X-RAY DIFFRACTION3C422 - 452
4X-RAY DIFFRACTION4D421 - 452

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more