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- PDB-4l1y: Crystal structure of Cimex nitrophorin A21V mutant -

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Basic information

Entry
Database: PDB / ID: 4l1y
TitleCrystal structure of Cimex nitrophorin A21V mutant
ComponentsSalivary nitrophorin
KeywordsTRANSPORT PROTEIN / beta sandwich / ferric heme / thiolate heme ligand
Function / homology
Function and homology information


vasodilation in another organism / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol dephosphorylation / nitric oxide transport / 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 / Nitrophorin Cim l NP
Similarity search - Component
Biological speciesCimex lectularius (bed bug)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.55 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 1.0Sep 17, 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_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_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: Salivary nitrophorin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2472
Polymers31,6301
Non-polymers6161
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.959, 42.228, 65.579
Angle α, β, γ (deg.)90.00, 94.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Salivary nitrophorin


Mass: 31630.396 Da / Num. of mol.: 1 / Fragment: unp residues 23-302
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.14 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000 , pH 8.5, 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: 0.9798 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 17, 2009 / 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: 1.55→29.35 Å / Num. all: 212447 / Num. obs: 37021 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.45 % / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 15.4
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 5.42 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 4.6 / Num. unique all: 3858 / % 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: 1.55→29.35 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.24 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25896 1957 5 %RANDOM
Rwork0.21955 ---
all0.22154 212447 --
obs0.22154 37021 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.939 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å2-0.16 Å2
2--0.3 Å20 Å2
3----0.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.236 Å
Refinement stepCycle: LAST / Resolution: 1.55→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 43 224 2496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.022328
X-RAY DIFFRACTIONr_bond_other_d0.0010.022163
X-RAY DIFFRACTIONr_angle_refined_deg2.1331.9793175
X-RAY DIFFRACTIONr_angle_other_deg0.99434995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8995279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.36125.288104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.70415398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.019158
X-RAY DIFFRACTIONr_chiral_restr0.160.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212634
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02532
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 128 -
Rwork0.311 2721 -
obs-2721 100 %

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