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

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Basic information

Entry
Database: PDB / ID: 4hpa
TitleCrystal structure of Nitrophorin 4 from Rhodnius prolixus Complexed with sulfide ion at pH 7.4
ComponentsNitrophorin-4
KeywordsTRANSPORT PROTEIN / HEME / Lipocalin / Nitrophorin / metal binding protein / sulfide
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
HYDROSULFURIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Nitrophorin-4
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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

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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)20,9433
Polymers20,2931
Non-polymers6512
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.169, 42.893, 52.255
Angle α, β, γ (deg.)90.00, 94.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-501-

HOH

21A-511-

HOH

31A-522-

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 / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE / Hydrogen sulfide


Mass: 34.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 1.93 Å3/Da / Density % sol: 36.36 %
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 15, 2011
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.5→30.5 Å / Num. obs: 24703 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 11.72 Å2
Reflection shellResolution: 1.5→1.54 Å / % possible all: 97.7

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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: 1.5→19.833 Å / Occupancy max: 1 / Occupancy min: 0.24 / FOM work R set: 0.9014 / SU ML: 0.15 / σ(F): 1.99 / Phase error: 16.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1814 1235 5 %RANDOM
Rwork0.1336 ---
all0.136 24695 --
obs0.136 24695 98.89 %-
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.639 Å2 / ksol: 0.475 e/Å3
Displacement parametersBiso max: 53.75 Å2 / Biso mean: 16.614 Å2 / Biso min: 4.33 Å2
Baniso -1Baniso -2Baniso -3
1-2.3167 Å20 Å22.0308 Å2
2--0.2526 Å2-0 Å2
3----2.5693 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.833 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1428 0 44 235 1707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071613
X-RAY DIFFRACTIONf_angle_d1.1562220
X-RAY DIFFRACTIONf_dihedral_angle_d12.824586
X-RAY DIFFRACTIONf_chiral_restr0.078241
X-RAY DIFFRACTIONf_plane_restr0.004284
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5-1.560.27751350.1829256498
1.56-1.6310.22341380.157260999
1.631-1.71690.21471350.1379257999
1.7169-1.82440.1891370.1253259199
1.8244-1.96520.18351380.1078261799
1.9652-2.16270.1441370.1163261499
2.1627-2.47520.1751370.11472608100
2.4752-3.11650.17631380.1387262299
3.1165-19.8350.17171400.1441265698

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