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- PDB-1ml7: Crystal structure of nitrophorin 4 complexed with 4-iodopyrazole -

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Basic information

Entry
Database: PDB / ID: 1ml7
TitleCrystal structure of nitrophorin 4 complexed with 4-iodopyrazole
Componentsnitrophorin 4
KeywordsLIGAND BINDING PROTEIN / NO carrier / ferric heme / iodopyrazole / lipocalin / beta barrel / conformational change
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
Chem-HEV / 4-IODOPYRAZOLE / Nitrophorin-4
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.25 Å
AuthorsBerry, R.E. / Ding, X.D. / Weichsel, A. / Montfort, W.R. / Walker, F.A.
Citation
Journal: J.Biol.Inorg.Chem. / Year: 2004
Title: Axial ligand complexes of the Rhodnius nitrophorins: reduction potentials, binding constants, EPR spectra, and structures of the 4-iodopyrazole and imidazole complexes of NP4
Authors: Berry, R.E. / Ding, X.D. / Shokhireva, T.K. / Weichsel, A. / Montfort, W.R. / Walker, F.A.
#1: Journal: Biochemistry / Year: 2001
Title: Ligand-Induced Heme Ruffling and Bent NO Geometry in Ultra-High-Resolution Structures of Nitophorin 4
Authors: Roberts, S.A. / Weichsel, A. / Qiu, Y. / Shelnutt, J.A. / Walker, F.A. / Montfort, W.R.
History
DepositionAug 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 2, 2015Group: Atomic model
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_struct_special_symmetry / pdbx_validate_chiral / struct_conn / struct_sheet / 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_sheet.number_strands / _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

Downloads & links

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Assembly

Deposited unit
A: nitrophorin 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3214
Polymers20,2931
Non-polymers1,0283
Water4,396244
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.404, 42.763, 52.769
Angle α, β, γ (deg.)90.00, 94.05, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-187-

PYZ

21A-207-

HOH

31A-208-

HOH

41A-266-

HOH

51A-432-

HOH

61A-446-

HOH

DetailsThe biological assembly is a monomer

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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) / Production host: Escherichia coli (E. coli) / References: UniProt: Q94734
#2: Chemical ChemComp-HEV / 5,8-DIMETHYL-1,2,3,4-TETRAVINYLPORPHINE-6,7-DIPROPIONIC ACID FERROUS COMPLEX / 1,3-DEDIMETHYL-1,3-DIVINYL HEME


Mass: 640.509 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H32FeN4O4
#3: Chemical ChemComp-PYZ / 4-IODOPYRAZOLE


Mass: 193.974 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H3IN2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 36.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 298K, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.8 Mammonium phosphate1reservoir
2100 mMTris-HCl1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 17, 2002
RadiationMonochromator: Cyclindrically bent triangular Si(111) asymmetric cut
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.25→22 Å / Num. all: 42458 / Num. obs: 42458 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 7.85 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.7
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 7.2 / Num. unique all: 3947 / % possible all: 92
Reflection
*PLUS
Lowest resolution: 21 Å / % possible obs: 98 % / Num. measured all: 219394
Reflection shell
*PLUS
% possible obs: 92 % / Rmerge(I) obs: 0.16

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Processing

Software
NameVersionClassification
MAR345data collection
CrystalCleardata reduction
SHELXSphasing
SHELXL-97refinement
CrystalClear(MSC/RIGAKU)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1IKJ

1ikj


Resolution: 1.25→20.4 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.194 2087 5 %random
Rwork0.142 ---
all0.145 42458 --
obs0.145 42458 97.9 %-
Displacement parametersBiso mean: 12.8 Å2
Refinement stepCycle: LAST / Resolution: 1.25→20.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1428 0 57 244 1729
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.04
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_from_restr_planes0.1
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.1
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.17

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