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- PDB-2at5: 1.22 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus ... -

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Basic information

Entry
Database: PDB / ID: 2at5
Title1.22 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus Containing Fe(III) Deuteroporphyrin IX Complexed With Nitric Oxide at pH 5.6
ComponentsNitrophorin 4
KeywordsTRANSPORT PROTEIN / Lipocalin / beta barrel / ferrous / heme analog / Fe(III) Deuteroporphyrin IX / 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
FE(III) DEUTEROPORPHYRIN IX / NITRIC OXIDE / PHOSPHATE ION / Nitrophorin-4
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.22 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 1.3Aug 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_chiral
Item: _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_bond.pdbx_aromatic_flag
Remark 600HETEROGEN Fe(III) Deuteroporphyrin IX is disordered by a rotation of 180 degrees around the CHA-Fe- ...HETEROGEN Fe(III) Deuteroporphyrin IX is disordered by a rotation of 180 degrees around the CHA-Fe-CHC axis which is reflected in conformation A and conformation B of the ligand. Nitric oxide occupies the sixth coordination position of the Fe(III) Deuteroporphyrin IX.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Nitrophorin 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9824
Polymers20,2931
Non-polymers6893
Water5,296294
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.210, 42.666, 53.005
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-267-

HOH

21X-323-

HOH

31X-426-

HOH

41X-446-

HOH

DetailsThe biological assembly is a monomer consisting of chain X and the Fe(III) Deuteroporphyrin IX, and can be generated by the identity operation: x,y,z

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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) / 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


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-FDE / FE(III) DEUTEROPORPHYRIN IX


Mass: 564.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H28FeN4O4
#4: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


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


Mass: 18.015 Da / Num. of mol.: 294 / 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: 1.61 Å3/Da / Density % sol: 22.79 %
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: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 30, 2003 / Details: Bent conical Si-mirror (Rh coating)
RadiationMonochromator: Bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.22→20.38 Å / Num. obs: 44702 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.93 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 24.3 / Scaling rejects: 4036
Reflection shellResolution: 1.22→1.26 Å / % possible obs: 96.1 % / Redundancy: 5.74 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 10.6 / Num. measured obs: 48 / Num. unique all: 4462 / Rsym value: 0.18 / % possible all: 95.8

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Processing

Software
NameVersionClassificationNB
d*TREK7.2SSIbetadata scaling
REFMACrefinement
PDB_EXTRACT1.7data extraction
CrystalClearV. 1.3 D*TREK (MSC/RIGAKU)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1X8O

1x8o


Resolution: 1.22→20.38 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.984 / SU ML: 0.02 / Isotropic thermal model: anisotropic / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / ESU R: 0.044 / ESU R Free: 0.041 / Stereochemistry target values: Engh & Huber
Details: Anisotropic refinement reduced Free R. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.148 2233 5 %RANDOM
Rwork0.118 ---
all0.119 44644 --
obs0.118 44644 95.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 7.583 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.21 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å / Luzzati d res low obs: 4.44 Å
Refinement stepCycle: LAST / Resolution: 1.22→20.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1714 0 85 307 2106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221822
X-RAY DIFFRACTIONr_bond_other_d0.0020.021522
X-RAY DIFFRACTIONr_angle_refined_deg1.6742.0252515
X-RAY DIFFRACTIONr_angle_other_deg0.92733594
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3875243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0329.09177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55615299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.032152
X-RAY DIFFRACTIONr_chiral_restr0.1090.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022158
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02353
X-RAY DIFFRACTIONr_nbd_refined0.470.2450
X-RAY DIFFRACTIONr_nbd_other0.230.21610
X-RAY DIFFRACTIONr_nbtor_refined0.1920.2846
X-RAY DIFFRACTIONr_nbtor_other0.0890.21020
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2206
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0160.21
X-RAY DIFFRACTIONr_metal_ion_refined0.2250.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2520.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.240
X-RAY DIFFRACTIONr_mcbond_it1.7381.51429
X-RAY DIFFRACTIONr_mcbond_other0.6081.5458
X-RAY DIFFRACTIONr_mcangle_it2.09521827
X-RAY DIFFRACTIONr_scbond_it3.133856
X-RAY DIFFRACTIONr_scangle_it3.8094.5686
X-RAY DIFFRACTIONr_rigid_bond_restr1.42334029
X-RAY DIFFRACTIONr_sphericity_free7.7373309
X-RAY DIFFRACTIONr_sphericity_bonded2.86733282
LS refinement shellResolution: 1.22→1.252 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.17 163 -
Rwork0.136 3139 -
all-3302 -
obs--95.9 %

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