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- PDB-1si6: Crystal structure of cimex nitrophorin complex with CO -

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Basic information

Entry
Database: PDB / ID: 1si6
TitleCrystal structure of cimex nitrophorin complex with CO
Componentssalivary nitrophorin
KeywordsTRANSPORT PROTEIN / ferrous heme / carbon monoxide / beta sandwich
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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Nitrophorin Cim l NP
Similarity search - Component
Biological speciesCimex lectularius (bed bug)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.45 Å
AuthorsWeichsel, A. / Montfort, W.R.
Citation
Journal: To be Published
Title: Structure of cimex nitrophorin complex with carbon monoxide
Authors: Weichsel, A. / Montfort, W.R.
#1: Journal: To be Published
Title: Structure of cimex nitrophorin and its complex with NO
Authors: Weichsel, A. / Maes, E.A. / Walker, F.A. / Montfort, W.R.
History
DepositionFeb 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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_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.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_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
X: salivary nitrophorin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3913
Polymers31,7461
Non-polymers6442
Water3,585199
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.155, 41.566, 65.388
Angle α, β, γ (deg.)90.00, 95.48, 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-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#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.: 199 / 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: 2.09 Å3/Da / Density % sol: 41.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: PEG 4000, Li2SO4, ethanol, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 14, 2003 / Details: bent Si-mirror
RadiationMonochromator: bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.45→15 Å / Num. all: 44739 / Num. obs: 44739 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 10.4
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 1.6 / Num. unique all: 4654 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDISPLAYFdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1NTF

1ntf


Resolution: 1.45→15 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 1.446 / SU ML: 0.056 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CO LIGAND PARTIALLY DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.25687 2277 5.1 %RANDOM
Rwork0.20286 ---
obs0.20551 42465 95.53 %-
all-42465 --
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: 25.303 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å2-1.49 Å2
2---0.04 Å20 Å2
3----0.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.093 Å0.107 Å
Luzzati sigma a-0.056 Å
Refinement stepCycle: LAST / Resolution: 1.45→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2247 0 45 199 2491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0212348
X-RAY DIFFRACTIONr_bond_other_d0.0020.022022
X-RAY DIFFRACTIONr_angle_refined_deg1.7952.0023204
X-RAY DIFFRACTIONr_angle_other_deg0.92234751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8245283
X-RAY DIFFRACTIONr_chiral_restr0.120.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022591
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02431
X-RAY DIFFRACTIONr_nbd_refined0.2890.2433
X-RAY DIFFRACTIONr_nbd_other0.250.22358
X-RAY DIFFRACTIONr_nbtor_other0.0860.21394
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2142
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1140.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2290.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.216
X-RAY DIFFRACTIONr_mcbond_it1.7291.51410
X-RAY DIFFRACTIONr_mcangle_it2.53722301
X-RAY DIFFRACTIONr_scbond_it3.1263938
X-RAY DIFFRACTIONr_scangle_it4.5074.5903
X-RAY DIFFRACTIONr_rigid_bond_restr1.79522348
X-RAY DIFFRACTIONr_sphericity_free6.3822202
X-RAY DIFFRACTIONr_sphericity_bonded3.85122289
LS refinement shellResolution: 1.45→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 158 -
Rwork0.229 3241 -
obs-3241 98 %

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