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- PDB-1y21: Crystal Structure of Cimex Nitrophorin NO Complex -

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Basic information

Entry
Database: PDB / ID: 1y21
TitleCrystal Structure of Cimex Nitrophorin NO Complex
Componentssalivary nitrophorin
KeywordsLIGAND BINDING PROTEIN / heme protein / beta-sandwich / NO carrier / ferrous NO complex / S-nitrosocysteine
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 / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsWeichsel, A. / Maes, E.M. / Andersen, J.F. / Valenzuela, J.G. / Shokhireva, T.K. / Walker, F.A. / Montfort, W.R.
Citation
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.H. / Walker, F.A. / Montfort, W.R.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2000
Title: Nitric Oxide Binding to Nitrophorin 4 Induces Complete Distal Pocket Burial
Authors: Weichsel, A. / Andersen, J.F. / Roberts, S.A.
History
DepositionNov 19, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionNov 30, 2004ID: 1NZH
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 29, 2012Group: Database references
Revision 1.4Aug 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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)32,5455
Polymers31,7461
Non-polymers7994
Water4,270237
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.065, 41.477, 65.346
Angle α, β, γ (deg.)90.00, 94.55, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
Detailsmonomer, the biological unit is identical to the asymmetric unit

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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: UniProt: O76745
#2: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 2 / 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: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 1.84 Å3/Da / Density % sol: 32.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: PEG 4000, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 1, 2002 / Details: osmic mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→64.55 Å / Num. all: 24549 / Num. obs: 24549 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 24.8 Å2 / Rsym value: 0.043 / Net I/σ(I): 20
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 6875 / Rsym value: 0.24 / % possible all: 98.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
d*TREKdata reduction
MLPHAREphasing
REFMAC5.1.22refinement
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1NTF

1ntf


Resolution: 1.75→64.55 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.629 / SU ML: 0.083 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.125 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20828 1255 4.9 %RANDOM
Rwork0.16766 ---
all0.1696 24549 --
obs0.1696 24549 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.019 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0.97 Å2
2--0.05 Å20 Å2
3----0.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.119 Å0.125 Å
Refinement stepCycle: LAST / Resolution: 1.75→64.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2227 0 55 237 2519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222335
X-RAY DIFFRACTIONr_bond_other_d0.0020.022018
X-RAY DIFFRACTIONr_angle_refined_deg1.8312.0073180
X-RAY DIFFRACTIONr_angle_other_deg0.91234738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8335279
X-RAY DIFFRACTIONr_chiral_restr0.1160.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022554
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02438
X-RAY DIFFRACTIONr_nbd_refined0.2190.2421
X-RAY DIFFRACTIONr_nbd_other0.2510.22375
X-RAY DIFFRACTIONr_nbtor_other0.0870.21382
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2180
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2050.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.214
X-RAY DIFFRACTIONr_mcbond_it1.3831.51404
X-RAY DIFFRACTIONr_mcangle_it2.38622284
X-RAY DIFFRACTIONr_scbond_it3.0933931
X-RAY DIFFRACTIONr_scangle_it4.8854.5896
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.329 97
Rwork0.279 1774
obs-1774

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