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- PDB-4jqh: Crystal structure of a new sGC activator (analogue of BAY 58-2667... -

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Basic information

Entry
Database: PDB / ID: 4jqh
TitleCrystal structure of a new sGC activator (analogue of BAY 58-2667) bound to nostoc H-NOX domain
ComponentsAlr2278 protein
KeywordsSIGNALING PROTEIN / GUANYLYL CYCLASE / analogue of BAY58-2667
Function / homology
Function and homology information


heme binding / metal ion binding
Similarity search - Function
H-NOX domain / H-NOX domain / Heme NO-binding / H-NOX domain superfamily / Haem-NO-binding / NO signalling/Golgi transport ligand-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-1MF / MALONIC ACID / Alr2278 protein
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKumar, V. / van den Akker, F.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Insights into soluble guanylyl cyclase activation derived from improved heme-mimetics.
Authors: von Wantoch Rekowski, M. / Kumar, V. / Zhou, Z. / Moschner, J. / Marazioti, A. / Bantzi, M. / Spyroulias, G.A. / van den Akker, F. / Giannis, A. / Papapetropoulos, A.
History
DepositionMar 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Apr 29, 2015Group: Non-polymer description
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alr2278 protein
B: Alr2278 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8316
Polymers42,3632
Non-polymers1,4684
Water2,090116
1
A: Alr2278 protein
hetero molecules

B: Alr2278 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8316
Polymers42,3632
Non-polymers1,4684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
Buried area2100 Å2
ΔGint-10 kcal/mol
Surface area17150 Å2
MethodPISA
2
A: Alr2278 protein
hetero molecules

A: Alr2278 protein
hetero molecules

A: Alr2278 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7469
Polymers63,5453
Non-polymers2,2016
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area4050 Å2
ΔGint-27 kcal/mol
Surface area24780 Å2
MethodPISA
3
B: Alr2278 protein
hetero molecules

B: Alr2278 protein
hetero molecules

B: Alr2278 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7469
Polymers63,5453
Non-polymers2,2016
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area4060 Å2
ΔGint-25 kcal/mol
Surface area24860 Å2
MethodPISA
4
A: Alr2278 protein
B: Alr2278 protein
hetero molecules

A: Alr2278 protein
B: Alr2278 protein
hetero molecules

A: Alr2278 protein
B: Alr2278 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,49218
Polymers127,0896
Non-polymers4,40312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area12980 Å2
ΔGint-81 kcal/mol
Surface area44770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.191, 122.191, 122.191
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Alr2278 protein


Mass: 21181.578 Da / Num. of mol.: 2 / Mutation: C139A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: alr2278 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3)pLysS / References: UniProt: Q8YUQ7, guanylate cyclase
#2: Chemical ChemComp-1MF / 4-{[(4-carboxybutyl)(2-{2-[(4'-phenoxybiphenyl-4-yl)methoxy]phenyl}ethyl)amino]methyl}benzoic acid


Mass: 629.741 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H39NO6
#3: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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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: 3.59 Å3/Da / Density % sol: 65.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.9M sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 3, 2012 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.522
11-K, -H, -L20.478
ReflectionResolution: 2.3→86.7 Å / Num. all: 27235 / Num. obs: 25770 / % possible obs: 94.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.5 % / Net I/σ(I): 28.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.5 % / % possible all: 97.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→86.42 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.775 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.031 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18983 1326 4.9 %RANDOM
Rwork0.1285 ---
all0.18983 27235 --
obs0.13157 25770 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.953 Å2
Refinement stepCycle: LAST / Resolution: 2.3→86.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2864 0 108 116 3088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213052
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.994122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9775364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.58824.825143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.04415493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5881510
X-RAY DIFFRACTIONr_chiral_restr0.090.2427
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212364
X-RAY DIFFRACTIONr_mcbond_it8.2231.51801
X-RAY DIFFRACTIONr_mcangle_it10.07722876
X-RAY DIFFRACTIONr_scbond_it16.04131251
X-RAY DIFFRACTIONr_scangle_it17.4214.51245
LS refinement shellResolution: 2.301→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 101 -
Rwork0.206 1832 -
obs--97.87 %

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