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- PDB-4xmc: Crystal structure of nitrophorin 7 from Rhodnius prolixus at pH 5.8 -

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Basic information

Entry
Database: PDB / ID: 4xmc
TitleCrystal structure of nitrophorin 7 from Rhodnius prolixus at pH 5.8
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 / Nitrophorin-7
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.421 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 13, 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
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-18 kcal/mol
Surface area9980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.419, 66.999, 38.997
Angle α, β, γ (deg.)90.00, 116.57, 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.: 80 / 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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 25%(w/v) PEG 3350, 0.1M MES monohydrate pH 5.8, 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: SLS / Beamline: X06SA / Wavelength: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 1.42→34.88 Å / Num. obs: 59987 / % possible obs: 91.3 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 11
Reflection shellResolution: 1.42→1.46 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 1.4 / % possible all: 71.4

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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: 1.421→34.877 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 19.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1939 3004 5.01 %
Rwork0.1608 --
obs0.1624 59987 91.63 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.894 Å2 / ksol: 0.364 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.4324 Å20 Å21.3171 Å2
2---3.14 Å20 Å2
3----0.2924 Å2
Refinement stepCycle: LAST / Resolution: 1.421→34.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1461 0 43 80 1584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061546
X-RAY DIFFRACTIONf_angle_d1.0422093
X-RAY DIFFRACTIONf_dihedral_angle_d13.865564
X-RAY DIFFRACTIONf_chiral_restr0.083220
X-RAY DIFFRACTIONf_plane_restr0.004259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4213-1.44460.38571020.30941857X-RAY DIFFRACTION63
1.4446-1.46950.31341330.25122561X-RAY DIFFRACTION87
1.4695-1.49620.25141430.23072670X-RAY DIFFRACTION89
1.4962-1.5250.31751360.20922638X-RAY DIFFRACTION90
1.525-1.55610.22921440.18892692X-RAY DIFFRACTION91
1.5561-1.58990.21651420.16582662X-RAY DIFFRACTION91
1.5899-1.62690.20671490.16142765X-RAY DIFFRACTION92
1.6269-1.66760.20321370.14052737X-RAY DIFFRACTION93
1.6676-1.71270.16491460.14162693X-RAY DIFFRACTION91
1.7127-1.76310.16131490.13452724X-RAY DIFFRACTION91
1.7631-1.820.20811450.13452808X-RAY DIFFRACTION96
1.82-1.8850.20211480.12742836X-RAY DIFFRACTION96
1.885-1.96050.16081470.11952843X-RAY DIFFRACTION96
1.9605-2.04970.14981500.12722838X-RAY DIFFRACTION95
2.0497-2.15780.18191470.13612803X-RAY DIFFRACTION95
2.1578-2.2930.23171520.1462794X-RAY DIFFRACTION94
2.293-2.470.21511430.16472707X-RAY DIFFRACTION92
2.47-2.71840.18611460.18392864X-RAY DIFFRACTION97
2.7184-3.11160.24421510.18022854X-RAY DIFFRACTION96
3.1116-3.91940.16961460.15642785X-RAY DIFFRACTION94
3.9194-34.80.17011480.16652852X-RAY DIFFRACTION96

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