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- PDB-4xmh: Crystal structure of nitrophorin 7 from Rhodnius prolixus at pH 7... -

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Basic information

Entry
Database: PDB / ID: 4xmh
TitleCrystal structure of nitrophorin 7 from Rhodnius prolixus at pH 7.8 complexed with Gly-Gly-Gly
Components
  • GLY-GLY-GLY
  • Nitrophorin-7
KeywordsTRANSPORT PROTEIN / Heme / NO transporter / oxidoreductase
Function / homology
Function and homology information


venom-mediated perturbation of biological process / modulation of process of another organism / nitrite dismutase / histamine binding / nitric oxide binding / vasodilation / toxin activity / 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 / Nitrophorin-7
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsOgata, H.
CitationJournal: F1000Res / Year: 2015
Title: Structure and dynamics of the membrane attaching nitric oxide transporter nitrophorin 7.
Authors: Knipp, M. / Ogata, H. / Soavi, G. / Cerullo, G. / Allegri, A. / Abbruzzetti, S. / Bruno, S. / Viappiani, C. / Bidon-Chanal, A. / Luque, F.J.
History
DepositionJan 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / citation / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.2Nov 20, 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-7
B: GLY-GLY-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7714
Polymers21,0622
Non-polymers7092
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-19 kcal/mol
Surface area9860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.374, 66.929, 38.885
Angle α, β, γ (deg.)90.00, 116.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nitrophorin-7 / NP7 / Nitrite dismutase


Mass: 20872.820 Da / Num. of mol.: 1 / Fragment: UNP residues 21-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodnius prolixus (insect) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PQK2, nitrite dismutase
#2: Protein/peptide GLY-GLY-GLY


Mass: 189.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 25%(w/v) PEG 3350, 0.1 M bis-Tris propane pH 7.8, 0.25%(w/v) Gly-Gly, 0.25%(w/v) Gly-Gly-Gly, 0.25%(w/v) Gly- Gly-Gly-Gly, 0.25%(w/v) pentaglycine, 0.02 M HEPES sodium pH 6.8.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.29→34.71 Å / Num. obs: 41095 / % possible obs: 92.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.024 / Net I/σ(I): 21.4
Reflection shellResolution: 1.29→1.37 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.3 / % possible all: 64.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 2011_08_24_1020)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MVF

3mvf


Resolution: 1.29→34.71 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 18.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1822 3737 5.02 %
Rwork0.1545 --
obs0.1559 41069 85.46 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.875 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.5121 Å2-0 Å2-2.0129 Å2
2---4.4986 Å20 Å2
3----3.7017 Å2
Refinement stepCycle: LAST / Resolution: 1.29→34.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1482 0 49 162 1693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061581
X-RAY DIFFRACTIONf_angle_d1.0672138
X-RAY DIFFRACTIONf_dihedral_angle_d13.659578
X-RAY DIFFRACTIONf_chiral_restr0.084223
X-RAY DIFFRACTIONf_plane_restr0.005266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2897-1.3060.2947290.3196544X-RAY DIFFRACTION18
1.306-1.32320.3245660.25641312X-RAY DIFFRACTION43
1.3232-1.34130.3133920.22771745X-RAY DIFFRACTION56
1.3413-1.36050.25031090.20971944X-RAY DIFFRACTION64
1.3605-1.38080.24961150.20142151X-RAY DIFFRACTION70
1.3808-1.40240.22631280.19032354X-RAY DIFFRACTION76
1.4024-1.42540.20511470.1812636X-RAY DIFFRACTION86
1.4254-1.44990.17381460.15892743X-RAY DIFFRACTION90
1.4499-1.47630.20131450.14422779X-RAY DIFFRACTION91
1.4763-1.50470.18971510.13792839X-RAY DIFFRACTION92
1.5047-1.53540.18471460.12992837X-RAY DIFFRACTION93
1.5354-1.56880.1711470.13252852X-RAY DIFFRACTION93
1.5688-1.60530.1431520.12762844X-RAY DIFFRACTION93
1.6053-1.64540.18581520.11732877X-RAY DIFFRACTION95
1.6454-1.68990.16331530.11252937X-RAY DIFFRACTION95
1.6899-1.73970.13871540.11912874X-RAY DIFFRACTION95
1.7397-1.79580.17351500.12392922X-RAY DIFFRACTION95
1.7958-1.860.16161520.12942924X-RAY DIFFRACTION95
1.86-1.93450.1521500.12842906X-RAY DIFFRACTION95
1.9345-2.02250.14481560.13742966X-RAY DIFFRACTION96
2.0225-2.12910.17851540.14592952X-RAY DIFFRACTION97
2.1291-2.26250.19181530.14832935X-RAY DIFFRACTION97
2.2625-2.43710.18781560.15482925X-RAY DIFFRACTION96
2.4371-2.68230.2021590.17092993X-RAY DIFFRACTION98
2.6823-3.07020.18511560.17872967X-RAY DIFFRACTION98
3.0702-3.86740.19071600.15692932X-RAY DIFFRACTION95
3.8674-34.72380.17421590.16442958X-RAY DIFFRACTION97

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