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- PDB-3c77: 1.08 A crystal structure of nitrophorin 4 from Rhodnius prolixus ... -

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Basic information

Entry
Database: PDB / ID: 3c77
Title1.08 A crystal structure of nitrophorin 4 from Rhodnius prolixus containing FE(III) deuteroporphyrin ix complexed with ammonia at ph 7.5
ComponentsNitrophorin-4
KeywordsTRANSPORT PROTEIN / LIPOCALN / BETA BARREL / FERRIC / HEME ANALOG / FE(III) DEUTEROPORPHYRIN IX / Iron / Metal-binding / Secreted / Vasoactive / Vasodilator
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
FE(III) DEUTEROPORPHYRIN IX / AMMONIA / Nitrophorin-4
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.08 Å
AuthorsAmoia, A.M. / Montfort, W.R.
CitationJournal: To be Published
Title: Heme Distortion in Nitrophorin 4: High Resolution Structures of Mutated Positions L123V and L133V and Heme Altered Proteins
Authors: Amoia, A.M. / Montfort, W.R.
History
DepositionFeb 6, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionMar 4, 2008ID: 2AT4
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / 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_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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.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_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

Downloads & links

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Assembly

Deposited unit
X: Nitrophorin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8743
Polymers20,2931
Non-polymers5812
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.156, 42.745, 52.821
Angle α, β, γ (deg.)90.00, 94.03, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-753-

HOH

21X-813-

HOH

31X-878-

HOH

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Components

#1: Protein Nitrophorin-4 / / NP4


Mass: 20292.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodnius prolixus (insect) / Plasmid: PET17B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q94734
#2: Chemical ChemComp-NH3 / AMMONIA / Ammonia


Mass: 17.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NH3
#3: Chemical ChemComp-FDE / FE(III) DEUTEROPORPHYRIN IX


Mass: 564.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H28FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsFE(III) DEUTEROPORPHYRIN IX IS DISORDERED BY A ROTATION OF 180 DEGREES AROUND THE CHA-FE-CHC AXIS ...FE(III) DEUTEROPORPHYRIN IX IS DISORDERED BY A ROTATION OF 180 DEGREES AROUND THE CHA-FE-CHC AXIS WHICH IS REFLECTED IN CONFORMATION A AND CONFORMATION B OF THE LIGAND. AMMONIA OCCUPIES THE SIXTH COORDINATION POSITION OF THE FE(III) DEUTEROPORPHYRIN IX.

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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: 1.64 Å3/Da / Density % sol: 24.3 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: AMMONIUM PHOSPHATE, pH 7.50, temperature 300.0K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 31, 2003 / Details: BENT CONICAL SI-MIRROR (RH COATING)
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: 1.07→21.8 Å / Num. obs: 65307 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 6.68 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 16.1
Reflection shellResolution: 1.07→1.11 Å / Redundancy: 6.06 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.18 / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalClearV. 1.3 D*TREK (MSC/RIGAKU)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1X8P

1x8p


Resolution: 1.08→21.8 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.765 / SU ML: 0.018 / Cross valid method: FREE R / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.033 / Stereochemistry target values: ENGH & HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.162 3207 5 %RANDOM
Rwork0.137 ---
obs0.137 63622 95.1 %-
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: 9.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å2-0.01 Å2
2---0.45 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.08→21.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1682 0 79 285 2046
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221784
X-RAY DIFFRACTIONr_bond_other_d0.0010.021506
X-RAY DIFFRACTIONr_angle_refined_deg1.7262.0282464
X-RAY DIFFRACTIONr_angle_other_deg0.85633549
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3435234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.45128.70177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.18215297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.623153
X-RAY DIFFRACTIONr_chiral_restr0.1030.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022101
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02351
X-RAY DIFFRACTIONr_nbd_refined0.420.2415
X-RAY DIFFRACTIONr_nbd_other0.20.21643
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2855
X-RAY DIFFRACTIONr_nbtor_other0.0870.21035
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2182
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0030.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0640.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1720.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.242
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9151.51371
X-RAY DIFFRACTIONr_mcbond_other0.7151.5439
X-RAY DIFFRACTIONr_mcangle_it2.35521771
X-RAY DIFFRACTIONr_scbond_it3.1423860
X-RAY DIFFRACTIONr_scangle_it3.8094.5691
X-RAY DIFFRACTIONr_rigid_bond_restr1.50833970
X-RAY DIFFRACTIONr_sphericity_free8.1493292
X-RAY DIFFRACTIONr_sphericity_bonded3.48333229
LS refinement shellResolution: 1.08→1.11 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.192 202 -
Rwork0.143 4319 -
obs--92.17 %

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