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- PDB-5mlg: Crystal structure of rat prorenin -

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Basic information

Entry
Database: PDB / ID: 5mlg
TitleCrystal structure of rat prorenin
ComponentsRenin
KeywordsHYDROLASE / prorenin / rat
Function / homology
Function and homology information


regulation of blood volume by renin-angiotensin / Metabolism of Angiotensinogen to Angiotensins / renin / mesonephros development / juxtaglomerular apparatus development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / regulation of MAPK cascade / response to immobilization stress ...regulation of blood volume by renin-angiotensin / Metabolism of Angiotensinogen to Angiotensins / renin / mesonephros development / juxtaglomerular apparatus development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / regulation of MAPK cascade / response to immobilization stress / amyloid-beta metabolic process / cell maturation / response to cAMP / angiotensin maturation / insulin-like growth factor receptor binding / hormone-mediated signaling pathway / kidney development / regulation of blood pressure / male gonad development / apical part of cell / cellular response to xenobiotic stimulus / peptidase activity / endopeptidase activity / response to lipopolysaccharide / aspartic-type endopeptidase activity / response to xenobiotic stimulus / signaling receptor binding / proteolysis / extracellular space / membrane
Similarity search - Function
Renin-like domain / 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 ...Renin-like domain / 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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 rat prorenin
Authors: Yan, Y. / Zhou, A. / Read, R.J.
History
DepositionDec 6, 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 / entity ...chem_comp / 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
Revision 1.3Nov 6, 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: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0962
Polymers42,8751
Non-polymers2211
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint3 kcal/mol
Surface area15800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.543, 142.543, 77.035
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 / Angiotensinogenase / prorenin


Mass: 42874.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ren1, Ren / Plasmid: pCEP4 / Cell (production host): HEK293 EBNA / Production host: Homo sapiens (human) / References: UniProt: P08424, 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


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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 4.66 Å3/Da / Density % sol: 74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.9M K/NaH2PO4, 0.1M HEPES PH7.3

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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: 2.6→50.4 Å / Num. obs: 23787 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Net I/σ(I): 14.3
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.929 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.787 / % possible all: 99.9

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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: 2.6→50.21 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.936 / SU B: 11.193 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.214 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23048 1077 4.5 %RANDOM
Rwork0.21794 ---
obs0.2185 22795 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 69.102 Å2
Baniso -1Baniso -2Baniso -3
1--4.86 Å20 Å20 Å2
2---4.86 Å20 Å2
3---9.73 Å2
Refinement stepCycle: 1 / Resolution: 2.6→50.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2812 0 14 1 2827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192897
X-RAY DIFFRACTIONr_bond_other_d0.0010.022656
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.9633935
X-RAY DIFFRACTIONr_angle_other_deg0.85736169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0535361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23924.034119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0715466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1011512
X-RAY DIFFRACTIONr_chiral_restr0.0630.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213199
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02592
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_it2.4496.9031453
X-RAY DIFFRACTIONr_mcbond_other2.4486.9021452
X-RAY DIFFRACTIONr_mcangle_it4.29510.3381811
X-RAY DIFFRACTIONr_mcangle_other4.29410.3411812
X-RAY DIFFRACTIONr_scbond_it2.2767.1441444
X-RAY DIFFRACTIONr_scbond_other2.2767.1461445
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.91210.6252125
X-RAY DIFFRACTIONr_long_range_B_refined6.776.3192893
X-RAY DIFFRACTIONr_long_range_B_other6.776.3172894
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.601→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.457 120 -
Rwork0.399 1627 -
obs--100 %

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