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- PDB-4evd: Crystal Structure HP-NAP from strain YS29 cadmium loaded (Cocryst... -

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Basic information

Entry
Database: PDB / ID: 4evd
TitleCrystal Structure HP-NAP from strain YS29 cadmium loaded (Cocrystallization 50mM)
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
: / DNA polymerase III subunit beta
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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)20,90517
Polymers19,1071
Non-polymers1,79916
Water1,53185
1
A: Neutrophil-activating protein
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)250,864204
Polymers229,28112
Non-polymers21,583192
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 area34660 Å2
ΔGint-274 kcal/mol
Surface area61090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.412, 187.412, 187.412
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432

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Components

#1: Protein Neutrophil-activating protein


Mass: 19106.736 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: YS29 / Gene: napA / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G1UIZ2
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 3.59 Å3/Da / Density % sol: 65.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50mM cadmium sulfate, 1.0M sodium acetate, 0.1M HEPES-NaOH, 0.1M L-Arginine, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 8, 2007 / Details: mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 14790 / % possible obs: 99.4 % / Redundancy: 10.4 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 38.1
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 8.2 / % possible all: 99.6

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Processing

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

3ta8


Resolution: 2.2→19.65 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.914 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 4.168 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1486 10.1 %RANDOM
Rwork0.213 ---
obs0.2155 14722 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 52.5 Å2 / Biso mean: 24.2293 Å2 / Biso min: 11.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1186 0 16 85 1287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221212
X-RAY DIFFRACTIONr_angle_refined_deg0.9611.9371632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6845142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73225.4161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73815233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.22152
X-RAY DIFFRACTIONr_chiral_restr0.0710.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02894
X-RAY DIFFRACTIONr_mcbond_it0.3251.5713
X-RAY DIFFRACTIONr_mcangle_it0.68521153
X-RAY DIFFRACTIONr_scbond_it1.1113499
X-RAY DIFFRACTIONr_scangle_it1.9644.5479
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 103 -
Rwork0.262 948 -
all-1051 -
obs--99.43 %

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