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- PDB-5ixr: Crystal Structure of C139A nostoc H-NOX domain with imidazole -

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Basic information

Entry
Database: PDB / ID: 5ixr
TitleCrystal Structure of C139A nostoc H-NOX domain with imidazole
ComponentsAlr2278 protein
KeywordsSIGNALING PROTEIN / Soluble guanylyl cyclase / H-NOX domain / Nitric oxide / Heme-Domain
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 / IMIDAZOLE / MALONATE ION / Alr2278 protein
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 C139A nostoc H-NOX domain with imidazole
Authors: Kumar, V. / van den Akker, F.
History
DepositionMar 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)42,2938
Polymers40,7182
Non-polymers1,5756
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.051, 123.051, 123.051
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 1 - 182 / Label seq-ID: 1 - 182

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.998149, -0.041543, -0.044418), (0.046363, -0.047085, -0.997814), (0.039361, -0.998027, 0.048924)-32.55166, -34.49109, -29.79983

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Components

#1: Protein Alr2278 protein


Mass: 20358.799 Da / Num. of mol.: 2 / Fragment: UNP residues 1-182 / Mutation: C139A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / UTEX 2576) (bacteria)
Strain: PCC 7120 / 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-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.7 Å3/Da / Density % sol: 66.8 % / Description: Red colored crystals
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.9M sodium malonate, pH 7.0,

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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 2, 2012 / 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, L10.504
11L, -K, H20.496
ReflectionResolution: 2.5→43.51 Å / Num. obs: 20550 / % possible obs: 99.45 % / Redundancy: 6.2 % / Biso Wilson estimate: 59.33 Å2 / Rsym value: 0.049 / Net I/σ(I): 24.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IAM

4iam


Resolution: 2.5→43.51 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.275 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.036 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17353 1109 5.1 %RANDOM
Rwork0.13056 ---
obs0.13282 20550 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 59.313 Å2
Baniso -1Baniso -2Baniso -3
1--17.46 Å28.93 Å2-22.17 Å2
2---19 Å2-18.58 Å2
3---36.45 Å2
Refinement stepCycle: 1 / Resolution: 2.5→43.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2864 0 110 35 3009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193099
X-RAY DIFFRACTIONr_bond_other_d0.0020.022799
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.9994218
X-RAY DIFFRACTIONr_angle_other_deg0.89736464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1435374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.824.966147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.60215501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8391510
X-RAY DIFFRACTIONr_chiral_restr0.1350.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023563
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02731
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_it4.685.7531469
X-RAY DIFFRACTIONr_mcbond_other4.6155.751468
X-RAY DIFFRACTIONr_mcangle_it6.7568.6291837
X-RAY DIFFRACTIONr_mcangle_other6.7638.631838
X-RAY DIFFRACTIONr_scbond_it5.336.0971630
X-RAY DIFFRACTIONr_scbond_other5.336.11631
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4228.9442377
X-RAY DIFFRACTIONr_long_range_B_refined10.02951.8067291
X-RAY DIFFRACTIONr_long_range_B_other10.02851.8127292
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCSNumber: 1647 / Type: TIGHT THERMAL / Rms dev position: 6.31 Å / Weight position: 0.5
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 71 -
Rwork0.205 1522 -
obs--99.62 %

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