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

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Basic information

Entry
Database: PDB / ID: 4xmf
TitleCrystal structure of nitrophorin 7 from Rhodnius prolixus at pH 7.8 complexed with histamine
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 / HISTAMINE / Nitrophorin-7
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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)21,4873
Polymers20,7601
Non-polymers7282
Water2,270126
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-21 kcal/mol
Surface area9740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.338, 66.722, 38.825
Angle α, β, γ (deg.)90.00, 116.87, 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 22-205
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-HSM / HISTAMINE


Mass: 111.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.13 Å3/Da / Density % sol: 42.35 %
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) Gly-Gly, 0.25%(w/v) Gly-Gly-Gly, 0.25%(w/v) Gly- Gly-Gly-Gly, 0.25%(w/v) pentaglycine, 0.02 M HEPES sodium pH 6.8.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Sep 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.6→30.74 Å / Num. obs: 22417 / % possible obs: 96.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.3
Reflection shellResolution: 1.6→1.64 Å / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.9 / % possible all: 95.5

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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: 1.6→30.74 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 21.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2071 1121 5 %
Rwork0.1583 --
obs0.1609 22417 97.26 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.967 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.7164 Å2-0 Å2-1.3211 Å2
2---0.462 Å2-0 Å2
3----1.2544 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1461 0 51 126 1638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071554
X-RAY DIFFRACTIONf_angle_d1.0242102
X-RAY DIFFRACTIONf_dihedral_angle_d14.442567
X-RAY DIFFRACTIONf_chiral_restr0.077220
X-RAY DIFFRACTIONf_plane_restr0.004260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.67280.30221370.2072611X-RAY DIFFRACTION96
1.6728-1.7610.2421370.17492604X-RAY DIFFRACTION96
1.761-1.87130.19611380.15572613X-RAY DIFFRACTION96
1.8713-2.01580.22181400.13682667X-RAY DIFFRACTION97
2.0158-2.21860.19791390.14732641X-RAY DIFFRACTION98
2.2186-2.53950.22431430.1572709X-RAY DIFFRACTION98
2.5395-3.1990.24641420.1762707X-RAY DIFFRACTION99
3.199-30.74540.1611450.14912744X-RAY DIFFRACTION99

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