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- PDB-2hys: Crystal structure of nitrophorin 2 complexed with cyanide -

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Basic information

Entry
Database: PDB / ID: 2hys
TitleCrystal structure of nitrophorin 2 complexed with cyanide
ComponentsNitrophorin-2
KeywordsTRANSPORT PROTEIN / beta barrel / lipocalin / ferric heme / cyanide
Function / homology
Function and homology information


histamine binding / nitric oxide binding / vasodilation / toxin 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
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Nitrophorin-2
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.2 Å
AuthorsWeichsel, A. / Montfort, W.R.
Citation
Journal: Inorg.Chem. / Year: 2007
Title: Assignment of the Ferriheme Resonances of the Low-Spin Complexes of Nitrophorins 1 and 4 by (1)H and (13)C NMR Spectroscopy: Comparison to Structural Data Obtained from X-ray Crystallography.
Authors: Shokhireva, T.Kh. / Weichsel, A. / Smith, K.M. / Berry, R.E. / Shokhirev, N.V. / Balfour, C.A. / Zhang, H. / Montfort, W.R. / Walker, F.A.
#1: Journal: J.Biol.Chem. / Year: 2000
Title: The crystal structure of nitrophorin 2. A trifunctional antihemostatic protein from the saliva of Rhodnius prolixus.
Authors: Andersen, J.F. / Montfort, W.R.
History
DepositionAug 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 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
A: Nitrophorin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7233
Polymers20,0801
Non-polymers6432
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.377, 34.377, 257.256
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
11A-435-

HOH

21A-455-

HOH

31A-562-

HOH

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Components

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


Mass: 20080.391 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: Q26241
#2: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 1.89 Å3/Da / Density % sol: 34.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 89% saturated sodium citrate, 100 mM hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 18, 2006 / Details: bent Si-mirror
RadiationMonochromator: diamond (111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.2→22 Å / Num. all: 42640 / Num. obs: 42640 / % possible obs: 84.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 24
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.2 / Num. unique all: 3225 / % possible all: 85

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-Icedata collection
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 1PEE

1pee


Resolution: 1.2→22 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.701 / SU ML: 0.034 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Fe-CN distance restrained to 2.0 A
RfactorNum. reflection% reflectionSelection details
Rfree0.21625 2127 5 %RANDOM
Rwork0.18563 ---
obs0.18715 40513 84.48 %-
all-40513 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.842 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2---0.36 Å20 Å2
3---0.72 Å2
Refine analyzeLuzzati coordinate error obs: 0.182 Å
Refinement stepCycle: LAST / Resolution: 1.2→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1453 0 45 172 1670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221539
X-RAY DIFFRACTIONr_angle_refined_deg2.0572.0532098
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.8835192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71225.90966
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8115278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.001152
X-RAY DIFFRACTIONr_chiral_restr0.1430.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021154
X-RAY DIFFRACTIONr_nbd_refined0.2280.2610
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21064
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2135
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.242
X-RAY DIFFRACTIONr_mcbond_it2.2861.5931
X-RAY DIFFRACTIONr_mcangle_it3.12321479
X-RAY DIFFRACTIONr_scbond_it3.863693
X-RAY DIFFRACTIONr_scangle_it5.1944.5611
X-RAY DIFFRACTIONr_rigid_bond_restr2.35531624
X-RAY DIFFRACTIONr_sphericity_free9.7573174
X-RAY DIFFRACTIONr_sphericity_bonded6.4631496
LS refinement shellResolution: 1.2→1.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 154 -
Rwork0.334 2916 -
obs-2916 83.51 %

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