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- PDB-2ofr: 1.00 A Crystal Structure Of V36A/D129A/L130A Mutant of Nitrophori... -

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Basic information

Entry
Database: PDB / ID: 2ofr
Title1.00 A Crystal Structure Of V36A/D129A/L130A Mutant of Nitrophorin 4 From Rhodnius Prolixus Complexed With Nitric Oxide at pH 5.6
ComponentsNitrophorin-4
KeywordsTRANSPORT PROTEIN / lipocalin / beta barrel / flexible loop mutant
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.
CitationJournal: To be Published
Title: Ligand Protection and Nitric Oxide Interactions with Heme in Nitrophorin 4: Kinetic and Structural Analyses of a Loop Mutant
Authors: Amoia, A.M. / Montfort, W.R.
History
DepositionJan 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 30, 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
X: Nitrophorin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9204
Polymers20,1791
Non-polymers7413
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.191, 42.637, 52.975
Angle α, β, γ (deg.)90.00, 94.12, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-313-

HOH

21X-330-

HOH

31X-347-

HOH

41X-368-

HOH

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Components

#1: Protein Nitrophorin-4 / NP4


Mass: 20178.520 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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#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.: 233 / 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: 1.96 Å3/Da / Density % sol: 37.21 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: ammonium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1→52.85 Å / Num. obs: 79668 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 37
Reflection shellResolution: 1→1.04 Å / Redundancy: 4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 5.33 / Rsym value: 0.39 / % possible all: 90.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalCleardata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1SXX

1sxx


Resolution: 1→9.47 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.551 / SU ML: 0.014 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14795 4022 5.1 %RANDOM
Rwork0.12586 ---
obs0.127 75093 94.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.202 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.03 Å2
2---0.17 Å20 Å2
3---0.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.136 Å / Luzzati d res low obs: 4 Å
Refinement stepCycle: LAST / Resolution: 1→9.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1793 0 50 233 2076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221914
X-RAY DIFFRACTIONr_bond_other_d0.0030.021225
X-RAY DIFFRACTIONr_angle_refined_deg1.9832.0272650
X-RAY DIFFRACTIONr_angle_other_deg1.133.0013039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7475262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39325.78383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81915323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.353153
X-RAY DIFFRACTIONr_chiral_restr0.1160.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022296
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02382
X-RAY DIFFRACTIONr_nbd_refined0.4680.2421
X-RAY DIFFRACTIONr_nbd_other0.240.21291
X-RAY DIFFRACTIONr_nbtor_refined0.1910.2848
X-RAY DIFFRACTIONr_nbtor_other0.0930.2914
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2690.2170
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2520.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2150.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9991.51511
X-RAY DIFFRACTIONr_mcbond_other0.7941.5472
X-RAY DIFFRACTIONr_mcangle_it2.37921917
X-RAY DIFFRACTIONr_scbond_it3.2233906
X-RAY DIFFRACTIONr_scangle_it3.9534.5727
X-RAY DIFFRACTIONr_rigid_bond_restr1.50733882
X-RAY DIFFRACTIONr_sphericity_free10.5063235
X-RAY DIFFRACTIONr_sphericity_bonded3.9633065
LS refinement shellResolution: 1→1.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 264 -
Rwork0.218 4905 -
obs--84.78 %

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