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- PDB-3t9j: Crystal structure HP-NAP from strain YS39 in apo form -

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Basic information

Entry
Database: PDB / ID: 3t9j
TitleCrystal structure HP-NAP from strain YS39 in apo form
ComponentsNeutrophil-activating protein
KeywordsMETAL TRANSPORT / DODECAMER / FOUR-HELIX BUNDLE
Function / homology
Function and homology information


oxidoreductase activity, acting on metal ions / ferric iron binding / 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
Neutrophil-activating protein
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTsuruta, O. / Yokoyama, H. / Fujii, S.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: A new crystal lattice structure of Helicobacter pylori neutrophil-activating protein (HP-NAP)
Authors: Tsuruta, O. / Yokoyama, H. / Fujii, S.
History
DepositionAug 3, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Nov 1, 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

Downloads & links

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Assembly

Deposited unit
A: Neutrophil-activating protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0692
Polymers19,0071
Non-polymers621
Water1,72996
1
A: Neutrophil-activating protein
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)228,82424
Polymers228,07912
Non-polymers74512
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation28_555x,-y+1/2,-z+1/21
crystal symmetry operation30_555z,-x+1/2,-y+1/21
crystal symmetry operation35_555y,-z+1/2,-x+1/21
crystal symmetry operation51_555-x+1/2,y,-z+1/21
crystal symmetry operation56_555-z+1/2,x,-y+1/21
crystal symmetry operation58_555-y+1/2,z,-x+1/21
crystal symmetry operation74_555-x+1/2,-y+1/2,z1
crystal symmetry operation79_555-z+1/2,-x+1/2,y1
crystal symmetry operation84_555-y+1/2,-z+1/2,x1
Buried area36280 Å2
ΔGint-191 kcal/mol
Surface area66560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.465, 189.465, 189.465
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-372-

HOH

21A-373-

HOH

31A-381-

HOH

41A-396-

HOH

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Components

#1: Protein Neutrophil-activating protein / Bacterioferritin / HP-NAP / Neutrophil-activating protein A / NAP A


Mass: 19006.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: YS39 / Gene: napA / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G1UIZ3
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 3.73 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 0.1M L-arginine, 20% ethylene glycol, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 1, 2010 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 15374 / % possible obs: 99.9 % / Redundancy: 13.5 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 66.4
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 11.2 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JI4

1ji4


Resolution: 2.2→19.34 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.358 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24812 765 5 %RANDOM
Rwork0.22333 ---
obs0.22465 14456 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.041 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1187 0 4 96 1287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221216
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8651.941634
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1985143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41525.33360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79815233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.76152
X-RAY DIFFRACTIONr_chiral_restr0.0650.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02894
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1710.2576
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2910.2833
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2101
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4771.5747
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.81821155
X-RAY DIFFRACTIONr_scbond_it1.0053534
X-RAY DIFFRACTIONr_scangle_it1.584.5479
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.203→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 58 -
Rwork0.25 1015 -
obs--100 %

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