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- PDB-1ike: Crystal Structure of Nitrophorin 4 from Rhodnius Prolixus Complex... -

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Basic information

Entry
Database: PDB / ID: 1ike
TitleCrystal Structure of Nitrophorin 4 from Rhodnius Prolixus Complexed with Histamine at 1.5 A Resolution
ComponentsNitrophorin 4
KeywordsTRANSPORT PROTEIN / nitric oxide transport / ferric heme / antihistamine / lipocalin
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 / HISTAMINE / Nitrophorin-4
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsRoberts, S.A. / Weichsel, A. / Qiu, Y. / Shelnutt, J.A. / Walker, F.A. / Montfort, W.R.
CitationJournal: Biochemistry / Year: 2001
Title: Ligand-induced heme ruffling and bent no geometry in ultra-high-resolution structures of nitrophorin 4.
Authors: Roberts, S.A. / Weichsel, A. / Qiu, Y. / Shelnutt, J.A. / Walker, F.A. / Montfort, W.R.
History
DepositionMay 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2016Group: Other
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.6Aug 16, 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
Revision 1.7Oct 9, 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
A: Nitrophorin 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0203
Polymers20,2931
Non-polymers7282
Water4,702261
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.180, 42.520, 52.860
Angle α, β, γ (deg.)90.00, 94.35, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-283-

HOH

21A-347-

HOH

31A-392-

HOH

41A-394-

HOH

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Components

#1: Protein Nitrophorin 4


Mass: 20292.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodnius prolixus (insect) / Plasmid: pET-17b-NP4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / 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-HSM / HISTAMINE


Mass: 111.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9N3 / Comment: neurotransmitter, hormone*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 1.94 Å3/Da / Density % sol: 36.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG4000, Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Details: graphite monochrometer
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→8.9 Å / Num. all: 22265 / Num. obs: 20817 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.6
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2769 / % possible all: 76

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Processing

Software
NameVersionClassification
MADNESSdata collection
SCALAdata scaling
SHELXL-97refinement
MADNESSdata reduction
CCP4(SCALA)data scaling
RefinementStarting model: PDB ENTRY 1D2U

1d2u


Resolution: 1.5→8.9 Å
Isotropic thermal model: Isotropic except for anisotropic Fe, S
σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Histamine occupies the sixth coordination position of the iron. The heme is disordered by a rotation of 180 degrees around the CHA-FE-CHC axis. The only evidence of this disorder is the ...Details: Histamine occupies the sixth coordination position of the iron. The heme is disordered by a rotation of 180 degrees around the CHA-FE-CHC axis. The only evidence of this disorder is the appearance of methyl groups CMB and CMC as vinyls. The loop containing residues 32-38 is disordered. There is no observed electron density for these residues and their positions and conformations are not reliable.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1076 -RANDOM
Rwork0.18 ---
obs0.18 20817 93.5 %-
all-22265 --
Displacement parametersBiso mean: 20 Å2
Refinement stepCycle: LAST / Resolution: 1.5→8.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1428 0 51 261 1740

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