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- PDB-1t68: Crystal structure of nitrophorin 2 complex with NO -

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Basic information

Entry
Database: PDB / ID: 1t68
TitleCrystal structure of nitrophorin 2 complex with NO
ComponentsNitrophorin 2
KeywordsTRANSPORT PROTEIN / beta barrel / lipocalin / heme / nitric oxide / ruffling
Function / homology
Function and homology information


histamine binding / nitric oxide binding / vasodilation / toxin activity / extracellular region / metal ion binding
Similarity search - Function
Nitrophorin / Nitrophorin domain / Nitrophorin / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NITRIC OXIDE / Nitrophorin-2
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.45 Å
AuthorsWeichsel, A. / Montfort, W.R.
Citation
Journal: To be Published
Title: Conformational change and heme ruffling in nitrophorin 2, a nitric oxide carrier from kissing bug
Authors: Weichsel, A. / Montfort, W.R.
#1: Journal: J.Biol.Chem. / Year: 2000
Title: The crystal structure of nitrophorin 2. A trifunctional antihemostatic protein from the saliva of Rhodnius prolixus.
Authors: Andersen, J.F. / Montfort, W.R.
#2: Journal: Biochemistry / Year: 2001
Title: Ligand-induced heme ruffling and bent NO geometry in ultra-high-resolution structures of nitrophorin 4
Authors: Roberts, S.A. / Weichsel, A. / Qui, Y. / Shelnutt, J.A. / Walker, F.A. / Montfort, W.R.
History
DepositionMay 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
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 / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Nitrophorin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7273
Polymers20,0801
Non-polymers6462
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.295, 125.444, 33.196
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11X-84-

LYS

21X-263-

HOH

31X-401-

HOH

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Components

#1: Protein Nitrophorin 2 / NP2 / Prolixin-S


Mass: 20080.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodnius prolixus (insect) / Plasmid: pET17B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q26241
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 39.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium citrate, pH 7.5, 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: Apr 15, 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→22.8 Å / Num. all: 26809 / Num. obs: 26809 / % possible obs: 89.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 13.2
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2879 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1EUO

1euo


Resolution: 1.45→22.8 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.929 / SU B: 1.284 / SU ML: 0.051 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.109 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23462 1291 4.8 %RANDOM
Rwork0.19291 ---
all0.19488 25400 --
obs0.19488 25400 88.91 %-
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: 20.273 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.089 Å0.109 Å
Luzzati sigma a-0.051 Å
Refinement stepCycle: LAST / Resolution: 1.45→22.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1416 0 45 102 1563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0211490
X-RAY DIFFRACTIONr_bond_other_d0.0050.021262
X-RAY DIFFRACTIONr_angle_refined_deg1.9892.0542024
X-RAY DIFFRACTIONr_angle_other_deg0.8932974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6055179
X-RAY DIFFRACTIONr_chiral_restr0.1210.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021639
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02262
X-RAY DIFFRACTIONr_nbd_refined0.1980.2271
X-RAY DIFFRACTIONr_nbd_other0.2660.21484
X-RAY DIFFRACTIONr_nbtor_other0.0910.2898
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.275
X-RAY DIFFRACTIONr_metal_ion_refined0.0620.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3480.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.215
X-RAY DIFFRACTIONr_mcbond_it1.9261.5894
X-RAY DIFFRACTIONr_mcangle_it2.89621434
X-RAY DIFFRACTIONr_scbond_it3.5383596
X-RAY DIFFRACTIONr_scangle_it5.0034.5590
X-RAY DIFFRACTIONr_rigid_bond_restr1.96721490
X-RAY DIFFRACTIONr_sphericity_free6.2932104
X-RAY DIFFRACTIONr_sphericity_bonded3.84821454
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 122 -
Rwork0.174 1998 -
obs-2120 98.1 %

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