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- PDB-5hwz: Crystal structure of nitrophorin 4 D30N mutant with nitrite -

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Basic information

Entry
Database: PDB / ID: 5hwz
TitleCrystal structure of nitrophorin 4 D30N mutant with nitrite
ComponentsNitrophorin-4
KeywordsTRANSPORT PROTEIN / Nitrophorin / Nitrite / Heme
Function / homology
Function and homology information


nitrite dismutase / histamine binding / nitric oxide binding / vasodilation / 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 / NITRITE ION / Nitrophorin-4
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsOgata, H. / He, C. / Lubitz, W.
CitationJournal: Chem Sci / Year: 2016
Title: Elucidation of the heme active site electronic structure affecting the unprecedented nitrite dismutase activity of the ferrihemebproteins, the nitrophorins.
Authors: He, C. / Ogata, H. / Lubitz, W.
History
DepositionJan 29, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 2.0Sep 12, 2018Group: Atomic model / Data collection / Database references / Category: atom_site / citation
Item: _atom_site.occupancy / _citation.journal_id_ISSN ..._atom_site.occupancy / _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
Revision 2.1Jan 10, 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
Revision 2.2Nov 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-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9543
Polymers20,2921
Non-polymers6622
Water2,126118
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-22 kcal/mol
Surface area8730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.779, 43.110, 52.623
Angle α, β, γ (deg.)90.00, 94.54, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-366-

HOH

21A-375-

HOH

31A-391-

HOH

41A-418-

HOH

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Components

#1: Protein Nitrophorin-4 / NP4 / Nitrite dismutase


Mass: 20291.678 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: D30N mutant / Source: (gene. exp.) Rhodnius prolixus (insect) / Production host: Escherichia coli (E. coli) / References: UniProt: Q94734, 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-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: Potassium phosphate

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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: Oct 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.45→26.23 Å / Num. obs: 27719 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.5
Reflection shellResolution: 1.45→1.49 Å / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 4.3 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX2010_07_29_2140refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MVF

3mvf


Resolution: 1.45→26.229 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 15.77
RfactorNum. reflection% reflection
Rfree0.1803 1386 5 %
Rwork0.1488 --
obs0.1504 27719 99.74 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Bsol: 41.598 Å2 / ksol: 0.442 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.6079 Å2-0 Å2-3.845 Å2
2---2.205 Å2-0 Å2
3----2.4029 Å2
Refinement stepCycle: LAST / Resolution: 1.45→26.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1428 0 46 118 1592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061589
X-RAY DIFFRACTIONf_angle_d1.0642174
X-RAY DIFFRACTIONf_dihedral_angle_d12.291563
X-RAY DIFFRACTIONf_chiral_restr0.075232
X-RAY DIFFRACTIONf_plane_restr0.004280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.50180.24031380.17452631X-RAY DIFFRACTION100
1.5018-1.5620.2121370.15182598X-RAY DIFFRACTION100
1.562-1.6330.1991370.13252615X-RAY DIFFRACTION100
1.633-1.71910.18021390.1322635X-RAY DIFFRACTION100
1.7191-1.82680.19251370.12052608X-RAY DIFFRACTION100
1.8268-1.96780.18811390.11962632X-RAY DIFFRACTION100
1.9678-2.16580.16161380.12852632X-RAY DIFFRACTION100
2.1658-2.47890.17211390.13852625X-RAY DIFFRACTION100
2.4789-3.12240.21361390.17332658X-RAY DIFFRACTION100
3.1224-26.23310.15361430.1632699X-RAY DIFFRACTION99

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