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- PDB-1sy1: 1.0 A Crystal Structure of T121V Mutant of Nitrophorin 4 Complexe... -

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Basic information

Entry
Database: PDB / ID: 1sy1
Title1.0 A Crystal Structure of T121V Mutant of Nitrophorin 4 Complexed with Nitric Oxide
ComponentsNitrophorin 4
KeywordsTRANSPORT PROTEIN / lipocalin / beta barrel / ferric 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: 1.01 Å
AuthorsMaes, E.M. / Weichsel, A. / Andersen, J.F. / Shepley, D. / Montfort, W.R.
Citation
Journal: Biochemistry / Year: 2004
Title: Role of binding site loops in controlling nitric oxide release: structure and kinetics of mutant forms of nitrophorin 4
Authors: Maes, E.M. / Weichsel, A. / Andersen, J.F. / Shepley, D. / Montfort, W.R.
#1: Journal: Biochemistry / Year: 2001
Title: Ligand-Induced Heme Ruffling and Bent NO Geometry in Ultra-High-Resolution Structures of Nitrophorin 4
History
DepositionMar 31, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 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
A: Nitrophorin 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0324
Polymers20,2911
Non-polymers7413
Water4,738263
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.395, 42.724, 53.032
Angle α, β, γ (deg.)90.00, 94.31, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-341-

HOH

21A-355-

HOH

31A-441-

HOH

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Components

#1: Protein Nitrophorin 4 / NP4


Mass: 20290.691 Da / Num. of mol.: 1 / Mutation: T121V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodnius prolixus (insect) / Organ: salivary gland / 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.: 263 / 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: 37.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Ammonium Phosphate 3.2 M, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.751 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 24, 2002 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: single crystal Si(311) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.751 Å / Relative weight: 1
ReflectionResolution: 1.01→30.6 Å / Num. all: 80037 / Num. obs: 80037 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.66 % / Biso Wilson estimate: 3.96 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 16.6
Reflection shellResolution: 1.01→1.04 Å / Redundancy: 3.46 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 6.2 / Num. unique all: 7313 / Rsym value: 0.175 / % possible all: 88.6

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Processing

Software
NameVersionClassification
REFMAC5.1.22refinement
Blu-Icedata collection
d*TREKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1KOI

1koi


Resolution: 1.01→26.44 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.221 / SU ML: 0.012 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.023 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14452 3967 5 %RANDOM
Rwork0.1293 ---
all0.13006 80037 --
obs0.13006 75071 96.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 6.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.01 Å2
2---0.01 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.012 Å0.023 Å
Luzzati sigma a-0.023 Å
Refinement stepCycle: LAST / Resolution: 1.01→26.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1448 0 50 265 1763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221547
X-RAY DIFFRACTIONr_bond_other_d0.0030.021301
X-RAY DIFFRACTIONr_angle_refined_deg1.7292.0562119
X-RAY DIFFRACTIONr_angle_other_deg2.57633064
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.455187
X-RAY DIFFRACTIONr_chiral_restr0.1030.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021697
X-RAY DIFFRACTIONr_gen_planes_other0.0220.02288
X-RAY DIFFRACTIONr_nbd_refined0.2360.2258
X-RAY DIFFRACTIONr_nbd_other0.2510.21442
X-RAY DIFFRACTIONr_nbtor_other0.0890.2879
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2149
X-RAY DIFFRACTIONr_metal_ion_refined0.380.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.239
X-RAY DIFFRACTIONr_mcbond_it1.1721.5919
X-RAY DIFFRACTIONr_mcangle_it1.77521476
X-RAY DIFFRACTIONr_scbond_it2.1373616
X-RAY DIFFRACTIONr_scangle_it3.0884.5617
X-RAY DIFFRACTIONr_rigid_bond_restr1.09321535
X-RAY DIFFRACTIONr_sphericity_free4.1622270
X-RAY DIFFRACTIONr_sphericity_bonded2.73421495
LS refinement shellResolution: 1.01→1.036 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.16 270
Rwork0.131 5440
obs-5440

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