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- PDB-5m6j: Crystal structure of nitrophorin 7 E27V mutant from Rhodnius prolixus -

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Basic information

Entry
Database: PDB / ID: 5m6j
TitleCrystal structure of nitrophorin 7 E27V mutant from Rhodnius prolixus
ComponentsNitrophorin-7
KeywordsTRANSPORT PROTEIN / NO transporter / heme protein / lipocalin fold
Function / homology
Function and homology information


intracellular nitric oxide homeostasis / vasodilation in another organism / response to histamine / nitrite dismutase / negative regulation of coagulation / histamine binding / nitric oxide binding / platelet aggregation / 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: 1.7 Å
AuthorsOgata, H.
CitationJournal: Sci Rep / Year: 2018
Title: Electrostatic Tuning of the Ligand Binding Mechanism by Glu27 in Nitrophorin 7.
Authors: Abbruzzetti, S. / Allegri, A. / Bidon-Chanal, A. / Ogata, H. / Soavi, G. / Cerullo, G. / Bruno, S. / Montali, C. / Luque, F.J. / Viappiani, C.
History
DepositionOct 25, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)21,3462
Polymers20,7301
Non-polymers6161
Water2,666148
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-18 kcal/mol
Surface area9760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.228, 66.885, 38.714
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: 20729.678 Da / Num. of mol.: 1
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 / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: NaOAc/HOAc

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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 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.7→34.63 Å / Num. obs: 72215 / % possible obs: 96.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 17.6
Reflection shellResolution: 1.7→1.74 Å / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 3 / % possible all: 95.3

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Processing

Software
NameVersionClassification
PHENIX2011_08_24_1020refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4xmc

4xmc


Resolution: 1.7→34.626 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 21.58
RfactorNum. reflection% reflection
Rfree0.2126 934 5 %
Rwork0.161 --
obs0.1635 18666 96.99 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Bsol: 28.266 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.6832 Å2-0 Å2-1.1894 Å2
2---0.4389 Å20 Å2
3----4.2443 Å2
Refinement stepCycle: LAST / Resolution: 1.7→34.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1459 0 43 148 1650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061551
X-RAY DIFFRACTIONf_angle_d1.0572102
X-RAY DIFFRACTIONf_dihedral_angle_d13.556565
X-RAY DIFFRACTIONf_chiral_restr0.081222
X-RAY DIFFRACTIONf_plane_restr0.004260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.78960.27521310.20782487X-RAY DIFFRACTION96
1.7896-1.90170.21321320.16732505X-RAY DIFFRACTION96
1.9017-2.04860.2311320.14522515X-RAY DIFFRACTION96
2.0486-2.25470.22631340.1532528X-RAY DIFFRACTION97
2.2547-2.58080.28181340.1652545X-RAY DIFFRACTION97
2.5808-3.25120.21791340.18022552X-RAY DIFFRACTION98
3.2512-34.63340.16271370.14592598X-RAY DIFFRACTION98

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