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- PDB-2at8: 0.96 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus ... -

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Basic information

Entry
Database: PDB / ID: 2at8
Title0.96 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus Containing Fe(III) 2,4 Dimethyl Deuteroporphyrin IX Complexed With Nitric Oxide at pH 5.6
ComponentsNitrophorin 4
KeywordsTRANSPORT PROTEIN / Lipocalin / beta barrel / ferrous / heme analog / Fe(III) 2 / 4 Dimethyl Deuteroporphyrin IX
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
FE(III) 2,4-DIMETHYL DEUTEROPORPHYRIN IX / NITRIC OXIDE / PHOSPHATE ION / Nitrophorin-4
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1 Å
AuthorsAmoia, A.M. / Montfort, W.R.
CitationJournal: To be Published
Title: Heme distortion in nitrophorin 4: high resolution structures of mutated positions L123V and L133V and heme altered proteins
Authors: Amoia, A.M. / Montfort, W.R.
History
DepositionAug 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Nitrophorin 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0104
Polymers20,2931
Non-polymers7173
Water4,071226
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.211, 42.582, 52.935
Angle α, β, γ (deg.)90.00, 94.61, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-267-

HOH

21X-323-

HOH

31X-426-

HOH

41X-446-

HOH

DetailsThe biological assembly is a monomer consisting of chain X and the Fe(III) 2,4 Dimethyl Deuteroporphyrin IX, and can be generated by the identity operation: x,y,z

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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: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q94734
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-FDD / FE(III) 2,4-DIMETHYL DEUTEROPORPHYRIN IX


Mass: 592.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H32FeN4O4
#4: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 1.59 Å3/Da / Density % sol: 22.15 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: ammonium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2005 / Details: Bent conical Si-mirror (Rh coating)
RadiationMonochromator: Bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.96→21.29 Å / Num. obs: 81981 / % possible obs: 86.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.16 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 22.6 / Scaling rejects: 31050
Reflection shellResolution: 0.96→0.99 Å / % possible obs: 89 % / Redundancy: 1.54 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.9 / Num. measured obs: 4909 / Num. unique all: 8392 / Rsym value: 0.41 / % possible all: 89

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Processing

Software
NameVersionClassificationNB
d*TREK7.2SSIbetadata scaling
REFMACrefinement
PDB_EXTRACT1.7data extraction
CrystalClearV. 1.3.6 D*TREK (MSC/RIGAKU)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1X8O

1x8o


Resolution: 1→21.29 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.922 / SU ML: 0.022 / Isotropic thermal model: anisotropic / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / ESU R: 0.035 / ESU R Free: 0.036 / Stereochemistry target values: Engh & Huber
Details: Anisotropic refinment reduced Free R. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.195 3642 5 %RANDOM
Rwork0.165 ---
all0.166 72220 --
obs0.166 72220 85.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20.03 Å2
2--0.03 Å20 Å2
3----0.29 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å / Luzzati d res low obs: 4 Å
Refinement stepCycle: LAST / Resolution: 1→21.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1722 0 48 229 1999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221831
X-RAY DIFFRACTIONr_angle_refined_deg1.7472.0262529
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3135245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27529.09177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.04215301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.299152
X-RAY DIFFRACTIONr_chiral_restr0.1160.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021446
X-RAY DIFFRACTIONr_nbd_refined0.4180.2968
X-RAY DIFFRACTIONr_nbtor_refined0.310.21252
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2203
X-RAY DIFFRACTIONr_metal_ion_refined0.280.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.234
X-RAY DIFFRACTIONr_mcbond_it1.7391.51156
X-RAY DIFFRACTIONr_mcangle_it2.39721838
X-RAY DIFFRACTIONr_scbond_it3.3963776
X-RAY DIFFRACTIONr_scangle_it4.3854.5689
LS refinement shellResolution: 1→1.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 276 -
Rwork0.308 5356 -
all-5632 -
obs--90.78 %

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