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- PDB-3tqj: Structure of the superoxide dismutase (Fe) (sodB) from Coxiella b... -

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Basic information

Entry
Database: PDB / ID: 3tqj
TitleStructure of the superoxide dismutase (Fe) (sodB) from Coxiella burnetii
ComponentsSuperoxide dismutase [Fe]
KeywordsOXIDOREDUCTASE / superoxide dismutase (Fe)
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding
Similarity search - Function
Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain
Similarity search - Domain/homology
: / Superoxide dismutase [Fe]
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.004 Å
AuthorsFranklin, M.C. / Cheung, J. / Cassidy, M. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jan 20, 2016Group: Database references
Revision 1.3Sep 13, 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_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 / _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_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: Superoxide dismutase [Fe]
B: Superoxide dismutase [Fe]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1884
Polymers49,0772
Non-polymers1122
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-9 kcal/mol
Surface area17220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.102, 65.285, 110.069
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Superoxide dismutase [Fe]


Mass: 24538.385 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA 493 Nine Mile Phase I / Gene: CBU_1708, sodB / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19685, superoxide dismutase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.2 Å3/Da / Density % sol: 44.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M imidazole, 10% PEG 8000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 28, 2011
RadiationMonochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. all: 29777 / Num. obs: 27752 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.5 % / Rsym value: 0.066 / Net I/σ(I): 34.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 1456 / Rsym value: 0.251 / % possible all: 71.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB CODE 1ISA

1isa


Resolution: 2.004→56.15 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.928 / SU B: 11.311 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.269 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27066 1388 5.1 %RANDOM
Rwork0.23301 ---
obs0.23494 27134 91.08 %-
all-29791 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.616 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å20 Å2
2---0.8 Å20 Å2
3---1.74 Å2
Refinement stepCycle: LAST / Resolution: 2.004→56.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3134 0 2 382 3518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0213244
X-RAY DIFFRACTIONr_bond_other_d0.0010.022190
X-RAY DIFFRACTIONr_angle_refined_deg0.8791.9144390
X-RAY DIFFRACTIONr_angle_other_deg0.78635320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.185382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.05724.706170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33815524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.0191510
X-RAY DIFFRACTIONr_chiral_restr0.0550.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213630
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02684
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1861.51912
X-RAY DIFFRACTIONr_mcbond_other0.0351.5772
X-RAY DIFFRACTIONr_mcangle_it0.35923074
X-RAY DIFFRACTIONr_scbond_it0.60231332
X-RAY DIFFRACTIONr_scangle_it0.9744.51316
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.004→2.056 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.524 70 -
Rwork0.373 1420 -
obs--69.21 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4325-0.02080.05892.5942-0.33091.31-0.01470.11030.1508-0.21250.018-0.2831-0.03270.0986-0.00340.0221-0.01450.02210.0886-0.00180.0581-9.79.529-10.6433
21.64410.1357-0.01452.85940.42011.3938-0.03530.1398-0.128-0.29630.0450.30310.0378-0.1123-0.00970.0414-0.0134-0.02420.08630.00740.0627-32.5535-9.6168-10.5027
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 193
2X-RAY DIFFRACTION1A1001
3X-RAY DIFFRACTION2B2 - 193
4X-RAY DIFFRACTION2B1001

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