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- PDB-4evb: Crystal Structure HP-NAP from strain YS39 zinc soaked (20mM) -

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Basic information

Entry
Database: PDB / ID: 4evb
TitleCrystal Structure HP-NAP from strain YS39 zinc soaked (20mM)
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 / molecular replacement / Resolution: 2.5 Å
AuthorsYokoyama, H. / Tsuruta, O. / Akao, N. / Fujii, S.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2012
Title: Crystal structure of Helicobacter pylori neutrophil-activating protein with a di-nuclear ferroxidase center in a zinc or cadmium-bound form
Authors: Yokoyama, H. / Tsuruta, O. / Akao, N. / Fujii, S.
#1: Journal: 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
DepositionApr 26, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_ref_seq_dif / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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: Neutrophil-activating protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,62310
Polymers19,0071
Non-polymers6169
Water1,36976
1
A: Neutrophil-activating protein
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)235,471120
Polymers228,07912
Non-polymers7,392108
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 area39720 Å2
ΔGint-366 kcal/mol
Surface area62990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.529, 185.529, 185.529
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-203-

ZN

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Components

#1: Protein Neutrophil-activating protein


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: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G1UIZ3
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 3.5 Å3/Da / Density % sol: 64.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 0.1M L-Arginine, 20% ethylene glycol, 20mM zinc sulfate, 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: AR-NW12A / Wavelength: 1.2892 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 20, 2009 / Details: mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2892 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 9990 / % possible obs: 99.2 % / Redundancy: 13.4 % / Biso Wilson estimate: 62.3 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 63.6
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 9.4 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0088refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TA8

3ta8


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.904 / Occupancy max: 1 / Occupancy min: 0.16 / SU B: 7.753 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.345 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2911 973 9.9 %RANDOM
Rwork0.2274 ---
obs0.2335 9792 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 87.37 Å2 / Biso mean: 50.3665 Å2 / Biso min: 27.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1179 0 16 76 1271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221212
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.9431630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.085142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45625.33360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.4315230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.771152
X-RAY DIFFRACTIONr_chiral_restr0.1030.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02890
X-RAY DIFFRACTIONr_mcbond_it0.6371.5712
X-RAY DIFFRACTIONr_mcangle_it1.34921147
X-RAY DIFFRACTIONr_scbond_it2.3343500
X-RAY DIFFRACTIONr_scangle_it4.0714.5483
LS refinement shellResolution: 2.501→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 64 -
Rwork0.312 635 -
all-699 -
obs--99.43 %

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