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- PDB-2imq: Crystal structure of ferrous cimex nitrophorin -

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Basic information

Entry
Database: PDB / ID: 2imq
TitleCrystal structure of ferrous cimex nitrophorin
ComponentsSalivary nitrophorin
KeywordsTRANSPORT PROTEIN / ferrous heme / beta-sandwich
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 / Nitrophorin Cim l NP
Similarity search - Component
Biological speciesCimex lectularius (bed bug)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.3 Å
AuthorsWeichsel, A. / Montfort, W.R.
Citation
Journal: To be Published
Title: Crystallographic and spectroscopic characterization of ferrous complexes of cimex nitrophorin, a heme-thiolate protein from the bedbug
Authors: Weichsel, A. / Badgandi, H. / Montfort, W.R.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Heme-assisted S-nitrosation of a proximal thiolate in a nitric oxide transport protein
Authors: Weichsel, A. / Maes, E.M. / Andersen, J.F. / Valenzuela, J.G. / Shokhireva, T.Kh. / Walker, F.A. / Montfort, W.R.
History
DepositionOct 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: 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.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_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 / _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
X: Salivary nitrophorin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3632
Polymers31,7461
Non-polymers6161
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.107, 41.491, 65.380
Angle α, β, γ (deg.)90.00, 95.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Salivary nitrophorin


Mass: 31746.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cimex lectularius (bed bug) / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / 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.: 200 / 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: 2.09 Å3/Da / Density % sol: 41.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 23% PEG 4000, 100 mM Tris HCl, 200 mM lithium sulfate, 15% ethanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2005 / Details: bent Si-mirrors
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: 1.3→28.4 Å / Num. all: 64243 / Num. obs: 64243 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 17.6
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.4 / Num. unique all: 6369 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
ADSCQuantumdata collection
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1NTF

1ntf


Resolution: 1.3→28.35 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.924 / SU ML: 0.037 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20844 3250 5.1 %RANDOM
Rwork0.17583 ---
all0.17753 60962 --
obs0.17753 60962 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.918 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0.97 Å2
2--0.37 Å20 Å2
3----0.63 Å2
Refine analyzeLuzzati coordinate error obs: 0.182 Å
Refinement stepCycle: LAST / Resolution: 1.3→28.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2251 0 43 201 2495
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222346
X-RAY DIFFRACTIONr_bond_other_d0.0010.022030
X-RAY DIFFRACTIONr_angle_refined_deg1.7541.9963201
X-RAY DIFFRACTIONr_angle_other_deg0.90534769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7475283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4629.151106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44615404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.609158
X-RAY DIFFRACTIONr_chiral_restr0.1190.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022583
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02431
X-RAY DIFFRACTIONr_nbd_refined0.2190.2425
X-RAY DIFFRACTIONr_nbd_other0.1970.22020
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21143
X-RAY DIFFRACTIONr_nbtor_other0.0880.21361
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2158
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.29
X-RAY DIFFRACTIONr_mcbond_it2.3971.51767
X-RAY DIFFRACTIONr_mcbond_other1.6751.5567
X-RAY DIFFRACTIONr_mcangle_it2.91322297
X-RAY DIFFRACTIONr_scbond_it4.19431106
X-RAY DIFFRACTIONr_scangle_it5.314.5901
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 235 -
Rwork0.216 4520 -
obs-4520 99.75 %

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