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- PDB-2vxh: The crystal structure of chlorite dismutase: a detox enzyme produ... -

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Basic information

Entry
Database: PDB / ID: 2vxh
TitleThe crystal structure of chlorite dismutase: a detox enzyme producing molecular oxygen
ComponentsCHLORITE DISMUTASE
KeywordsOXIDOREDUCTASE / HEME-BASED ENZYME / CHLORATE RESPIRATION / MOLECULAR OXYGEN PRODUCTION
Function / homology
Function and homology information


oxidoreductase activity / heme binding / metal ion binding
Similarity search - Function
Heme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
CARBONATE ION / PROTOPORPHYRIN IX CONTAINING FE / THIOCYANATE ION / Chlorite dismutase / Chlorite dismutase
Similarity search - Component
Biological speciesAZOSPIRA ORYZAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsDe Geus, D.C. / Thomassen, E.A.J. / Hagedoorn, P.L. / Pannu, N.S. / Abrahams, J.P.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal Structure of Chlorite Dismutase, a Detoxifying Enzyme Producing Molecular Oxygen
Authors: De Geus, D.C. / Thomassen, E.A.J. / Hagedoorn, P.L. / Pannu, N.S. / Van Duijn, E. / Abrahams, J.P.
History
DepositionJul 4, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHLORITE DISMUTASE
B: CHLORITE DISMUTASE
C: CHLORITE DISMUTASE
D: CHLORITE DISMUTASE
E: CHLORITE DISMUTASE
F: CHLORITE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,29823
Polymers170,9506
Non-polymers4,34717
Water9,998555
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25520 Å2
ΔGint-199.5 kcal/mol
Surface area55360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.458, 169.335, 60.792
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUGLNGLNAA10 - 21713 - 220
21GLUGLUGLNGLNBB10 - 21713 - 220
31GLUGLUGLNGLNCC10 - 21713 - 220
41GLUGLUGLNGLNDD10 - 21713 - 220
51GLUGLUGLNGLNEE10 - 21713 - 220
61GLUGLUGLNGLNFF10 - 21713 - 220
12THRTHRASPASPAA231 - 248234 - 251
22THRTHRASPASPBB231 - 248234 - 251
32THRTHRASPASPCC231 - 248234 - 251
42THRTHRASPASPDD231 - 248234 - 251
52THRTHRASPASPEE231 - 248234 - 251
62THRTHRASPASPFF231 - 248234 - 251

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Components

#1: Protein
CHLORITE DISMUTASE /


Mass: 28491.680 Da / Num. of mol.: 6 / Fragment: RESIDUES 35-282
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AZOSPIRA ORYZAE (bacteria) / Strain: GR-1 / Description: DSM 11199 / Plasmid: PET28A-CDBC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: Q673K5, UniProt: E2DI02*PLUS, chlorite O2-lyase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CNS
#4: Chemical
ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CO3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST 3 AMINO ACIDS GSH -2 TO 0 ARE A REMAINDER OF A LINKER AFTER THROMBIN CLEAVAGE. THE ...THE FIRST 3 AMINO ACIDS GSH -2 TO 0 ARE A REMAINDER OF A LINKER AFTER THROMBIN CLEAVAGE. THE UNIPROT ENTRY B2D1S8 INCLUDES A SIGNAL PEPTIDE IN ITS SEQUENCE. THIS PROTEIN HAS BEEN OVEREXPRESSED IN ITS ACTIVE FORM (D.C DE GEUS ET AL.(2008)ACTA CRYSTALLOGRAPHICA SECTION F, IN PRESS) AND DOES NOT INCLUDE THIS SIGNAL PEPTIDE.

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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: 2.54 Å3/Da / Density % sol: 51.6 % / Description: NONE
Crystal growpH: 5.5
Details: 100 MM MES PH 5.5, 25 %(W/V) PEG MME 2000, 0.3 M KSCN, 5 %(V/V) GLYCEROL, 180 MM AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98340, 1.73990, 1.73820
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98341
21.73991
31.73821
ReflectionResolution: 2.1→40.13 Å / Num. obs: 100003 / % possible obs: 100 % / Redundancy: 13.8 % / Biso Wilson estimate: 26.559 Å2 / Rmerge(I) obs: 0.11
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 14.09 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
CRANKphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.1→50.68 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.909 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FOLLOWING DISORDERED REGIONS WERE NOT MODELED. CHAIN A -2 TO 7 AND 230 TO 248 CHAIN B -2 TO 8 AND 227 TO 248 CHAIN C -2 TO 10 AND 228 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FOLLOWING DISORDERED REGIONS WERE NOT MODELED. CHAIN A -2 TO 7 AND 230 TO 248 CHAIN B -2 TO 8 AND 227 TO 248 CHAIN C -2 TO 10 AND 228 TO 248 CHAIN D -2 TO 7 AND 228 TO 248 CHAIN E -2 TO 7 AND 228 TO 251 CHAIN F -2 TO 8 AND 228 TO 251.
RfactorNum. reflection% reflectionSelection details
Rfree0.25486 4994 5 %RANDOM
Rwork0.2187 ---
obs0.2205 94936 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.167 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å20 Å20 Å2
2---0.88 Å20 Å2
3---1.8 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10939 0 296 555 11790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02211505
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2982.03815667
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.74451363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73624.198486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.265151971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0061560
X-RAY DIFFRACTIONr_chiral_restr0.0950.21733
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028588
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.25438
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.27759
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2712
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3050.280
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6071.56885
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.178211158
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.63134620
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7174.54509
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A903tight positional0.130.05
2B903tight positional0.060.05
3C903tight positional0.090.05
4D903tight positional0.050.05
5E903tight positional0.050.05
6F903tight positional0.070.05
1A897medium positional0.370.5
2B897medium positional0.310.5
3C897medium positional0.440.5
4D897medium positional0.350.5
5E897medium positional0.360.5
6F897medium positional0.370.5
1A903tight thermal0.110.5
2B903tight thermal0.10.5
3C903tight thermal0.140.5
4D903tight thermal0.150.5
5E903tight thermal0.160.5
6F903tight thermal0.120.5
1A897medium thermal0.712
2B897medium thermal0.662
3C897medium thermal0.792
4D897medium thermal0.742
5E897medium thermal0.912
6F897medium thermal0.692
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.296 381
Rwork0.25 6889

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