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- PDB-2qqy: Crystal structure of ferritin like, diiron-carboxylate proteins f... -

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Basic information

Entry
Database: PDB / ID: 2qqy
TitleCrystal structure of ferritin like, diiron-carboxylate proteins from Bacillus anthracis str. Ames
ComponentsSigma B operon
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / dodecameric alpha-helical / ferritin fold / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


ferroxidase activity / ferric iron binding / intracellular iron ion homeostasis / heme binding / cytosol
Similarity search - Function
Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBacillus anthracis str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKim, Y. / Joachimiak, G. / Wu, R. / Patterson, S. / Gornicki, P. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Ferritin like, Diiron-carboxylate Proteins from Bacillus anthracis str. Ames.
Authors: Kim, Y. / Joachimiak, G. / Wu, R. / Patterson, S. / Gornicki, P. / Joachimiak, A.
History
DepositionJul 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sigma B operon


Theoretical massNumber of molelcules
Total (without water)17,4151
Polymers17,4151
Non-polymers00
Water2,306128
1
A: Sigma B operon
x 12


Theoretical massNumber of molelcules
Total (without water)208,97512
Polymers208,97512
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
Buried area28970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.225, 100.225, 100.225
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Sigma B operon / Putative bacterial ferritin


Mass: 17414.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. (bacteria) / Species: Bacillus anthracis / Strain: Ames / Gene: BAS0929, BA_0993, GBAA0993 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9K5J5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.45 Å3/Da / Density % sol: 49.74 %
Crystal growTemperature: 289 K
Details: 0.5 M Lithium sulfate, 2 % PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 3, 2007 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL, SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→31.69 Å / Num. obs: 11458 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 39.6 % / Rsym value: 0.086 / Net I/σ(I): 15.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 32.2 % / Mean I/σ(I) obs: 11.9 / Rsym value: 0.439 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXCDphasing
SHELXEmodel building
MLPHAREphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→31.69 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.911 / SU B: 4.169 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.183
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1125 9.8 %RANDOM
Rwork0.197 ---
obs0.202 10304 99.5 %-
all-10304 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.75 Å2
Refinement stepCycle: LAST / Resolution: 2→31.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1122 0 0 128 1250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221189
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.9751608
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1365148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.26325.46964
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.26215232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.794158
X-RAY DIFFRACTIONr_chiral_restr0.0960.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02910
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.2610
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2835
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2106
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2261.5760
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.64821168
X-RAY DIFFRACTIONr_scbond_it3.2013495
X-RAY DIFFRACTIONr_scangle_it4.9444.5440
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 81 -
Rwork0.198 740 -
obs--96.93 %
Refinement TLS params.Method: refined / Origin x: 0 Å / Origin y: 0 Å / Origin z: 0 Å
111213212223313233
T0 Å20 Å20 Å2-0 Å20 Å2--0 Å2
L0 °20 °20 °2-0 °20 °2--0 °2
S0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °

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