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- PDB-2all: Crystal structure of L122V/L132V mutant of nitrophorin 2 -

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Basic information

Entry
Database: PDB / ID: 2all
TitleCrystal structure of L122V/L132V mutant of nitrophorin 2
ComponentsNitrophorin 2
KeywordsTRANSPORT PROTEIN / beta barrel / lipocalin / ferric heme / double mutant
Function / homology
Function and homology information


histamine binding / nitric oxide binding / vasodilation / toxin 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 / Nitrophorin-2
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.47 Å
AuthorsWeichsel, A. / Berry, R.E. / Walker, F.A. / Montfort, W.R.
Citation
Journal: To be Published
Title: Crystal structures, ligand induced conformational change and heme deformation in complexes of nitrophorin 2, a nitric oxide transport protein from rhodnius prolixus
Authors: Weichsel, A. / Berry, R.E. / Walker, F.A. / Montfort, W.R.
#1: Journal: J.Biol.Chem. / Year: 2000
Title: The crystal structure of nitrophorin 2
Authors: Andersen, J.F. / Montfort, W.R.
History
DepositionAug 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_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 9, 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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6692
Polymers20,0521
Non-polymers6161
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.440, 126.340, 33.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11X-204-

HOH

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Components

#1: Protein Nitrophorin 2 / NP2 / Prolixin-S


Mass: 20052.336 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: Q26241
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 1.74 Å3/Da / Density % sol: 28.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.1808 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 31, 2003 / Details: bent Si-mirror
RadiationMonochromator: diamond (111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1808 Å / Relative weight: 1
ReflectionResolution: 1.47→30 Å / Num. all: 29090 / Num. obs: 29090 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 20.5 Å2 / Rsym value: 0.08 / Net I/σ(I): 20.8
Reflection shellResolution: 1.47→1.52 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 2489 / Rsym value: 0.19 / % possible all: 84

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
XDISPLAYFdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1EUO

1euo


Resolution: 1.47→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.097 / SU ML: 0.037 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1773 1474 5.1 %RANDOM
Rwork0.13713 ---
all0.13922 27616 --
obs0.13922 27616 97.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.765 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2---0.11 Å20 Å2
3----0.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.155 Å
Refinement stepCycle: LAST / Resolution: 1.47→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1487 0 43 204 1734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221582
X-RAY DIFFRACTIONr_bond_other_d0.0010.021359
X-RAY DIFFRACTIONr_angle_refined_deg1.8542.0432168
X-RAY DIFFRACTIONr_angle_other_deg1.22333221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6525200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00430.89667
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.42315284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.414152
X-RAY DIFFRACTIONr_chiral_restr0.1190.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021756
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02277
X-RAY DIFFRACTIONr_nbd_refined0.230.2277
X-RAY DIFFRACTIONr_nbd_other0.1860.21297
X-RAY DIFFRACTIONr_nbtor_refined0.180.2740
X-RAY DIFFRACTIONr_nbtor_other0.0890.2904
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2156
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.231
X-RAY DIFFRACTIONr_mcbond_it2.0881.51217
X-RAY DIFFRACTIONr_mcbond_other0.7741.5389
X-RAY DIFFRACTIONr_mcangle_it2.50421544
X-RAY DIFFRACTIONr_scbond_it3.7443776
X-RAY DIFFRACTIONr_scangle_it4.8114.5612
X-RAY DIFFRACTIONr_rigid_bond_restr1.77733526
X-RAY DIFFRACTIONr_sphericity_free10.3123205
X-RAY DIFFRACTIONr_sphericity_bonded3.92832894
LS refinement shellResolution: 1.467→1.505 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 81 -
Rwork0.173 1613 -
obs-1613 77.81 %

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