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- PDB-4gnw: Crystal structure of nitrophorin 4 triple mutant complex with ammonia -

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Basic information

Entry
Database: PDB / ID: 4gnw
TitleCrystal structure of nitrophorin 4 triple mutant complex with ammonia
ComponentsNitrophorin-4
KeywordsTRANSPORT PROTEIN / beta barrel / lipocalin / ferric heme / 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 / AMMONIA / PHOSPHATE ION / Nitrophorin-4
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 A resolution: transport of nitric oxide by a lipocalin-based heme protein
Authors: Andresen, J.F. / Weichsel, A. / Balfour, C.A. / Champagne, D.E. / Montfort, W.R.
History
DepositionAug 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_conn_angle / 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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrophorin-4
B: Nitrophorin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0368
Polymers40,5792
Non-polymers1,4576
Water8,089449
1
A: Nitrophorin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0184
Polymers20,2901
Non-polymers7283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nitrophorin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0184
Polymers20,2901
Non-polymers7283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.740, 69.740, 141.676
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 / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NH3 / AMMONIA / Ammonia


Mass: 17.031 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NH3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H2O

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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: 2.45 Å3/Da / Density % sol: 49.81 %
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: dimond (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→60.4 Å / Num. all: 140391 / Num. obs: 140391 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 13.6
Reflection shellResolution: 1.15→1.19 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 1.6 / Num. unique all: 12869 / % possible all: 91.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.6.0117refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NP4

1np4


Resolution: 1.15→60.4 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.246 / SU ML: 0.025 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18059 7000 5 %RANDOM
Rwork0.16196 ---
all0.1629 133362 --
obs0.1629 133362 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.042 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å20 Å2
3----0.21 Å2
Refine analyzeLuzzati coordinate error obs: 0.178 Å
Refinement stepCycle: LAST / Resolution: 1.15→60.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2856 0 98 449 3403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.023524
X-RAY DIFFRACTIONr_bond_other_d0.0010.022230
X-RAY DIFFRACTIONr_angle_refined_deg1.62.0214877
X-RAY DIFFRACTIONr_angle_other_deg0.91935500
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0935446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.52725.973149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64915576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.122154
X-RAY DIFFRACTIONr_chiral_restr0.0990.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024127
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02745
X-RAY DIFFRACTIONr_rigid_bond_restr3.46835754
X-RAY DIFFRACTIONr_sphericity_free23.95594
X-RAY DIFFRACTIONr_sphericity_bonded9.80555995
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 427 -
Rwork0.39 8638 -
obs-8638 90.23 %

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