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- PDB-2asn: Crystal structure of D1A mutant of nitrophorin 2 complexed with i... -

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Basic information

Entry
Database: PDB / ID: 2asn
TitleCrystal structure of D1A mutant of nitrophorin 2 complexed with imidazole
ComponentsNitrophorin 2
KeywordsTRANSPORT PROTEIN / beta barrel / lipocalin / ferric heme / imidazole
Function / homology
Function and homology information


histamine binding / nitric oxide binding / vasodilation / 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-2
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsWeichsel, A. / Berry, R.E. / Walker, F.A. / Montfort, W.R.
Citation
Journal: To be Published
Title: Crystal structures, ligand induced conformational change and heme deformation in complexes of nitrophorin 2, a nitric oxide transport protein from rhodnius prolixus
Authors: Weichsel, A. / Berry, R.E. / Walker, F.A. / Montfort, W.R.
#1: Journal: J.Biol.Chem. / Year: 2000
Title: The crystal structure of nitrophorin 2
Authors: Andersen, J.F. / Montfort, W.R.
History
DepositionAug 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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_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_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_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
X: Nitrophorin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5913
Polymers19,9051
Non-polymers6862
Water2,936163
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.389, 34.389, 256.725
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11X-435-

HOH

21X-455-

HOH

31X-557-

HOH

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Components

#1: Protein Nitrophorin 2 / / NP2 / Prolixin-S


Mass: 19905.186 Da / Num. of mol.: 1 / Fragment: residues 25-202
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): BL21(DE3) / References: UniProt: Q26241
#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-IMD / IMIDAZOLE / Imidazole


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


Mass: 18.015 Da / Num. of mol.: 163 / 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: 1.91 Å3/Da / Density % sol: 35.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.1808 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 31, 2003 / Details: bent Si-mirror
RadiationMonochromator: diamond (111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1808 Å / Relative weight: 1
ReflectionResolution: 1.7→16.3 Å / Num. all: 13482 / Num. obs: 13482 / % possible obs: 73.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 18.7 Å2 / Rsym value: 0.05 / Net I/σ(I): 8.9
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 544 / Rsym value: 0.138 / % possible all: 38

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1PEE

1pee


Resolution: 1.7→16.3 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.899 / SU ML: 0.065 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20925 680 5 %RANDOM
Rwork0.15209 ---
all0.1549 13482 --
obs0.1549 12802 73.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.071 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.16 Å2
Refine analyzeLuzzati sigma a obs: 0.171 Å
Refinement stepCycle: LAST / Resolution: 1.7→16.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1419 0 48 163 1630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221506
X-RAY DIFFRACTIONr_bond_other_d0.0010.021294
X-RAY DIFFRACTIONr_angle_refined_deg1.7822.0532053
X-RAY DIFFRACTIONr_angle_other_deg0.86233051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1035186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30830.95263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63415266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.058152
X-RAY DIFFRACTIONr_chiral_restr0.1080.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021661
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02270
X-RAY DIFFRACTIONr_nbd_refined0.1930.2264
X-RAY DIFFRACTIONr_nbd_other0.1910.21209
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2703
X-RAY DIFFRACTIONr_nbtor_other0.090.2879
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2136
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1860.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.223
X-RAY DIFFRACTIONr_mcbond_it1.6411.51183
X-RAY DIFFRACTIONr_mcbond_other0.2941.5371
X-RAY DIFFRACTIONr_mcangle_it1.86221451
X-RAY DIFFRACTIONr_scbond_it2.9793806
X-RAY DIFFRACTIONr_scangle_it3.7114.5596
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 26 -
Rwork0.141 573 -
obs-573 45.66 %

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