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- PDB-2al0: Crystal structure of nitrophorin 2 ferrous aqua complex -

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Basic information

Entry
Database: PDB / ID: 2al0
TitleCrystal structure of nitrophorin 2 ferrous aqua complex
ComponentsNitrophorin 2
KeywordsTRANSPORT PROTEIN / beta barrel / lipocalin / ferrous heme
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
CITRIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Nitrophorin-2
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 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 4, 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 1.3Aug 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 / 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 1.4Oct 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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8893
Polymers20,0801
Non-polymers8092
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.405, 34.405, 255.181
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11X-202-

CIT

21X-515-

HOH

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Components

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


Mass: 20080.391 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: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 1.65 Å3/Da / Density % sol: 24.9 %
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-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2004 / Details: bent Si-mirror
RadiationMonochromator: bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.6→23 Å / Num. all: 21168 / Num. obs: 21168 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 28.7 Å2 / Rsym value: 0.05 / Net I/σ(I): 21
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 2039 / Rsym value: 0.23 / % possible all: 97

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Processing

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

1pee


Resolution: 1.6→23 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.832 / SU ML: 0.066 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22927 1084 5.1 %RANDOM
Rwork0.18212 ---
all0.18449 19970 --
obs0.18449 19970 97.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.075 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2---0.2 Å20 Å2
3---0.39 Å2
Refine analyzeLuzzati coordinate error obs: 0.182 Å
Refinement stepCycle: LAST / Resolution: 1.6→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1434 0 56 143 1633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221528
X-RAY DIFFRACTIONr_bond_other_d0.0010.021291
X-RAY DIFFRACTIONr_angle_refined_deg1.8932.0552085
X-RAY DIFFRACTIONr_angle_other_deg0.92333050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1345187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08130.90966
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01615268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.196152
X-RAY DIFFRACTIONr_chiral_restr0.1250.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021694
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02267
X-RAY DIFFRACTIONr_nbd_refined0.2270.2231
X-RAY DIFFRACTIONr_nbd_other0.1820.21142
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2719
X-RAY DIFFRACTIONr_nbtor_other0.0860.2835
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.299
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2880.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.242
X-RAY DIFFRACTIONr_mcbond_it1.751.51162
X-RAY DIFFRACTIONr_mcbond_other0.3611.5374
X-RAY DIFFRACTIONr_mcangle_it2.02521466
X-RAY DIFFRACTIONr_scbond_it3.0853757
X-RAY DIFFRACTIONr_scangle_it3.9884.5614
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 76 -
Rwork0.223 1453 -
obs-1453 96.22 %

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