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- PDB-4amt: Crystal structure at 2.6A of human prorenin -

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Basic information

Entry
Database: PDB / ID: 4amt
TitleCrystal structure at 2.6A of human prorenin
ComponentsRENIN
KeywordsHYDROLASE / HORMONE
Function / homology
Function and homology information


renin / juxtaglomerular apparatus development / 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 ...renin / juxtaglomerular apparatus development / 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 / Metabolism of Angiotensinogen to Angiotensins / cell maturation / response to cAMP / hormone-mediated signaling pathway / kidney development / insulin-like growth factor receptor binding / regulation of blood pressure / male gonad development / cellular response to xenobiotic stimulus / apical part of cell / peptidase activity / response to lipopolysaccharide / aspartic-type endopeptidase activity / signaling receptor binding / proteolysis / extracellular space / extracellular region / plasma membrane
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 speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZhou, A.
CitationJournal: To be Published
Title: The Crystal Structure of Prorenin
Authors: Zhou, A.
History
DepositionMar 13, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5777
Polymers42,3641
Non-polymers1,2136
Water1629
1
A: RENIN
hetero molecules

A: RENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,15414
Polymers84,7282
Non-polymers2,42612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area5980 Å2
ΔGint-118.8 kcal/mol
Surface area30840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.320, 141.320, 75.850
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 / PRORENIN / ANGIOTENSINOGENASE


Mass: 42364.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCEP4 / Cell line (production host): HEK293 EBNA / Production host: HOMO SAPIENS (human) / References: UniProt: P00797, renin
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.21 Å3/Da / Density % sol: 70.82 % / Description: NONE
Crystal growDetails: 1.0 M LITHIUM SULFATE, 0.1 M CITRATE PH 5.6, 0.5 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.6→44.69 Å / Num. obs: 22788 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.9
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.718 / Mean I/σ(I) obs: 1.8 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
CCP4data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V0Z

2v0z


Resolution: 2.6→35.33 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.898 / SU B: 32.726 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R: 0.364 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30024 1162 5.1 %RANDOM
Rwork0.26449 ---
obs0.26626 21623 98.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 80.37 Å2
Baniso -1Baniso -2Baniso -3
1--4.98 Å20 Å20 Å2
2---4.98 Å20 Å2
3---9.95 Å2
Refinement stepCycle: LAST / Resolution: 2.6→35.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2716 0 74 9 2799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222852
X-RAY DIFFRACTIONr_bond_other_d0.0010.021924
X-RAY DIFFRACTIONr_angle_refined_deg1.0981.993863
X-RAY DIFFRACTIONr_angle_other_deg0.7783.0034663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8595345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.43923.448116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78915466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1011515
X-RAY DIFFRACTIONr_chiral_restr0.060.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213085
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02588
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_it0.2421.51722
X-RAY DIFFRACTIONr_mcbond_other0.0251.5717
X-RAY DIFFRACTIONr_mcangle_it0.46122781
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.16931130
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8854.51082
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: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.468 86 -
Rwork0.414 1607 -
obs--99.12 %
Refinement TLS params.Method: refined / Origin x: -20.9138 Å / Origin y: 2.2415 Å / Origin z: 12.8802 Å
111213212223313233
T0.6258 Å20.0697 Å2-0.1099 Å2-0.6553 Å2-0.0076 Å2--0.8953 Å2
L1.6065 °20.7297 °20.7883 °2-6.4287 °21.7963 °2--1.9469 °2
S0.2378 Å °-0.1073 Å °-1.169 Å °-0.0125 Å °0.1707 Å °-0.2994 Å °0.2193 Å °0.1791 Å °-0.4086 Å °

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