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

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Basic information

Entry
Database: PDB / ID: 4hpb
TitleCrystal structure of Nitrophorin 4 from Rhodnius prolixus Complexed with Beta-Mercaptoethanol 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
BETA-MERCAPTOETHANOL / PROTOPORPHYRIN IX CONTAINING FE / Nitrophorin-4
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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)20,9873
Polymers20,2931
Non-polymers6952
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.288, 43.185, 52.618
Angle α, β, γ (deg.)90.00, 94.38, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-351-

HOH

21A-387-

HOH

31A-398-

HOH

41A-432-

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-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 1.96 Å3/Da / Density % sol: 37.31 %
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: 1.6→30.7 Å / Num. obs: 20819 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 14.38 Å2
Reflection shellResolution: 1.6→1.64 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: 1.6→19.967 Å / Occupancy max: 1 / Occupancy min: 0.05 / FOM work R set: 0.9066 / SU ML: 0.18 / σ(F): 2.01 / Phase error: 16.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1795 1040 5 %RANDOM
Rwork0.1421 ---
all0.144 20811 --
obs0.144 20811 99.6 %-
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.207 Å2 / ksol: 0.472 e/Å3
Displacement parametersBiso max: 56.88 Å2 / Biso mean: 18.5687 Å2 / Biso min: 7.25 Å2
Baniso -1Baniso -2Baniso -3
1-8.1969 Å20 Å22.7411 Å2
2--5.2541 Å2-0 Å2
3----13.451 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 0 47 153 1589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061540
X-RAY DIFFRACTIONf_angle_d1.042100
X-RAY DIFFRACTIONf_dihedral_angle_d13.302547
X-RAY DIFFRACTIONf_chiral_restr0.072225
X-RAY DIFFRACTIONf_plane_restr0.004265
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.68440.21331450.1665276699
1.6844-1.78980.23651500.15232838100
1.7898-1.92790.19781460.11982788100
1.9279-2.12170.17721490.1134281899
2.1217-2.42830.16631490.1292848100
2.4283-3.05760.18241490.14162830100
3.0576-19.9690.16521520.1581288399

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