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- PDB-2a3f: Crystal structure of nitrophorin 2 aqua complex -

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Basic information

Entry
Database: PDB / ID: 2a3f
TitleCrystal structure of nitrophorin 2 aqua complex
ComponentsNitrophorin 2
KeywordsTRANSPORT PROTEIN / beta barrel / lipocalin / ferric 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
PROTOPORPHYRIN IX CONTAINING FE / Nitrophorin-2
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 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
DepositionJun 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 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 / pdbx_struct_special_symmetry / 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 1.4Nov 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
X: Nitrophorin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6972
Polymers20,0801
Non-polymers6161
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.608, 125.773, 33.395
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-263-

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2 Å3/Da / Density % sol: 39 %
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: Apr 8, 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: 1.4→26 Å / Num. all: 31128 / Num. obs: 31128 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 20.9 Å2 / Rsym value: 0.09 / Net I/σ(I): 20
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 3089 / Rsym value: 0.25 / % possible all: 93

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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: 1.4→26 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.472 / SU ML: 0.045 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21391 1563 5.1 %RANDOM
Rwork0.17755 ---
all0.1794 ---
obs0.1794 29280 91.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.996 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å20 Å2
2--0.49 Å20 Å2
3---0.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.073 Å0.084 Å
Luzzati sigma a-0.045 Å
Refinement stepCycle: LAST / Resolution: 1.4→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1422 0 48 104 1574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221506
X-RAY DIFFRACTIONr_bond_other_d0.0020.021287
X-RAY DIFFRACTIONr_angle_refined_deg1.9882.0552049
X-RAY DIFFRACTIONr_angle_other_deg1.58533037
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2885181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.15330.93864
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22915268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.47152
X-RAY DIFFRACTIONr_chiral_restr0.1320.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021659
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02263
X-RAY DIFFRACTIONr_nbd_refined0.1980.2263
X-RAY DIFFRACTIONr_nbd_other0.190.21222
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2718
X-RAY DIFFRACTIONr_nbtor_other0.0960.2925
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.287
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2220.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0870.210
X-RAY DIFFRACTIONr_mcbond_it2.5861.51116
X-RAY DIFFRACTIONr_mcbond_other1.1161.5370
X-RAY DIFFRACTIONr_mcangle_it3.23621445
X-RAY DIFFRACTIONr_scbond_it4.343733
X-RAY DIFFRACTIONr_scangle_it5.6244.5601
X-RAY DIFFRACTIONr_rigid_bond_restr2.33333309
X-RAY DIFFRACTIONr_sphericity_free11.533104
X-RAY DIFFRACTIONr_sphericity_bonded5.72332757
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0.072 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 125 -
Rwork0.194 2091 -
obs-2216 90.45 %

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