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

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Basic information

Entry
Database: PDB / ID: 4hpc
TitleCrystal structure of Nitrophorin 4 from Rhodnius prolixus Complexed with Cysteine 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
CYSTEINE / PROTOPORPHYRIN IX CONTAINING FE / Nitrophorin-4
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 / pdbx_struct_special_symmetry / 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 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitrophorin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0303
Polymers20,2931
Non-polymers7382
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.236, 43.152, 52.442
Angle α, β, γ (deg.)90.00, 94.31, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

21A-444-

HOH

31A-467-

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-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 1.95 Å3/Da / Density % sol: 37.01 %
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: Aug 12, 2010
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.4→30.6 Å / Num. obs: 30890 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.06 Å2
Reflection shellResolution: 1.4→1.44 Å / % possible all: 99.6

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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: 1.4→19.945 Å / Occupancy max: 1 / Occupancy min: 0.26 / FOM work R set: 0.921 / SU ML: 0.15 / σ(F): 2 / Phase error: 14.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1687 1544 5 %RANDOM
Rwork0.1375 ---
all0.139 30882 --
obs0.139 30882 99.69 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.436 Å2 / ksol: 0.437 e/Å3
Displacement parametersBiso max: 51.55 Å2 / Biso mean: 18.0621 Å2 / Biso min: 6.26 Å2
Baniso -1Baniso -2Baniso -3
1-1.9539 Å20 Å20.8407 Å2
2--0.7618 Å2-0 Å2
3----2.7156 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 0 50 176 1615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071549
X-RAY DIFFRACTIONf_angle_d1.1432117
X-RAY DIFFRACTIONf_dihedral_angle_d13.838554
X-RAY DIFFRACTIONf_chiral_restr0.083229
X-RAY DIFFRACTIONf_plane_restr0.004267
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4-1.44520.22521380.157262399
1.4452-1.49690.20771400.144265599
1.4969-1.55680.15251400.11572656100
1.5568-1.62760.18421390.11482638100
1.6276-1.71330.16521410.11322692100
1.7133-1.82060.15921380.1122620100
1.8206-1.96110.17561430.11412706100
1.9611-2.15820.16951390.11732652100
2.1582-2.470.19021400.13122658100
2.47-3.11010.15831420.15362696100
3.1101-19.94710.15591440.1592742100

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