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- PDB-1ji4: NAP protein from helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 1ji4
TitleNAP protein from helicobacter pylori
ComponentsNEUTROPHIL-ACTIVATING PROTEIN A
KeywordsMETAL TRANSPORT / dodecamer / four-helix bundle
Function / homology
Function and homology information


Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / : / ferric iron binding / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
Dps protein family signature 2. / Dps protein family signature 1. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily ...Dps protein family signature 2. / Dps protein family signature 1. / DNA-binding protein Dps, conserved site / 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
: / DNA protection during starvation protein
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsZanotti, G. / Papinutto, E. / Dundon, W.G. / Battistutta, R. / Seveso, M. / Del Giudice, G. / Rappuoli, R. / Montecucco, C.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Structure of the Neutrophil-activating Protein from Helicobacter pylori
Authors: Zanotti, G. / Papinutto, E. / Dundon, W.G. / Battistutta, R. / Seveso, M. / Del Giudice, G. / Rappuoli, R. / Montecucco, C.
#1: Journal: Nat.Struct.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.
#2: Journal: Nat.Struct.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
DepositionJun 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / 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 A
B: NEUTROPHIL-ACTIVATING PROTEIN A
C: NEUTROPHIL-ACTIVATING PROTEIN A
D: NEUTROPHIL-ACTIVATING PROTEIN A
E: NEUTROPHIL-ACTIVATING PROTEIN A
F: NEUTROPHIL-ACTIVATING PROTEIN A
G: NEUTROPHIL-ACTIVATING PROTEIN A
H: NEUTROPHIL-ACTIVATING PROTEIN A
I: NEUTROPHIL-ACTIVATING PROTEIN A
J: NEUTROPHIL-ACTIVATING PROTEIN A
K: NEUTROPHIL-ACTIVATING PROTEIN A
L: NEUTROPHIL-ACTIVATING PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,61348
Polymers203,52512
Non-polymers2,08836
Water11,638646
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39070 Å2
ΔGint-519 kcal/mol
Surface area63670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.778, 133.225, 95.228
Angle α, β, γ (deg.)90.00, 93.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NEUTROPHIL-ACTIVATING PROTEIN A / NAP A / BACTERIOFERRITIN


Mass: 16960.396 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: NAPA / Production host: Bacillus subtilis (bacteria) / References: UniProt: P43313
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 12 / Source method: obtained synthetically
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 646 / 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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: ammonium acetate, citrate buffer, MPD, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.2 Mammonium acetate1reservoir
20.1 Mcitrate1reservoirpH5.6
330 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.3 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 12, 2000
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 71729 / Num. obs: 71729 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 39.2 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 11.3
Reflection shellResolution: 2.5→2.66 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.087 / Mean I/σ(I) obs: 5.9 / Num. unique all: 9698 / % possible all: 90.9
Reflection
*PLUS
Lowest resolution: 50 Å / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
Highest resolution: 2.52 Å / % possible obs: 90.9 % / Num. unique obs: 9698 / Rmerge(I) obs: 0.087

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QGH

1qgh


Resolution: 2.52→20.81 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1727967.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
Details: Only one monomer was treated independently and all the others were generated from the transformation matrices according to the Strict-ncs of CNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 7263 10.1 %RANDOM
Rwork0.215 ---
all-71706 --
obs-71706 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.12 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso mean: 29.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.77 Å20 Å24.86 Å2
2---5.07 Å20 Å2
3---7.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.52→20.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14352 0 24 742 15118
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d19.9
X-RAY DIFFRACTIONc_improper_angle_d1.41
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.286 997 10.3 %
Rwork0.278 8692 -
obs-9698 76.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4MPD.PARAM
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.224 / Rfactor Rwork: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.41
LS refinement shell
*PLUS
Rfactor Rfree: 0.286 / Rfactor Rwork: 0.278

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