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- PDB-3a3k: Reversibly bound chloride in the atrial natriuretic peptide recep... -

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Basic information

Entry
Database: PDB / ID: 3a3k
TitleReversibly bound chloride in the atrial natriuretic peptide receptor hormone-binding domain
ComponentsAtrial natriuretic peptide receptor A
KeywordsLYASE / NATRIURETIC PEPTIDE RECEPTOR / GUANYLYL-CYCLASE-COUPLED RECEPTOR / chloride binding motif / SIGNAL TRANSDUCTION / SIGNALING PROTEIN / MEMBRANE PROTEIN / cGMP biosynthesis / Chloride / Disulfide bond / Glycoprotein / GTP-binding / Membrane / Nucleotide-binding / Phosphoprotein / Receptor / Transmembrane
Function / homology
Function and homology information


Physiological factors / natriuretic peptide receptor activity / positive regulation of cGMP-mediated signaling / receptor guanylyl cyclase signaling pathway / peptide receptor activity / guanylate cyclase / guanylate cyclase activity / cGMP biosynthetic process / hormone binding / adenylate cyclase activity ...Physiological factors / natriuretic peptide receptor activity / positive regulation of cGMP-mediated signaling / receptor guanylyl cyclase signaling pathway / peptide receptor activity / guanylate cyclase / guanylate cyclase activity / cGMP biosynthetic process / hormone binding / adenylate cyclase activity / dopamine metabolic process / cGMP-mediated signaling / peptide hormone binding / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / cell surface receptor signaling pathway / receptor complex / protein kinase activity / intracellular signal transduction / GTP binding / ATP binding / plasma membrane
Similarity search - Function
Adenylyl cyclase class-4/guanylyl cyclase / Natriuretic peptides receptors signature. / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / Response regulator ...Adenylyl cyclase class-4/guanylyl cyclase / Natriuretic peptides receptors signature. / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / Response regulator / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / Atrial natriuretic peptide receptor 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsOgawa, H. / Qiu, Y. / Ogata, C.M. / Misono, K.S.
CitationJournal: Protein Sci. / Year: 2010
Title: Reversibly bound chloride in the atrial natriuretic peptide receptor hormone-binding domain: Possible allosteric regulation and a conserved structural motif for the chloride-binding site.
Authors: Ogawa, H. / Qiu, Y. / Philo, J.S. / Arakawa, T. / Ogata, C.M. / Misono, K.S.
History
DepositionJun 14, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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 / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / 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_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Atrial natriuretic peptide receptor A
B: Atrial natriuretic peptide receptor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,05220
Polymers96,8702
Non-polymers3,18218
Water4,720262
1
A: Atrial natriuretic peptide receptor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7669
Polymers48,4351
Non-polymers1,3318
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Atrial natriuretic peptide receptor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,28611
Polymers48,4351
Non-polymers1,85110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.521, 120.521, 160.613
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-543-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Atrial natriuretic peptide receptor A / Atrial natriuretic peptide A-type receptor / ANPRA / ANP-A / NPR-A / Guanylate cyclase / GC-A


Mass: 48434.828 Da / Num. of mol.: 2 / Fragment: UNP residues 29-463
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Npr1 / Plasmid: PCDNA3-NPRA-ECD / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHINESE HAMSTER / References: UniProt: P18910, guanylate cyclase

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Sugars , 2 types, 7 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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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Non-polymers , 3 types, 273 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 3.01 Å3/Da / Density % sol: 59.14 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9195 Å
DetectorType: SBC-2 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9195 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / % possible obs: 98.3 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 22
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 3.9 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→19.92 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.882 / SU B: 7.916 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.504 / ESU R Free: 0.274
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 1936 5 %RANDOM
Rwork0.20517 ---
obs0.20711 36455 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.339 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6740 0 187 262 7189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227110
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.9829699
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5165851
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29923.23322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.275151084
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6781554
X-RAY DIFFRACTIONr_chiral_restr0.0760.21065
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025412
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.23163
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.24780
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2330
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5631.54342
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0126853
X-RAY DIFFRACTIONr_scbond_it1.25233142
X-RAY DIFFRACTIONr_scangle_it2.0754.52846
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 135 -
Rwork0.243 2266 -
obs--100 %

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