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- PDB-4grj: Crystal structure of nitrophorin 4 triple mutant complex with NO -

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Basic information

Entry
Database: PDB / ID: 4grj
TitleCrystal structure of nitrophorin 4 triple mutant complex with NO
ComponentsNitrophorin-4
KeywordsTRANSPORT PROTEIN / beta barrel / lipocalin / nitric oxide transport / nitric oxide binding
Function / homology
Function and homology information


nitrite dismutase / histamine binding / nitric oxide binding / vasodilation / oxidoreductase 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 / NITRIC OXIDE / PHOSPHATE ION / Nitrophorin-4
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.15 Å
AuthorsWeichsel, A. / Issaian, A.V. / Montfort, W.R.
Citation
Journal: To be Published
Title: Crystal structures of nitrophorin 4 triple mutant
Authors: Issaian, V.A. / Weichsel, A. / Montfort, W.R.
#1: Journal: Structure / Year: 1998
Title: The crystal structure of nitrophorin 4 at 1.5 resolution: transport of nitric oxide by a lipocalin-based heme protein
Authors: Andersen, J.F. / Weichsel, A. / Balfour, C.A. / Champagne, D.E. / Montfort, W.R.
#2: Journal: Biochemistry / Year: 2005
Title: Ultrahigh resolution structures of nitrophorin 4: Heme distortion in ferrous CO and NO complexes
Authors: Maes, E.M. / Roberts, S.A. / Weichsel, A. / Montfort, W.R.
History
DepositionAug 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.2Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 27, 2024Group: Structure summary / Category: 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-4
B: Nitrophorin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0628
Polymers40,5792
Non-polymers1,4836
Water8,089449
1
A: Nitrophorin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0314
Polymers20,2901
Non-polymers7413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nitrophorin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0314
Polymers20,2901
Non-polymers7413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.640, 69.640, 141.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Nitrophorin-4 / NP4


Mass: 20289.709 Da / Num. of mol.: 2 / Mutation: D30N, E32Q, D35N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodnius prolixus (insect) / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q94734
#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.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.85 M ammonium phosphate, 100 mM 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: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 5, 2011 / Details: bent Si-mirror
RadiationMonochromator: diamond (111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.15→60.31 Å / Num. all: 136529 / Num. obs: 136529 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 12.1
Reflection shellResolution: 1.15→1.19 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.4 / Num. unique all: 13678 / % possible all: 98

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Processing

Software
NameClassification
Blu-Icedata collection
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4GNW

4gnw


Resolution: 1.15→60.31 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.342 / SU ML: 0.027 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18533 6765 5 %RANDOM
Rwork0.16032 ---
all0.1616 129575 --
obs0.1616 129575 96.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.535 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å20 Å2
2---0.1 Å20 Å2
3---0.15 Å2
Refine analyzeLuzzati coordinate error obs: 0.177 Å
Refinement stepCycle: LAST / Resolution: 1.15→60.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2856 0 100 449 3405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.023626
X-RAY DIFFRACTIONr_bond_other_d0.0040.022319
X-RAY DIFFRACTIONr_angle_refined_deg1.62.0215013
X-RAY DIFFRACTIONr_angle_other_deg0.98135725
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3515464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.89225.906149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8115606
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.295155
X-RAY DIFFRACTIONr_chiral_restr0.1010.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024261
X-RAY DIFFRACTIONr_gen_planes_other0.010.02764
X-RAY DIFFRACTIONr_rigid_bond_restr4.02835945
X-RAY DIFFRACTIONr_sphericity_free25.871592
X-RAY DIFFRACTIONr_sphericity_bonded11.18256195
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 460 -
Rwork0.352 9222 -
obs-9222 98.18 %

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