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- PDB-1yjh: Crystal Structure of Cimex Nitrophorin Ferrous NO Complex -

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Basic information

Entry
Database: PDB / ID: 1yjh
TitleCrystal Structure of Cimex Nitrophorin Ferrous NO Complex
Componentssalivary nitrophorin
KeywordsOXYGEN STORAGE/TRANSPORT / ferrous heme / nitric oxide / beta sandwich / five-coordinate iron / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol dephosphorylation / nitric oxide transport / vasodilation / iron ion binding / heme binding / extracellular space
Similarity search - Function
: / Inositol polyphosphate-related phosphatase / Endonuclease/Exonuclease/phosphatase family 2 / Inositol polyphosphate phosphatase, catalytic domain homologues / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NITRIC OXIDE / : / Nitrophorin Cim l NP
Similarity search - Component
Biological speciesCimex lectularius (bed bug)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.65 Å
AuthorsWeichsel, A. / Badgandi, H. / Montfort, W.R.
Citation
Journal: To be Published
Title: Crystal Structure of Cimex Nitrophorin NO Complex
Authors: Weichsel, A. / Badgandi, H. / Montfort, W.R.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Heme-assisted S-nitrosation of a proximal thiolate in a nitric oxide transport protein
Authors: Weichsel, A. / Maes, E.M. / Andersen, J.F. / Valenzuela, J.G. / Shokhireva, T.K. / Walker, F.A. / Montfort, W.R.
History
DepositionJan 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: salivary nitrophorin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3933
Polymers31,7461
Non-polymers6462
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.000, 41.560, 65.370
Angle α, β, γ (deg.)90.00, 95.29, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein salivary nitrophorin


Mass: 31746.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cimex lectularius (bed bug) / Organ: salivary glands / Plasmid: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: GenBank: 3388165, UniProt: O76745*PLUS
#2: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 1.9 Å3/Da / Density % sol: 34.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, Li2SO4, ethanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 6, 2004
Details: Flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(311) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.65→37.5 Å / Num. all: 30416 / Num. obs: 30416 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 16.3
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 2 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 4.2 / Num. unique all: 2616 / % possible all: 83.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
d*TREKdata reduction
REFMAC5.2refinement
d*TREKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1NTF

1ntf


Resolution: 1.65→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.545 / SU ML: 0.087 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24992 1495 4.9 %RANDOM
Rwork0.20314 ---
all0.2054 28744 --
obs0.2054 28744 95.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å2-1.85 Å2
2--0.12 Å20 Å2
3----0.56 Å2
Refine analyzeLuzzati coordinate error obs: 0.126 Å
Refinement stepCycle: LAST / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2242 0 45 207 2494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222342
X-RAY DIFFRACTIONr_bond_other_d0.0010.022020
X-RAY DIFFRACTIONr_angle_refined_deg1.9181.9973191
X-RAY DIFFRACTIONr_angle_other_deg1.29734749
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9245279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.14129.167108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.6615404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.648158
X-RAY DIFFRACTIONr_chiral_restr0.1140.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022570
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02428
X-RAY DIFFRACTIONr_nbd_refined0.2220.2423
X-RAY DIFFRACTIONr_nbd_other0.1970.22059
X-RAY DIFFRACTIONr_nbtor_refined0.180.21106
X-RAY DIFFRACTIONr_nbtor_other0.090.21306
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2177
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0490.21
X-RAY DIFFRACTIONr_metal_ion_refined0.070.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0990.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.27
X-RAY DIFFRACTIONr_mcbond_it1.5391.51764
X-RAY DIFFRACTIONr_mcbond_other0.3381.5564
X-RAY DIFFRACTIONr_mcangle_it1.81422283
X-RAY DIFFRACTIONr_scbond_it2.78931121
X-RAY DIFFRACTIONr_scangle_it3.494.5906
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 93 -
Rwork0.241 1786 -
obs-1786 80.51 %

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