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- PDB-4xmd: Crystal structure of nitrophorin 7 from Rhodnius prolixus at pH 7.8 -

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Basic information

Entry
Database: PDB / ID: 4xmd
TitleCrystal structure of nitrophorin 7 from Rhodnius prolixus at pH 7.8
ComponentsNitrophorin-7
KeywordsTRANSPORT PROTEIN / Heme / NO transpoter / 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 / 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 20, 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)21,3762
Polymers20,7601
Non-polymers6161
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-17 kcal/mol
Surface area9900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.312, 66.807, 39.026
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.15 Å3/Da / Density % sol: 42.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 25%(w/v) PEG 3350, 0.1 M bis-Tris propane pH 7.8, 0.02 M HEPES pH 6.8, 0.25%(w/v) naphthalene-1,3,6-trisulfonic acid trisodium salt hydrate, 0.25%(w/v) 2,6-naphthalenedisulfonic acid ...Details: 25%(w/v) PEG 3350, 0.1 M bis-Tris propane pH 7.8, 0.02 M HEPES pH 6.8, 0.25%(w/v) naphthalene-1,3,6-trisulfonic acid trisodium salt hydrate, 0.25%(w/v) 2,6-naphthalenedisulfonic acid disodium salt, 0.25%(w/v) 4-aminobenzoic acid, 0.25%(w/v) 5-sulfosalicylic acid dehydrate.

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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: Jul 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.6→30.42 Å / Num. obs: 23143 / % possible obs: 99.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.5
Reflection shellResolution: 1.6→1.64 Å / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1565)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MVF

3mvf


Resolution: 1.6→30.42 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1916 1158 5 %
Rwork0.1347 --
obs0.1376 23137 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→30.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1461 0 43 199 1703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061553
X-RAY DIFFRACTIONf_angle_d1.0262106
X-RAY DIFFRACTIONf_dihedral_angle_d14.069567
X-RAY DIFFRACTIONf_chiral_restr0.045222
X-RAY DIFFRACTIONf_plane_restr0.004261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.67280.26441450.18882742X-RAY DIFFRACTION100
1.6728-1.7610.25931440.15312742X-RAY DIFFRACTION100
1.761-1.87130.22641430.14352703X-RAY DIFFRACTION100
1.8713-2.01580.19061450.12482767X-RAY DIFFRACTION100
2.0158-2.21860.19291440.12762725X-RAY DIFFRACTION100
2.2186-2.53950.18871450.13422758X-RAY DIFFRACTION100
2.5395-3.19890.21071450.14132754X-RAY DIFFRACTION100
3.1989-30.40.16121470.12532788X-RAY DIFFRACTION100

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