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- PDB-4np1: NITROPHORIN 1 COMPLEX WITH NITRIC OXIDE -

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Basic information

Entry
Database: PDB / ID: 4np1
TitleNITROPHORIN 1 COMPLEX WITH NITRIC OXIDE
ComponentsNITROPHORIN 1
KeywordsVASODILATOR / NITRIC OXIDE TRANSPORT / HEME / ANTIHISTAMINE / LIPOCALIN
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
PROTOPORPHYRIN IX CONTAINING FE / NITRIC OXIDE / 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. / Walker, F.A. / Montfort, W.R.
Citation
Journal: To be Published
Title: Nitric Oxide Binding to the Ferri-and Ferroheme States of Nitrophorin 1, a Reversible No-Binding Heme Protein from the Saliva of the Blood-Sucking Insect, Rhodnius Prolixus
Authors: Ding, X.D. / Weichsel, A. / Andersen, J.F. / Shokhireva, T.Kh. / Balfour, C. / Pierik, A. / Averill, B.A. / Montfort, W.R. / Walker, F.A.
#1: 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.
#2: 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
DepositionJun 26, 1998Processing site: BNL
Revision 1.0Nov 11, 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.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_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 23, 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

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Assembly

Deposited unit
A: NITROPHORIN 1
B: NITROPHORIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,69510
Polymers41,0222
Non-polymers1,6738
Water2,540141
1
A: NITROPHORIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3475
Polymers20,5111
Non-polymers8364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NITROPHORIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3475
Polymers20,5111
Non-polymers8364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.410, 74.290, 66.120
Angle α, β, γ (deg.)90.00, 99.19, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.686192, -0.040491, -0.726292), (-0.057147, -0.998364, 0.001667), (-0.725172, 0.040362, -0.687384)
Vector: 43.1843, 76.9003, 97.4409)

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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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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

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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: Nov 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: 18071 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 28 Å2 / Rsym value: 0.058 / Net I/σ(I): 9.2
Reflection shellResolution: 2.2→2.35 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.258 / % possible all: 87.7

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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: 0.016 / Data cutoff high absF: 1000000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.3 354 5 %RANDOM
Rwork0.19 ---
obs0.19 13528 84.7 %-
Displacement parametersBiso mean: 36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.31 Å
Luzzati d res low-15 Å
Luzzati sigma a0.26 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 0 100 141 3127
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.7
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_d1.18
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.71.5
X-RAY DIFFRACTIONx_mcangle_it4.52
X-RAY DIFFRACTIONx_scbond_it3.82
X-RAY DIFFRACTIONx_scangle_it5.82.5
Refine LS restraints NCSNCS model details: UNRESTRAINED
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.06 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.28 22 5 %
Rwork0.29 1100 -
obs--58 %
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

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