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- PDB-2ji3: X-ray structure of the iron-peroxide intermediate of superoxide r... -

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Basic information

Entry
Database: PDB / ID: 2ji3
TitleX-ray structure of the iron-peroxide intermediate of superoxide reductase (E114A mutant) from Desulfoarculus baarsii
ComponentsDesulfoferrodoxin
KeywordsOXIDOREDUCTASE / RAMAN SPECTROSCOPY / SUPEROXIDE REDUCTASE / INTERMEDIATE TRAPPING / MICROSPECTROPHOTOMETRY / DETOXIFICATION / ELECTRON TRANSPORT / IRON / TRANSPORT / REDOX STATES / METAL-BINDING
Function / homology
Function and homology information


superoxide reductase / superoxide reductase activity / removal of superoxide radicals / iron ion binding
Similarity search - Function
Desulphoferrodoxin, N-terminal domain / Desulfoferrodoxin / Desulfoferrodoxin, N-terminal domain / Desulfoferrodoxin, N-terminal domain superfamily / Desulfoferrodoxin, N-terminal domain / SOR catalytic domain / Desulfoferrodoxin, ferrous iron-binding domain / Desulfoferrodoxin, ferrous iron-binding domain superfamily / Desulfoferrodoxin / Rubrerythrin, domain 2 ...Desulphoferrodoxin, N-terminal domain / Desulfoferrodoxin / Desulfoferrodoxin, N-terminal domain / Desulfoferrodoxin, N-terminal domain superfamily / Desulfoferrodoxin, N-terminal domain / SOR catalytic domain / Desulfoferrodoxin, ferrous iron-binding domain / Desulfoferrodoxin, ferrous iron-binding domain superfamily / Desulfoferrodoxin / Rubrerythrin, domain 2 / Single Sheet / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / NITRATE ION / PEROXIDE ION / Desulfoferrodoxin
Similarity search - Component
Biological speciesDesulfarculus baarsii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKatona, G. / Carpentier, P. / Niviere, V. / Amara, P. / Adam, V. / Ohana, J. / Tsanov, N. / Bourgeois, D.
CitationJournal: Science / Year: 2007
Title: Raman-assisted crystallography reveals end-on peroxide intermediates in a nonheme iron enzyme.
Authors: Katona, G. / Carpentier, P. / Niviere, V. / Amara, P. / Adam, V. / Ohana, J. / Tsanov, N. / Bourgeois, D.
History
DepositionFeb 24, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.pdbx_description / _entity.pdbx_mutation / _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_seq_type / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Revision 1.4Jun 27, 2018Group: Data collection / Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _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.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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.5May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.6May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.7Dec 13, 2023Group: 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_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_asym_id / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Desulfoferrodoxin
B: Desulfoferrodoxin
C: Desulfoferrodoxin
D: Desulfoferrodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,23920
Polymers56,4734
Non-polymers76516
Water5,567309
1
A: Desulfoferrodoxin
B: Desulfoferrodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,67411
Polymers28,2372
Non-polymers4389
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: Desulfoferrodoxin
D: Desulfoferrodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5649
Polymers28,2372
Non-polymers3277
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)69.450, 82.900, 202.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.229898, 0.079956, -0.969925), (0.08761, -0.990873, -0.102449), (-0.969263, -0.108528, 0.220795)50.928, 53.3133, 44.9648
2given(-0.967133, -0.236001, -0.094647), (0.240878, -0.969569, -0.043754), (-0.081441, -0.065115, 0.994549)42.1051, 44.6491, -43.914
3given(0.327951, 0.03336, -0.944105), (-0.320849, 0.943905, -0.078099), (0.88854, 0.328528, 0.320258)87.2087, 18.311, -10.7855

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Desulfoferrodoxin / Dfx / Superoxide reductase / SOR


Mass: 14118.362 Da / Num. of mol.: 4 / Mutation: E114A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfarculus baarsii (bacteria) / Gene: dfx, rbo, Deba_2050 / Plasmid: PMLE47A / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q46495, superoxide reductase

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Non-polymers , 5 types, 325 molecules

#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-PER / PEROXIDE ION / Peroxide


Mass: 31.999 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 114 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 114 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, GLU 114 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 114 TO ALA ENGINEERED RESIDUE IN CHAIN C, GLU 114 TO ALA ENGINEERED RESIDUE IN CHAIN D, GLU 114 TO ALA

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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: 2.6 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 16 % PEG 4000, 100 MM TRIS/HNO3 PH9.0, 0.2 M CA(NO3)2 AND 25 MG/ML PROTEIN MIXED 1:1, HANGING DROP VAPOUR DIFFUSION, 20C, pH 9.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 8, 2006 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) OR SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.95→47.1 Å / Num. obs: 42838 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.27
Reflection shellResolution: 1.94→2.06 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.09 / % possible all: 94.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VZI

1vzi


Resolution: 1.95→47.13 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 224508.68 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD AMPLITUDE
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2147 5.1 %RANDOM
Rwork0.217 ---
obs0.217 42472 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.2546 Å2 / ksol: 0.336778 e/Å3
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å20 Å2
2---6.35 Å20 Å2
3---5.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 1.95→47.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3899 0 22 309 4230
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.232
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it3.072.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.336 349 5 %
Rwork0.303 6667 -
obs--99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PER.PARION.TOP
X-RAY DIFFRACTION4ION.PARAMPER.TOP

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