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- PDB-4hpd: Crystal structure of Nitrophorin 4 from Rhodnius prolixus Complex... -

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Basic information

Entry
Database: PDB / ID: 4hpd
TitleCrystal structure of Nitrophorin 4 from Rhodnius prolixus Complexed with homocysteine at pH 7.4
ComponentsNitrophorin-4
KeywordsTRANSPORT PROTEIN / HEME / Lipocalin / Nitrophorin / metal binding protein
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
2-AMINO-4-MERCAPTO-BUTYRIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Nitrophorin-4
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsNishikawa, K. / Ogata, H. / Knipp, M.
CitationJournal: J.Inorg.Biochem. / Year: 2013
Title: Complexes of ferriheme nitrophorin 4 with low-molecular weight thiol(ate)s occurring in blood plasma
Authors: He, C. / Nishikawa, K. / Erdem, O.F. / Reijerse, E. / Ogata, H. / Lubitz, W. / Knipp, M.
History
DepositionOct 23, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Mar 6, 2024Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.5Nov 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)21,0443
Polymers20,2931
Non-polymers7522
Water3,873215
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.082, 42.982, 52.321
Angle α, β, γ (deg.)90.00, 93.93, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-364-

HOH

21A-399-

HOH

31A-458-

HOH

41A-468-

HOH

51A-503-

HOH

61A-507-

HOH

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Components

#1: Protein Nitrophorin-4 / NP4


Mass: 20292.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodnius prolixus (insect) / Plasmid: PET17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q94734
#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-HCS / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / L-Homocysteine


Type: L-peptide linking / Mass: 135.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 36.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 3.2M AMMONIUM PHOSPHATE, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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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: Mar 23, 2010
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.3→29.5 Å / Num. obs: 38103 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.02 Å2
Reflection shellResolution: 1.3→1.33 Å / % possible all: 94.5

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Processing

Software
NameClassification
XDSdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MVF

3mvf


Resolution: 1.3→19.873 Å / Occupancy max: 1 / Occupancy min: 0.28 / FOM work R set: 0.9084 / SU ML: 0.15 / σ(F): 1.99 / Phase error: 15.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1787 1905 5 %RANDOM
Rwork0.1447 ---
all0.1464 38097 --
obs0.1464 38097 99.42 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.592 Å2 / ksol: 0.431 e/Å3
Displacement parametersBiso max: 48.43 Å2 / Biso mean: 17.5758 Å2 / Biso min: 5.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.5263 Å2-0 Å2-0.3066 Å2
2---0.3591 Å2-0 Å2
3----0.1672 Å2
Refinement stepCycle: LAST / Resolution: 1.3→19.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1428 0 51 215 1694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071584
X-RAY DIFFRACTIONf_angle_d1.1812168
X-RAY DIFFRACTIONf_dihedral_angle_d12.443572
X-RAY DIFFRACTIONf_chiral_restr0.085234
X-RAY DIFFRACTIONf_plane_restr0.005276
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3-1.33250.30171280.2234242594
1.3325-1.36850.19081370.18352608100
1.3685-1.40880.22641350.15612568100
1.4088-1.45420.2151360.15672574100
1.4542-1.50620.18331360.13392577100
1.5062-1.56650.1821350.11882568100
1.5665-1.63780.16591370.12182608100
1.6378-1.72410.16211360.12152581100
1.7241-1.8320.17371360.11732583100
1.832-1.97330.18481370.1232608100
1.9733-2.17170.15521370.12732609100
2.1717-2.48540.16691370.13692596100
2.4854-3.12940.19421380.15732616100
3.1294-19.87490.16691400.1601267199

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