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- PDB-2pyb: Napa protein from borrelia burgdorferi -

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Basic information

Entry
Database: PDB / ID: 2pyb
TitleNapa protein from borrelia burgdorferi
ComponentsNeutrophil activating protein
KeywordsMETAL TRANSPORT / Ferritin / Dps / FOUR-HELIX BUNDLE
Function / homology
Function and homology information


ferric iron binding / intracellular iron ion homeostasis / cytosol
Similarity search - Function
DNA-binding protein Dps / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Neutrophil activating protein A (NapA)
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZanotti, G. / Papinutto, E. / De Bernard, M.
Citation
Journal: Biochim.Biophys.Acta / Year: 2010
Title: Structure and immunomodulatory property relationship in NapA of Borrelia burgdorferi.
Authors: Codolo, G. / Papinutto, E. / Polenghi, A. / D'Elios, M.M. / Zanotti, G. / de Bernard, M.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: Structure of the neutrophil-activating protein from Helicobacter pylori
Authors: Zanotti, G. / Papinutto, E. / Dundon, W. / Battistutta, R. / Seveso, M. / Dal Giudice, G. / Montecucco, C.
#2: Journal: Nat.Struct.Mol.Biol. / Year: 1998
Title: The Crystal Structure of Dps, a Ferritin Homolog that Binds and Protects DNA
Authors: Grant, R.A. / Filman, D.J. / Finkel, S.E. / Kolter, R. / Hogle, J.M.
#3: Journal: Nat.Struct.Mol.Biol. / Year: 2000
Title: The Dodecameric Ferritin from Listeria Innocua Contains a Novel Intersubunit Iron Binding Site
Authors: Ilari, A. / Stefanini, S. / Chiancone, E. / Tsernoglou, D.
History
DepositionMay 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 26, 2016Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _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
A: Neutrophil activating protein
B: Neutrophil activating protein
C: Neutrophil activating protein
D: Neutrophil activating protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,54512
Polymers71,0984
Non-polymers4478
Water43224
1
A: Neutrophil activating protein
B: Neutrophil activating protein
C: Neutrophil activating protein
D: Neutrophil activating protein
hetero molecules

A: Neutrophil activating protein
B: Neutrophil activating protein
C: Neutrophil activating protein
D: Neutrophil activating protein
hetero molecules

A: Neutrophil activating protein
B: Neutrophil activating protein
C: Neutrophil activating protein
D: Neutrophil activating protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,63436
Polymers213,29412
Non-polymers1,34024
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area47760 Å2
ΔGint-467 kcal/mol
Surface area70180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)93.078, 93.078, 227.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThe biological assembly is a dodecamer, generate by the 3-fold axis from the tetramer contained in the asymmetric unit

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Components

#1: Protein
Neutrophil activating protein / NapA


Mass: 17774.498 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Strain: B31 / Gene: NAPA / Plasmid: pSM214G-NapA / Production host: BACILLUS SUBTILIS (bacteria) / Strain (production host): SMS 118 / References: UniProt: O51633
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5
Details: 0.1M sodium acetate and 26-30% MPD, pH 4.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 15, 2002
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 22533 / Num. obs: 22533 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 52.5 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 6.4
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 1.3 / Num. unique all: 2778 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→37.99 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2005816.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The data is merohedral twinning with twinning operator: (h,-h-k,-l) and the twinned fraction 0.45.
RfactorNum. reflection% reflectionSelection details
Rfree0.2754 1661 7.4 %RANDOM
Rwork0.2419 ---
obs0.2419 22533 99.8 %-
all-22533 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 75.516 Å2 / ksol: 0.341731 e/Å3
Displacement parametersBiso mean: 52.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å24.89 Å20 Å2
2--0.34 Å20 Å2
3----0.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.63 Å0.54 Å
Luzzati d res low-5 Å
Luzzati sigma a0.99 Å0.74 Å
Refinement stepCycle: LAST / Resolution: 2.6→37.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4984 0 8 24 5016
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it1.962
X-RAY DIFFRACTIONc_scbond_it1.682
X-RAY DIFFRACTIONc_scangle_it2.462.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.4512 272 7.3 %
Rwork0.3736 3445 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ion.param

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