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- PDB-3dtz: Crystal structure of Putative Chlorite dismutase TA0507 -

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Basic information

Entry
Database: PDB / ID: 3dtz
TitleCrystal structure of Putative Chlorite dismutase TA0507
ComponentsPutative Chlorite dismutase TA0507
Keywordsstructural genomics / unknown function / Putatvie Chlorite dismutase TA0507 Thermoplasma acidophilum / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyHeme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel / oxidoreductase activity / heme binding / metal ion binding / FORMIC ACID / Chlorite dismutase
Function and homology information
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.81 Å
AuthorsChang, C. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of Putative Chlorite dismutase TA0507
Authors: Chang, C. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionJul 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 30, 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_site
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_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: Putative Chlorite dismutase TA0507
B: Putative Chlorite dismutase TA0507
C: Putative Chlorite dismutase TA0507
D: Putative Chlorite dismutase TA0507
E: Putative Chlorite dismutase TA0507
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,3098
Polymers144,1715
Non-polymers1383
Water18,5911032
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16010 Å2
ΔGint-59 kcal/mol
Surface area42280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.403, 135.728, 74.147
Angle α, β, γ (deg.)90.00, 110.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative Chlorite dismutase TA0507


Mass: 28834.248 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: Ta0507 / Plasmid: pET derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q9HKT8
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1032 / 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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 0.1M Tris pH 7.8, 0.2M Ammonium Formate, 18%PEG3350., pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97857 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 13, 2008
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. all: 111997 / Num. obs: 110752 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 4.52
Reflection shellResolution: 1.81→1.83 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 3.96 / Num. unique all: 2526 / % possible all: 91.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.81→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.602 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20591 5538 5 %RANDOM
Rwork0.16705 ---
all0.169 110556 --
obs0.169 110556 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.053 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å2-0.38 Å2
2---0.49 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.81→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8943 0 9 1032 9984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0229405
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.96312792
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.69351158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.40222.067445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39151612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7781595
X-RAY DIFFRACTIONr_chiral_restr0.1020.21383
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027223
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.24663
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.26665
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2915
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8671.55788
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36729130
X-RAY DIFFRACTIONr_scbond_it2.23334214
X-RAY DIFFRACTIONr_scangle_it3.2324.53634
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.809→1.855 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 375 -
Rwork0.224 7303 -
obs-7678 93.98 %
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)
10.5156-0.05710.18351.22050.48090.82620.02070.13740.1083-0.2190.0112-0.0478-0.20960.0435-0.03190.0035-0.00180.0045-0.05590.0354-0.041151.011644.280854.6039
20.9011-0.1339-0.02360.4325-0.18930.85540.0320.1514-0.0362-0.11440.00360.01660.0810.048-0.0356-0.02690.00450.0044-0.0293-0.0297-0.062953.095816.592452.5734
30.64490.09320.24320.48540.12011.16420.0592-0.0003-0.13050.0702-0.0165-0.01850.21910.1145-0.0427-0.01060.0235-0.007-0.05620.003-0.045657.52727.355978.1545
40.6869-0.14140.37331.2562-0.0240.84160.0271-0.07250.03840.1261-0.0322-0.074-0.02390.06810.005-0.0304-0.01150.0056-0.0154-0.0101-0.083459.126528.422295.2841
50.736-0.016-0.00350.9552-0.27771.0742-0.0135-0.08140.22340.0794-0.056-0.0972-0.24710.04020.0696-0.0102-0.0102-0.0245-0.1053-0.00950.017954.889751.477780.4391
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 224
2X-RAY DIFFRACTION2B1 - 224
3X-RAY DIFFRACTION3C1 - 224
4X-RAY DIFFRACTION4D1 - 224
5X-RAY DIFFRACTION5E1 - 224

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