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- PDB-3mvf: Crystal Structure of Nitrophorin 4 from Rhodnius prolixus Complex... -

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Basic information

Entry
Database: PDB / ID: 3mvf
TitleCrystal Structure of Nitrophorin 4 from Rhodnius prolixus Complexed with Nitrite at pH 7.4
ComponentsNitrophorin-4
KeywordsTRANSPORT PROTEIN / heme / hemoglobin / iron / lipocalin / nitric oxide / nitrite / 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 / NITRITE ION / Nitrophorin-4
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsOgata, H. / He, C. / Knipp, M.
CitationJournal: Biochemistry / Year: 2010
Title: Formation of the complex of nitrite with the ferriheme b beta-barrel proteins nitrophorin 4 and nitrophorin 7.
Authors: He, C. / Ogata, H. / Knipp, M.
History
DepositionMay 4, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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)21,0014
Polymers20,2931
Non-polymers7083
Water4,017223
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nitrophorin-4
hetero molecules

A: Nitrophorin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0028
Polymers40,5852
Non-polymers1,4176
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1430 Å2
ΔGint-5 kcal/mol
Surface area17670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.301, 42.909, 52.460
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-226-

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-NO2 / NITRITE ION / Nitrite


Mass: 46.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 1.94 Å3/Da / Density % sol: 36.75 %
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: 0.91892 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 23, 2010
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91892 Å / Relative weight: 1
ReflectionResolution: 1.4→30.53 Å / Num. obs: 30694 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.038
Reflection shellResolution: 1.4→1.44 Å / Rmerge(I) obs: 0.193 / % possible all: 93.7

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→15 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.765 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18717 1533 5 %RANDOM
Rwork0.13641 ---
obs0.13889 29136 100 %-
all-30669 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.999 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å2-0.14 Å2
2---0.41 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1428 0 49 223 1700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221512
X-RAY DIFFRACTIONr_angle_refined_deg2.2192.0432058
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1055183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.225.75866
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13715246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.406152
X-RAY DIFFRACTIONr_chiral_restr0.1750.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021143
X-RAY DIFFRACTIONr_mcbond_it2.8981.5918
X-RAY DIFFRACTIONr_mcangle_it4.15321458
X-RAY DIFFRACTIONr_scbond_it5.5013594
X-RAY DIFFRACTIONr_scangle_it7.3284.5600
X-RAY DIFFRACTIONr_rigid_bond_restr2.86831512
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 114 -
Rwork0.16 2169 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -8.2211 Å / Origin y: -0.3259 Å / Origin z: -13.2321 Å
111213212223313233
T0.0014 Å20.0001 Å2-0.0028 Å2-0.0007 Å20 Å2--0.0059 Å2
L0.0088 °2-0.0015 °20.0004 °2-0.0131 °2-0.0032 °2--0.0062 °2
S0.0003 Å °0.0006 Å °0.0004 Å °0.0002 Å °0.0003 Å °0.0014 Å °0.0004 Å °-0.0003 Å °-0.0006 Å °

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