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- PDB-2at0: 1.00 A Crystal Structure Of L133V Mutant of Nitrophorin 4 From Rh... -

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Entry
Database: PDB / ID: 2at0
Title1.00 A Crystal Structure Of L133V Mutant of Nitrophorin 4 From Rhodnius Prolixus Complexed With Nitric Oxide at pH 5.6
ComponentsNitrophorin 4
KeywordsTRANSPORT PROTEIN / Lipocalin / beta barrel / ferrous heme / nitric oxide
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 / 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 1.3Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / 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 / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_alt_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600HETEROGEN The heme is disordered by a rotation of 180 degrees around the CHA-Fe-CHC axis, which is ...HETEROGEN The heme is disordered by a rotation of 180 degrees around the CHA-Fe-CHC axis, which is reflected in conformation A and conformation D of the ligand.

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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)21,0204
Polymers20,2791
Non-polymers7413
Water5,116284
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.286, 42.699, 52.970
Angle α, β, γ (deg.)90.00, 94.27, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-295-

HOH

21X-364-

HOH

31X-423-

HOH

41X-569-

HOH

DetailsThe biological assembly is a monomer consisting of chain X and the heme, and can be generated by the identity operation: x,y,z

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Components

#1: Protein Nitrophorin 4 / / NP4


Mass: 20278.637 Da / Num. of mol.: 1 / Mutation: L133V
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 / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide / Nitric oxide


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


Mass: 18.015 Da / Num. of mol.: 284 / 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: 1.62 Å3/Da / Density % sol: 23.63 %
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: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 20, 2005
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1→36.51 Å / Num. obs: 83901 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 9.3 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 13.9
Reflection shellResolution: 1→1.05 Å / % possible obs: 98.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 5.3 / Num. measured obs: 12069 / Num. unique all: 12069 / Rsym value: 0.178 / % possible all: 98

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT1.7data extraction
Blu-Icedata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 1X8O

1x8o


Resolution: 1→36.47 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.514 / SU ML: 0.013
Isotropic thermal model: anisotropic; residues 32-35 isotropic due to lack of density
Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / ESU R: 0.026 / ESU R Free: 0.026 / Stereochemistry target values: Engh & Huber
Details: Anisotropic refinment reduced Free R. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.154 4242 5.1 %RANDOM
Rwork0.139 ---
all0.14 83900 --
obs0.14 83900 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.753 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å2-0.13 Å2
2---0.18 Å20 Å2
3---0.05 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å / Luzzati d res low obs: 4 Å
Refinement stepCycle: LAST / Resolution: 1→36.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1689 0 179 287 2155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221800
X-RAY DIFFRACTIONr_angle_refined_deg1.4892.0282474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1585230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.90529.01281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.28615302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.788152
X-RAY DIFFRACTIONr_chiral_restr0.10.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021399
X-RAY DIFFRACTIONr_nbd_refined0.270.2873
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21222
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2248
X-RAY DIFFRACTIONr_metal_ion_refined0.3020.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.294
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.080.258
X-RAY DIFFRACTIONr_mcbond_it1.2781.51111
X-RAY DIFFRACTIONr_mcangle_it1.86421765
X-RAY DIFFRACTIONr_scbond_it2.2523794
X-RAY DIFFRACTIONr_scangle_it2.9534.5707
X-RAY DIFFRACTIONr_rigid_bond_restr1.15331870
X-RAY DIFFRACTIONr_sphericity_free4.2723365
X-RAY DIFFRACTIONr_sphericity_bonded3.54231710
LS refinement shellResolution: 1→1.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 292 -
Rwork0.19 5413 -
all-5705 -
obs--92.42 %

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