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- PDB-1u0x: Crystal structure of nitrophorin 4 under pressure of xenon (200 psi) -

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Basic information

Entry
Database: PDB / ID: 1u0x
TitleCrystal structure of nitrophorin 4 under pressure of xenon (200 psi)
ComponentsNitrophorin 4
KeywordsTRANSPORT PROTEIN / beta-barrel / lipocalin / ferric heme / xenon
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 / AMMONIA / XENON / Nitrophorin-4
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.45 Å
AuthorsNienhaus, K. / Maes, E.M. / Weichsel, A. / Montfort, W.R. / Nienhaus, G.U.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Structural dynamics controls nitric oxide affinity in nitrophorin 4
Authors: Nienhaus, K. / Maes, E.M. / Weichsel, A. / Montfort, W.R. / Nienhaus, G.U.
#1: Journal: Biochemistry / Year: 2001
Title: Ligand-Induced Heme Ruffling and Bent NO Geometry in Ultra-High-Resolution Structures of Nitrophorin 4
Authors: Roberts, S.A. / Weichsel, A. / Qui, Y. / Shelnutt, J.A. / Walker, F.A. / Montfort, W.R.
#2: Journal: Nat.Struct.Biol. / Year: 2000
Title: Nitric Oxide Binding to Nitrophorin 4 Induces Complete Distal Pocket Burial
Authors: Weichsel, A. / Andersen, J.F. / Roberts, S.A. / Montfort, W.R.
History
DepositionJul 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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 / pdbx_struct_special_symmetry / 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.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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitrophorin 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1895
Polymers20,2931
Non-polymers8964
Water5,873326
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.196, 42.461, 52.990
Angle α, β, γ (deg.)90.00, 94.24, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-260-

HOH

21A-327-

HOH

31A-394-

HOH

41A-425-

HOH

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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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NH3 / AMMONIA


Mass: 17.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NH3
#4: Chemical ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Xe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 1.9 Å3/Da / Density % sol: 34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 1, 2001 / Details: osmic mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→30.3 Å / Num. all: 26873 / Num. obs: 26873 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 11.8 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.9
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 6.8 / Num. unique all: 2149 / % possible all: 78

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1D2U

1d2u


Resolution: 1.45→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.012 / SU ML: 0.04 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17527 1362 5.1 %RANDOM
Rwork0.14308 ---
all0.1447 26873 --
obs0.1447 25510 96.82 %-
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: 10.001 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.12 Å2
2---0.06 Å20 Å2
3---0.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.073 Å0.072 Å
Luzzati sigma a0.04 Å-
Refinement stepCycle: LAST / Resolution: 1.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1557 0 46 326 1929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221656
X-RAY DIFFRACTIONr_bond_other_d0.0020.021392
X-RAY DIFFRACTIONr_angle_refined_deg1.8082.0422280
X-RAY DIFFRACTIONr_angle_other_deg1.8333292
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3215206
X-RAY DIFFRACTIONr_chiral_restr0.1060.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021876
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02311
X-RAY DIFFRACTIONr_nbd_refined0.2410.2348
X-RAY DIFFRACTIONr_nbd_other0.2570.21720
X-RAY DIFFRACTIONr_nbtor_other0.0880.21000
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2273
X-RAY DIFFRACTIONr_metal_ion_refined0.0240.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2420.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.260
X-RAY DIFFRACTIONr_mcbond_it1.0461.5992
X-RAY DIFFRACTIONr_mcangle_it1.85621613
X-RAY DIFFRACTIONr_scbond_it2.4843658
X-RAY DIFFRACTIONr_scangle_it3.794.5655
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0.073 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 77 -
Rwork0.238 1377 -
obs-2023 72 %

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