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- PDB-1t0t: Crystallographic structure of a putative chlorite dismutase -

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Basic information

Entry
Database: PDB / ID: 1t0t
TitleCrystallographic structure of a putative chlorite dismutase
ComponentsAPC35880
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / pentamer / icosahedral / PROTEIN STRUCTURE INITIATIVE / MCSG / PSI / Midwest Center for Structural Genomics
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-CH group of donors, oxygen as acceptor / hydrogen peroxide-dependent heme synthase / heme B biosynthetic process / peroxidase activity / heme binding / metal ion binding
Similarity search - Function
Apc35880; domain 1 / Coproheme decarboxylase / Heme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Coproheme decarboxylase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsGilski, M. / Borek, D. / Chen, Y. / Collart, F. / Joachimiak, A. / Otwinowski, Z. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of APC35880 protein from Bacillus Stearothermophilus
Authors: Gilski, M. / Borek, D. / Chen, Y. / Collart, F. / Joachimiak, A. / Otwinowski, Z.
History
DepositionApr 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 13, 2017Group: Refinement description / Category: refine / Item: _refine.pdbx_method_to_determine_struct
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THIS SEQUENCE HAS NOT YET BEEN DEPOSITED IN ANY SEQUENCE DATABASE

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
V: APC35880
W: APC35880
X: APC35880
Y: APC35880
Z: APC35880
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,84115
Polymers144,0885
Non-polymers1,75310
Water23,8701325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20570 Å2
ΔGint-86 kcal/mol
Surface area48210 Å2
MethodPISA
2
V: APC35880
W: APC35880
X: APC35880
Y: APC35880
Z: APC35880
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)1,750,098180
Polymers1,729,05760
Non-polymers21,041120
Water1,08160
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 area353990 Å2
ΔGint-1030 kcal/mol
Surface area471350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.839, 202.839, 202.839
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
APC35880


Mass: 28817.609 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
References: UniProt: Q5KUD5*PLUS
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1325 / 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: 2.7 Å3/Da / Density % sol: 53.7 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 273K / Temp details: 273

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979338
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Oct 15, 2003
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979338 Å / Relative weight: 1
ReflectionResolution: 1.75→25 Å / Num. obs: 136920 / Observed criterion σ(I): 1
Reflection shellResolution: 1.75→1.79 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0001refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→25 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.051 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.194 6934 5 %RANDOM
Rwork0.156 ---
obs0.158 131204 99.8 %-
all-138148 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.18 Å2
Refinement stepCycle: LAST / Resolution: 1.75→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9980 0 145 1295 11420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02210345
X-RAY DIFFRACTIONr_bond_other_d0.0010.029235
X-RAY DIFFRACTIONr_angle_refined_deg1.7161.94913970
X-RAY DIFFRACTIONr_angle_other_deg0.9553.00221230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55651210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67123.462520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39151745
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1541575
X-RAY DIFFRACTIONr_chiral_restr0.1170.21470
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.0211370
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022275
X-RAY DIFFRACTIONr_nbd_refined0.2420.22096
X-RAY DIFFRACTIONr_nbd_other0.2380.29355
X-RAY DIFFRACTIONr_nbtor_refined0.1970.25017
X-RAY DIFFRACTIONr_nbtor_other0.0870.26008
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.21092
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0690.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.279
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3470.2298
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2690.274
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.611.57702
X-RAY DIFFRACTIONr_mcbond_other0.5411.52465
X-RAY DIFFRACTIONr_mcangle_it2.92229765
X-RAY DIFFRACTIONr_scbond_it4.68535121
X-RAY DIFFRACTIONr_scangle_it6.2714.54205
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 491 -
Rwork0.175 9663 -
obs--100 %

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