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- PDB-2eu7: Crystal structure of D1A mutant of nitrophorin 2 complexed with a... -

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Basic information

Entry
Database: PDB / ID: 2eu7
TitleCrystal structure of D1A mutant of nitrophorin 2 complexed with ammonia
ComponentsNitrophorin 2
KeywordsTRANSPORT PROTEIN / beta barrel / lipocalin / ferric heme / 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 / AMMONIA / Nitrophorin-2
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.2 Å
AuthorsWeichsel, 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. A trifunctional antihemostatic protein from the saliva of Rhodnius prolixus
Authors: Andersen, J.F. / Montfort, W.R.
History
DepositionOct 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 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_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 1.5Oct 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)20,5393
Polymers19,9051
Non-polymers6342
Water4,288238
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.770, 125.300, 34.080
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-245-

HOH

21X-357-

HOH

31X-404-

HOH

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Components

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


Mass: 19905.186 Da / Num. of mol.: 1 / Fragment: residues 25-202 / Mutation: D1A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodnius prolixus (insect) / Plasmid: pET-24a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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-NH3 / AMMONIA


Mass: 17.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NH3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1mM protein, 3.2M ammonium phosphate, 100mM Tris HCl, pH 7.5, 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: Mar 11, 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: 1.2→6 Å / Num. all: 47640 / Num. obs: 47640 / % possible obs: 88.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 14 Å2 / Rsym value: 0.14 / Net I/σ(I): 9.2
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 5261 / Rsym value: 0.24 / % possible all: 99.1

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Processing

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

1euo


Resolution: 1.2→6 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.908 / SU B: 1.288 / SU ML: 0.028 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21512 2426 5.1 %RANDOM
Rwork0.17665 ---
all0.17862 ---
obs0.17862 45095 88.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.402 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refine analyzeLuzzati coordinate error obs: 0.167 Å
Refinement stepCycle: LAST / Resolution: 1.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1424 0 44 238 1706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221508
X-RAY DIFFRACTIONr_bond_other_d0.0010.021273
X-RAY DIFFRACTIONr_angle_refined_deg2.0832.0482059
X-RAY DIFFRACTIONr_angle_other_deg0.90833004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.515186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.63330.95263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44815261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.734152
X-RAY DIFFRACTIONr_chiral_restr0.1330.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021684
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02269
X-RAY DIFFRACTIONr_nbd_refined0.2440.2270
X-RAY DIFFRACTIONr_nbd_other0.1830.21291
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2730
X-RAY DIFFRACTIONr_nbtor_other0.0950.2923
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2162
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.270.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.230
X-RAY DIFFRACTIONr_mcbond_it2.6351.51198
X-RAY DIFFRACTIONr_mcbond_other0.9871.5375
X-RAY DIFFRACTIONr_mcangle_it2.94721470
X-RAY DIFFRACTIONr_scbond_it3.973782
X-RAY DIFFRACTIONr_scangle_it4.714.5587
X-RAY DIFFRACTIONr_rigid_bond_restr2.00333505
X-RAY DIFFRACTIONr_sphericity_free10.543239
X-RAY DIFFRACTIONr_sphericity_bonded5.08432740
LS refinement shellResolution: 1.2→1.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 205 -
Rwork0.191 3527 -
obs-3527 98.57 %

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