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- PDB-1sy2: 1.0 A Crystal Structure of D129A/L130A Mutant of Nitrophorin 4 -

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Basic information

Entry
Database: PDB / ID: 1sy2
Title1.0 A Crystal Structure of D129A/L130A Mutant of Nitrophorin 4
ComponentsNitrophorin 4
KeywordsTRANSPORT PROTEIN / lipocalin / beta barrel / ferric heme
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 / AMMONIUM ION / Nitrophorin-4
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1 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 / struct_conn ...database_2 / 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 / _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.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 1.5Nov 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 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8413
Polymers20,2071
Non-polymers6352
Water4,648258
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.149, 42.804, 52.881
Angle α, β, γ (deg.)90.00, 93.93, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-208-

HOH

21A-444-

HOH

31A-445-

HOH

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Components

#1: Protein Nitrophorin 4 / NP4


Mass: 20206.574 Da / Num. of mol.: 1 / Mutation: D129A, L130A
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-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#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.: 258 / 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: 37.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium Phosphate 2.8 M, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 16, 2002 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 0.99→21.4 Å / Num. all: 85962 / Num. obs: 85962 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.62 % / Biso Wilson estimate: 6.62 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 27.3
Reflection shellResolution: 0.99→1.03 Å / Redundancy: 3.34 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 7.7 / Num. unique all: 8609 / Rsym value: 0.157 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
Blu-Icedata collection
d*TREKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1D2U

1d2u


Resolution: 1→21.4 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.246 / SU ML: 0.014 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1696 4104 5 %RANDOM
Rwork0.15559 ---
all0.1563 85962 --
obs0.1563 77984 97.27 %-
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: 8.691 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0.03 Å2
2--0.05 Å20 Å2
3---0.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.014 Å0.027 Å
Luzzati sigma a-0.026 Å
Refinement stepCycle: LAST / Resolution: 1→21.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1450 0 44 258 1752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221542
X-RAY DIFFRACTIONr_bond_other_d0.0020.021302
X-RAY DIFFRACTIONr_angle_refined_deg1.662.0432116
X-RAY DIFFRACTIONr_angle_other_deg0.79433053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5325193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0980.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021732
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02291
X-RAY DIFFRACTIONr_nbd_refined0.2170.2279
X-RAY DIFFRACTIONr_nbd_other0.2540.21490
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.110.2904
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2134
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0090.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2190.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0580.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.291.5932
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.98721493
X-RAY DIFFRACTIONr_scbond_it2.1553604
X-RAY DIFFRACTIONr_scangle_it3.1654.5607
X-RAY DIFFRACTIONr_rigid_bond_restr1.0921536
X-RAY DIFFRACTIONr_sphericity_free3.6252258
X-RAY DIFFRACTIONr_sphericity_bonded2.91521493
LS refinement shellResolution: 1→1.026 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.186 281
Rwork0.164 5777
obs-5777

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