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- PDB-5mkt: Crystal structure of mouse prorenin -

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Basic information

Entry
Database: PDB / ID: 5mkt
TitleCrystal structure of mouse prorenin
ComponentsRenin-1
KeywordsHYDROLASE / prorenin
Function / homology
Function and homology information


regulation of blood volume by renin-angiotensin / cellular response to xenobiotic stimulus => GO:0071466 / Metabolism of Angiotensinogen to Angiotensins / renin / response to xenobiotic stimulus => GO:0009410 / mesonephros development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / regulation of MAPK cascade ...regulation of blood volume by renin-angiotensin / cellular response to xenobiotic stimulus => GO:0071466 / Metabolism of Angiotensinogen to Angiotensins / renin / response to xenobiotic stimulus => GO:0009410 / mesonephros development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / regulation of MAPK cascade / response to immobilization stress / angiotensin maturation / amyloid-beta metabolic process / cell maturation / response to cAMP / insulin-like growth factor receptor binding / hormone-mediated signaling pathway / kidney development / response to organic substance / regulation of blood pressure / male gonad development / apical part of cell / peptidase activity / endopeptidase activity / response to lipopolysaccharide / aspartic-type endopeptidase activity / signaling receptor binding / proteolysis / extracellular space / membrane / cytoplasm
Similarity search - Function
Renin-like domain / Aspartic peptidase, N-terminal / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site ...Renin-like domain / Aspartic peptidase, N-terminal / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsYan, Y. / Read, R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust082961/Z/07/Z United Kingdom
British Heart FoundationPG/12/41/29679 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of mouse prorenin
Authors: Yan, Y. / Zhou, A. / Read, R.J.
History
DepositionDec 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Renin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0002
Polymers42,7781
Non-polymers2211
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint3 kcal/mol
Surface area15660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.232, 141.232, 82.961
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Renin-1 / / Angiotensinogenase / Kidney renin


Mass: 42778.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ren1, Ren, Ren-1 / Plasmid: pCEP4 / Cell line (production host): HEK293 EBNA / Production host: Homo sapiens (human) / References: UniProt: P06281, renin
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 4.92 Å3/Da / Density % sol: 75 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 0.75 K/Na H2PO4, 0.1M HEPES PH 7.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.2→50.25 Å / Num. all: 13590 / Num. obs: 71150 / % possible obs: 99.9 % / Redundancy: 5.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Net I/σ(I): 9.5
Reflection shellResolution: 3.2→3.42 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.739 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.827 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AMT

4amt


Resolution: 3.2→50.21 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.897 / SU B: 30.333 / SU ML: 0.457 / Cross valid method: THROUGHOUT / ESU R: 0.764 / ESU R Free: 0.422 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29723 703 5.2 %RANDOM
Rwork0.26308 ---
obs0.26499 12878 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 126.261 Å2
Baniso -1Baniso -2Baniso -3
1--9.25 Å20 Å20 Å2
2---9.25 Å20 Å2
3---18.51 Å2
Refinement stepCycle: 1 / Resolution: 3.2→50.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2435 0 14 0 2449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192505
X-RAY DIFFRACTIONr_bond_other_d0.0010.022258
X-RAY DIFFRACTIONr_angle_refined_deg1.0121.9643412
X-RAY DIFFRACTIONr_angle_other_deg0.82435234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6775324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35624.45792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59615370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.865157
X-RAY DIFFRACTIONr_chiral_restr0.0550.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212784
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02495
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_it2.06413.2131311
X-RAY DIFFRACTIONr_mcbond_other2.06313.2111310
X-RAY DIFFRACTIONr_mcangle_it3.72919.8021630
X-RAY DIFFRACTIONr_mcangle_other3.72819.8041631
X-RAY DIFFRACTIONr_scbond_it1.41713.0831194
X-RAY DIFFRACTIONr_scbond_other1.41713.0841195
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.67919.6431783
X-RAY DIFFRACTIONr_long_range_B_refined5.1822479
X-RAY DIFFRACTIONr_long_range_B_other5.1812480
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 40 -
Rwork0.409 950 -
obs--99.9 %

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