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- PDB-4xmg: Crystal structure of nitrophorin 7 from Rhodnius prolixus at pH 7... -

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Basic information

Entry
Database: PDB / ID: 4xmg
TitleCrystal structure of nitrophorin 7 from Rhodnius prolixus at pH 7.8 complexed with imidazole
ComponentsNitrophorin-7
KeywordsTRANSPORT PROTEIN / Heme / NO transporter / oxidoreductase
Function / homology
Function and homology information


venom-mediated perturbation of biological process / modulation of process of another organism / nitrite dismutase / histamine binding / nitric oxide binding / vasodilation / toxin activity / oxidoreductase 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 / IMIDAZOLE / Nitrophorin-7
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsOgata, H.
CitationJournal: F1000Res / Year: 2015
Title: Structure and dynamics of the membrane attaching nitric oxide transporter nitrophorin 7.
Authors: Knipp, M. / Ogata, H. / Soavi, G. / Cerullo, G. / Allegri, A. / Abbruzzetti, S. / Bruno, S. / Viappiani, C. / Bidon-Chanal, A. / Luque, F.J.
History
DepositionJan 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 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
A: Nitrophorin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4453
Polymers20,7601
Non-polymers6862
Water2,162120
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-14 kcal/mol
Surface area9690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.264, 66.747, 38.561
Angle α, β, γ (deg.)90.00, 116.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nitrophorin-7 / NP7 / Nitrite dismutase


Mass: 20759.660 Da / Num. of mol.: 1 / Fragment: UNP residues 22-105
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodnius prolixus (insect) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PQK2, nitrite dismutase
#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-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 25%(w/v) PEG 3350, 0.1 M bis-Tris propane pH 7.8. 0.25%(w/v) hexamminecobalt(III) chloride, 0.25%(w/v) salicylamide, 0.25%(w/v) sulfanilamide, 0.25%(w/v) vanilic acid, 0.02 M HEPES sodium pH 6.8.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.8 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.8→34.25 Å / Num. obs: 15836 / % possible obs: 97.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 9.2
Reflection shellResolution: 1.8→1.85 Å / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 3 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 2011_08_24_1020)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MVF

3mvf


Resolution: 1.8→34.245 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 22.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 792 5 %
Rwork0.178 --
obs0.18 15833 97.96 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.634 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.9689 Å20 Å22.5951 Å2
2---4.9168 Å2-0 Å2
3----5.0521 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1461 0 48 120 1629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081558
X-RAY DIFFRACTIONf_angle_d1.1572109
X-RAY DIFFRACTIONf_dihedral_angle_d15.049567
X-RAY DIFFRACTIONf_chiral_restr0.088221
X-RAY DIFFRACTIONf_plane_restr0.004262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.91280.35541310.25852501X-RAY DIFFRACTION97
1.9128-2.06050.26561300.1952461X-RAY DIFFRACTION98
2.0605-2.26780.22461320.17942510X-RAY DIFFRACTION97
2.2678-2.59590.21311310.18012493X-RAY DIFFRACTION98
2.5959-3.27010.23881330.17692525X-RAY DIFFRACTION99
3.2701-34.25110.17691350.16182551X-RAY DIFFRACTION98

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