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- PDB-5ixz: Crystal structure of the signaling protein complex 5 -

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Basic information

Entry
Database: PDB / ID: 5ixz
TitleCrystal structure of the signaling protein complex 5
ComponentsAlr2278 protein
KeywordsSIGNALING PROTEIN / Soluble guanylyl cyclase / H-NOX domain / Nitric oxide / Heme-Binding Domain / DMSO
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
PROTOPORPHYRIN IX CONTAINING FE / MALONATE ION / Alr2278 protein
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKumar, V. / van den Akker, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01 HL075329 United States
CitationJournal: To Be Published
Title: Crystal structure of the signaling protein complex 5
Authors: Kumar, V. / van den Akker, F.
History
DepositionMar 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Alr2278 protein
B: Alr2278 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2097
Polymers40,7182
Non-polymers1,4915
Water19811
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.267, 123.267, 123.267
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: 20358.799 Da / Num. of mol.: 2 / Fragment: UNP resiudes 1-182
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: alr2278 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YUQ7
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.72 Å3/Da / Density % sol: 66.92 % / Description: Red-colored crystals
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: BL7-1 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 17, 2015 / Details: Mirrors
RadiationMonochromator: Graphite / Protocol: 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, L10.491
11L, -K, H20.509
ReflectionResolution: 2.4→38.98 Å / Num. obs: 23398 / % possible obs: 99.78 % / Redundancy: 7.2 % / Biso Wilson estimate: 71.5 Å2 / Rmerge(I) obs: 0.15 / Rsym value: 0.065 / Net I/σ(I): 11.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.54 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IAM

4iam


Resolution: 2.4→38.98 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.941 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17747 1206 4.9 %RANDOM
Rwork0.14889 ---
obs0.15038 23398 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 93.567 Å2
Baniso -1Baniso -2Baniso -3
1--54.69 Å232.78 Å2-23.6 Å2
2---49.25 Å259.55 Å2
3---103.94 Å2
Refinement stepCycle: 1 / Resolution: 2.4→38.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2864 0 101 11 2976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193044
X-RAY DIFFRACTIONr_bond_other_d0.0020.022770
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.9974141
X-RAY DIFFRACTIONr_angle_other_deg0.9136385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9155362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.79224.789142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.23615492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1861510
X-RAY DIFFRACTIONr_chiral_restr0.1020.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023474
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02712
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_it3.9119.2021454
X-RAY DIFFRACTIONr_mcbond_other3.8859.21453
X-RAY DIFFRACTIONr_mcangle_it5.41513.81814
X-RAY DIFFRACTIONr_mcangle_other5.42313.8011815
X-RAY DIFFRACTIONr_scbond_it4.1849.5751590
X-RAY DIFFRACTIONr_scbond_other4.189.5731588
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.21414.1832327
X-RAY DIFFRACTIONr_long_range_B_refined8.13873.5163350
X-RAY DIFFRACTIONr_long_range_B_other8.13773.5153350
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.401→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 79 -
Rwork0.219 1736 -
obs--99.94 %

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