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- PDB-3tgb: Crystal structure of L130R mutant of Nitrophorin 4 from Rhodnius ... -

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Basic information

Entry
Database: PDB / ID: 3tgb
TitleCrystal structure of L130R mutant of Nitrophorin 4 from Rhodnius prolixus complexed with imidazole at pH 7.4
ComponentsNitrophorin-4
KeywordsMETAL BINDING PROTEIN / heme / lipocalin / nitrophorin
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 / IMIDAZOLE / Nitrophorin-4
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsOgata, H. / He, C. / Knipp, M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2012
Title: Guanidine-Ferroheme Coordination in the Mutant Protein Nitrophorin 4(L130R).
Authors: He, C. / Fuchs, M.R. / Ogata, H. / Knipp, M.
History
DepositionAug 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)21,0223
Polymers20,3371
Non-polymers6862
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.719, 43.058, 52.469
Angle α, β, γ (deg.)90.00, 94.43, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-258-

HOH

21A-303-

HOH

31A-326-

HOH

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Components

#1: Protein Nitrophorin-4 / NP4


Mass: 20336.699 Da / Num. of mol.: 1 / Mutation: L130R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodnius prolixus (insect) / Production host: Escherichia coli (E. coli) / 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-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 1.93 Å3/Da / Density % sol: 36.29 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: Ammonium phosphate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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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: Dec 15, 2010
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.35→21.72 Å / Num. obs: 34144 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.038
Reflection shellResolution: 1.35→1.39 Å / Rmerge(I) obs: 0.351 / % possible all: 99.9

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Processing

Software
NameClassification
XDSdata scaling
MOLREPphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→21.72 Å / SU ML: 0.14 / σ(F): 2 / Phase error: 16.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1856 1708 5 %RANDOM
Rwork0.1429 ---
obs0.145 32436 99.82 %-
all-34144 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.564 Å2 / ksol: 0.453 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.922 Å2-0 Å2-3.7173 Å2
2---1.5253 Å2-0 Å2
3----1.3967 Å2
Refinement stepCycle: LAST / Resolution: 1.35→21.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1431 0 48 189 1668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071648
X-RAY DIFFRACTIONf_angle_d1.1032261
X-RAY DIFFRACTIONf_dihedral_angle_d13.136587
X-RAY DIFFRACTIONf_chiral_restr0.079238
X-RAY DIFFRACTIONf_plane_restr0.004296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.38980.24181420.18662682X-RAY DIFFRACTION100
1.3898-1.43460.20891410.16572688X-RAY DIFFRACTION100
1.4346-1.48590.21921410.14732683X-RAY DIFFRACTION100
1.4859-1.54530.17651410.12412680X-RAY DIFFRACTION100
1.5453-1.61560.1831420.122691X-RAY DIFFRACTION100
1.6156-1.70080.16651420.11652706X-RAY DIFFRACTION100
1.7008-1.80730.15741420.11612685X-RAY DIFFRACTION100
1.8073-1.94680.19641430.12072716X-RAY DIFFRACTION100
1.9468-2.14250.15341420.12572704X-RAY DIFFRACTION100
2.1425-2.45220.18631410.12842688X-RAY DIFFRACTION100
2.4522-3.08810.19811450.15992738X-RAY DIFFRACTION100
3.0881-21.72260.1871460.16112775X-RAY DIFFRACTION100

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