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- PDB-2o09: Crystal structure of the H-NOX domain from Nostoc sp. PCC 7120 -

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Basic information

Entry
Database: PDB / ID: 2o09
TitleCrystal structure of the H-NOX domain from Nostoc sp. PCC 7120
ComponentsAlr2278 protein
KeywordsSIGNALING PROTEIN / heme / NO / CO / guanylyl cyclase
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 / Alr2278 protein
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsMa, X. / van den Akker, F.
CitationJournal: Embo J. / Year: 2007
Title: NO and CO differentially activate soluble guanylyl cyclase via a heme pivot-bend mechanism.
Authors: Ma, X. / Sayed, N. / Beuve, A. / van den Akker, F.
History
DepositionNov 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_conn.ptnr2_label_seq_id / _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)43,6604
Polymers42,4272
Non-polymers1,2332
Water4,125229
1
A: Alr2278 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8302
Polymers21,2141
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alr2278 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8302
Polymers21,2141
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.420, 123.420, 123.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-592-

HOH

21B-575-

HOH

31B-597-

HOH

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Components

#1: Protein Alr2278 protein


Mass: 21213.643 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: alr2278 / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 3.69 Å3/Da / Density % sol: 66.68 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 1.4M tri-sodium citrate dihydrate, pH 5.6-6.6, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→22 Å / Num. all: 36257 / Num. obs: 35861 / % possible obs: 98.9 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 18.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 1.7 / Num. unique all: 3525 / % possible all: 98.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→21.82 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.707 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1818 5 %RANDOM
Rwork0.185 ---
obs0.187 35861 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.385 Å2
Refinement stepCycle: LAST / Resolution: 2.1→21.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2866 0 86 229 3181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223035
X-RAY DIFFRACTIONr_angle_refined_deg1.2212.0424130
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2765362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3224.789142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03315494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2191510
X-RAY DIFFRACTIONr_chiral_restr0.0690.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022336
X-RAY DIFFRACTIONr_nbd_refined0.2120.31306
X-RAY DIFFRACTIONr_nbtor_refined0.3120.52069
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.5354
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.377
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.522
X-RAY DIFFRACTIONr_mcbond_it2.01921860
X-RAY DIFFRACTIONr_mcangle_it3.30942872
X-RAY DIFFRACTIONr_scbond_it3.99641364
X-RAY DIFFRACTIONr_scangle_it5.54461254
LS refinement shellResolution: 2.1→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 133 -
Rwork0.239 2483 -
obs-2616 98.12 %

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