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- PDB-1ntf: Crystal Structure of Cimex Nitrophorin -

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Basic information

Entry
Database: PDB / ID: 1ntf
TitleCrystal Structure of Cimex Nitrophorin
Componentssalivary nitrophorin
KeywordsTRANSPORT PROTEIN / ferric heme protein / beta sandwich / NO carrier
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 / Nitrophorin Cim l NP
Similarity search - Component
Biological speciesCimex lectularius (bed bug)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.8 Å
AuthorsWeichsel, A. / Maes, E.M. / Andersen, J.F. / Valenzuela, J.G. / 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. / Walker, F.A. / Montfort, W.R.
#1: Journal: Nat.Struct.Biol. / Year: 2000
Title: Nitric Oxide Binding to Nitrophorin 4 Induces Complete Distal Pocket Burial
Authors: Weichsel, A. / Andersen, J.F. / Roberts, S.A. / Montfort, W.R.
History
DepositionJan 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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

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Assembly

Deposited unit
A: salivary nitrophorin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3632
Polymers31,7461
Non-polymers6161
Water2,936163
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.200, 42.100, 65.850
Angle α, β, γ (deg.)90.00, 95.88, 90.00
Int Tables number4
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) / Plasmid: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: O76745
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 163 / 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: 1.99 Å3/Da / Density % sol: 37.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: PEG 4000, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
122 %PEG40001reservoir
2200 mM1reservoirLi2SO4
3100 mMTris-HCl1reservoirpH8.6
420 mMsodium citrate1droppH5.6, or 100mMpotassium phosphate pH8.1

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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: Jul 8, 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: 1.8→21 Å / Num. all: 25024 / Num. obs: 24988 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 19.9 Å2 / Rsym value: 0.064 / Net I/σ(I): 11
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 1859 / Rsym value: 0.31 / % possible all: 96.5
Reflection
*PLUS
Highest resolution: 1.8 Å / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 96.5 % / Rmerge(I) obs: 0.31

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Processing

Software
NameVersionClassification
REFMAC5.1.22refinement
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→21 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.971 / SU ML: 0.087 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.115 / ESU R Free: 0.116 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19788 1214 4.8 %RANDOM
Rwork0.151 ---
all0.1532 23852 --
obs0.15323 23852 99.66 %-
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: 22.693 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å2-0.94 Å2
2--0.03 Å20 Å2
3---0.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.11 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2227 0 43 163 2433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222326
X-RAY DIFFRACTIONr_bond_other_d0.0020.022012
X-RAY DIFFRACTIONr_angle_refined_deg1.9682.0043171
X-RAY DIFFRACTIONr_angle_other_deg0.94534723
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.885279
X-RAY DIFFRACTIONr_chiral_restr0.1220.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022554
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02438
X-RAY DIFFRACTIONr_nbd_refined0.2040.2362
X-RAY DIFFRACTIONr_nbd_other0.2470.22286
X-RAY DIFFRACTIONr_nbtor_other0.090.21426
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2106
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2120.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3760.213
X-RAY DIFFRACTIONr_mcbond_it1.3661.51398
X-RAY DIFFRACTIONr_mcangle_it2.52822278
X-RAY DIFFRACTIONr_scbond_it3.5853928
X-RAY DIFFRACTIONr_scangle_it5.7034.5893
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.356 79
Rwork0.284 1780
obs-1780
Refinement
*PLUS
Rfactor Rfree: 0.2 / Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.022
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2

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