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- PDB-3np1: CRYSTAL STRUCTURE OF THE COMPLEX OF NITROPHORIN 1 FROM RHODNIUS P... -

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Basic information

Entry
Database: PDB / ID: 3np1
TitleCRYSTAL STRUCTURE OF THE COMPLEX OF NITROPHORIN 1 FROM RHODNIUS PROLIXUS WITH CYANIDE
ComponentsNITROPHORIN 1
KeywordsNITRIC OXIDE TRANSPORT / FERRIC HEME / HISTAMINE / ANTIHISTAMINE / VASODILATOR / LIPOCALIN / CYANIDE
Function / homology
Function and homology information


histamine binding / nitric oxide binding / vasodilation / 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
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / Nitrophorin-1
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.3 Å
AuthorsWeichsel, A. / Andersen, J.F. / Champagne, D.E. / Walker, F.A. / Montfort, W.R.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: Crystal structures of a nitric oxide transport protein from a blood-sucking insect.
Authors: Weichsel, A. / Andersen, J.F. / Champagne, D.E. / Walker, F.A. / Montfort, W.R.
#1: Journal: Biochemistry / Year: 1997
Title: Nitric Oxide Binding and Crystallization of Recombinant Nitrophorin I, a Nitric Oxide Transport Protein from the Blood-Sucking Bug Rhodnius Prolixus
Authors: Andersen, J.F. / Champagne, D.E. / Weichsel, A. / Ribeiro, J.M. / Balfour, C.A. / Dress, V. / Montfort, W.R.
History
DepositionJan 22, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Refinement description / Category: diffrn_detector / pdbx_database_status / software
Item: _diffrn_detector.detector / _pdbx_database_status.process_site / _software.name
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 1.5Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 1
B: NITROPHORIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4978
Polymers41,0222
Non-polymers1,4756
Water2,162120
1
A: NITROPHORIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2484
Polymers20,5111
Non-polymers7373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NITROPHORIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2484
Polymers20,5111
Non-polymers7373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.390, 74.220, 66.230
Angle α, β, γ (deg.)90.00, 99.51, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.697379, -0.038635, -0.715661), (-0.053702, -0.998556, 0.001578), (-0.714688, 0.037332, -0.698446)
Vector: 42.167, 76.6498, 97.6618)

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Components

#1: Protein NITROPHORIN 1 / NP1


Mass: 20510.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodnius prolixus (insect) / Cell line: BL21 / Organ: SALIVARY GLAND / Plasmid: PET17B-NP1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q26239
#2: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growpH: 7.5
Details: 2.8 M AMMONIUM PHOSPHATE, 0.1 M TRIS.HCL, PH 7.5, ROOM TEMPERATURE
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Andersen, J.F., (1997) Biochemistry, 36, 4423.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
210 mMpotassium phosphate1drop
32.6 Mammonium phosphate1reservoir
40.1 Mpotassium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Oct 17, 1997 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→28 Å / Num. obs: 16620 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 25 Å2 / Rsym value: 0.056 / Net I/σ(I): 10
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.22 / % possible all: 97.2
Reflection
*PLUS
Num. measured all: 46715 / Rmerge(I) obs: 0.053

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Processing

Software
NameVersionClassification
MADNESdata collection
AGROVATA/ROTAVATAdata reduction
X-PLOR3.851model building
X-PLOR3.851refinement
MADNESdata reduction
Agrovatadata scaling
ROTAVATAdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 1NP1

1np1


Resolution: 2.3→15 Å / Rfactor Rfree error: 0.013 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT CORRECTION WITH K = 0.3435, B = 94.9.
RfactorNum. reflection% reflectionSelection details
Rfree0.28 492 5 %RANDOM
Rwork0.19 ---
obs0.19 14049 71.4 %-
Displacement parametersBiso mean: 32 Å2
Refine analyzeLuzzati sigma a obs: 0.42 Å
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 0 277 127 3290
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d30.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.971.5
X-RAY DIFFRACTIONx_mcangle_it4.682
X-RAY DIFFRACTIONx_scbond_it4.322
X-RAY DIFFRACTIONx_scangle_it6.232.5
Refine LS restraints NCSNCS model details: UNRESTRAINED
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.081 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.415 26 5 %
Rwork0.277 1296 -
obs--69.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19X.HEMETOPH19X.HEME
X-RAY DIFFRACTION3PARAM.PO4TOP.PO4
X-RAY DIFFRACTION4PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg30.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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