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- PDB-4l20: Crystal structure of Cimex nitrophorin A21V mutant ferrous NO complex -

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Basic information

Entry
Database: PDB / ID: 4l20
TitleCrystal structure of Cimex nitrophorin A21V mutant ferrous NO complex
ComponentsSalivary nitrophorin
KeywordsTRANSPORT PROTEIN / beta sandwich / ferrous heme / thiolate heme ligand / s-nitrosocysteine
Function / homology
Function and homology information


phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol dephosphorylation / nitric oxide transport / vasodilation / iron ion binding / heme binding / extracellular space
Similarity search - Function
: / Inositol polyphosphate-related phosphatase / Endonuclease/Exonuclease/phosphatase family 2 / Inositol polyphosphate phosphatase, catalytic domain homologues / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NITRIC OXIDE / Nitrophorin Cim l NP
Similarity search - Component
Biological speciesCimex lectularius (bed bug)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.68 Å
AuthorsBadgandi, H.B. / Weichsel, A. / Montfort, W.R.
CitationJournal: To be Published
Title: Proximal Cysteine Protonation in Cimex Nitrophorin is key to efficient NO transport and release.
Authors: Badgandi, H.B. / Hazzard, J.T. / Weichsel, A. / Tollin, G. / Montfort, W.R.
History
DepositionJun 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Salivary nitrophorin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3063
Polymers31,6591
Non-polymers6462
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.963, 41.814, 65.241
Angle α, β, γ (deg.)90.00, 94.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Salivary nitrophorin


Mass: 31659.396 Da / Num. of mol.: 1 / Fragment: unp residues 23-302 / Mutation: A21V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cimex lectularius (bed bug) / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: O76745
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.1 Å3/Da / Density % sol: 41.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000 , pH 5.6, 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: 0.9798 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 23, 2008 / Details: bent (Si)-mirror
RadiationMonochromator: diamond (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.68→40.73 Å / Num. all: 158351 / Num. obs: 30208 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.24 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 13.6
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 4.2 / Num. unique all: 3023 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
REFMAC5.7.003refinement
CrystalCleardata reduction
CrystalCleardata scaling
REFMAC5.7.003phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1NTF

1ntf


Resolution: 1.68→35.16 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.175 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22145 1528 5.1 %RANDOM
Rwork0.1756 ---
all0.17798 158351 --
obs0.17798 28675 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.284 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0.2 Å2
2---0.03 Å2-0 Å2
3----0 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.68→35.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2231 0 45 187 2463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022367
X-RAY DIFFRACTIONr_bond_other_d0.0020.022195
X-RAY DIFFRACTIONr_angle_refined_deg1.9331.9813233
X-RAY DIFFRACTIONr_angle_other_deg0.93935076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.975289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.9125.227110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57215409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.932159
X-RAY DIFFRACTIONr_chiral_restr0.1240.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212696
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02543
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 97 -
Rwork0.238 2121 -
obs-3023 100 %

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