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- PDB-6vjr: Oxygen tolerant Archeal 4hydroxybutyrylCoA dehydratase (4HBD) fro... -

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Basic information

Entry
Database: PDB / ID: 6vjr
TitleOxygen tolerant Archeal 4hydroxybutyrylCoA dehydratase (4HBD) from N. maritimus
ComponentsVinylacetyl-CoA Delta-isomerase
KeywordsPROTEIN BINDING / oxygen tolerance / iron-sulfur cluster / ammonia-oxidizing archaea / bioenergy / C-cycling
Function / homology
Function and homology information


vinylacetyl-CoA Delta-isomerase / vinylacetyl-CoA delta-isomerase activity / oxidoreductase activity, acting on the CH-CH group of donors / 4 iron, 4 sulfur cluster binding / nucleotide binding / metal ion binding
Similarity search - Function
HpaB/PvcC/4-BUDH / HpaB/PvcC/4-BUDH N-terminal / HpaB/PvcC/4-BUDH C-terminal / 4-hydroxyphenylacetate 3-hydroxylase C terminal / 4-hydroxyphenylacetate 3-hydroxylase N terminal / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 ...HpaB/PvcC/4-BUDH / HpaB/PvcC/4-BUDH N-terminal / HpaB/PvcC/4-BUDH C-terminal / 4-hydroxyphenylacetate 3-hydroxylase C terminal / 4-hydroxyphenylacetate 3-hydroxylase N terminal / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / : / IRON/SULFUR CLUSTER / Unknown ligand / Vinylacetyl-CoA Delta-isomerase
Similarity search - Component
Biological speciesNitrosopumilus maritimus SCM1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsDeMirci, H. / Mathews, I.I. / Wakatsuki, S. / Kulakman, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306 United States
CitationJournal: To Be Published
Title: Structural adaptation of oxygen tolerance in a key archaeal carbon fixation enzyme
Authors: Demirci, H. / Wakatsuki, S.
History
DepositionJan 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Aug 13, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / atom_type / audit_author / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_src_gen / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_asym / struct_conf / struct_conn / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_contact_author.id / _pdbx_entry_details.has_protein_modification / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_R_Free_selection_details / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_residues_total / _software.classification / _software.name / _software.version / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Model completeness / Details: New refinement / Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vinylacetyl-CoA Delta-isomerase
B: Vinylacetyl-CoA Delta-isomerase
C: Vinylacetyl-CoA Delta-isomerase
D: Vinylacetyl-CoA Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,49934
Polymers224,7434
Non-polymers5,75630
Water28,2111566
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37820 Å2
ΔGint-474 kcal/mol
Surface area57520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.530, 72.954, 180.517
Angle α, β, γ (deg.)90.00, 98.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Vinylacetyl-CoA Delta-isomerase


Mass: 56185.863 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosopumilus maritimus SCM1 (archaea)
Strain: SCM1 / Gene: Nmar_0207 / Production host: Escherichia coli (E. coli)
References: UniProt: A9A1Y2, vinylacetyl-CoA Delta-isomerase

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Non-polymers , 7 types, 1596 molecules

#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#6: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1566 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 51.52 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 8
Details: 0.1 M Li2SO4, 0.1 M Tris, pH 8 25 % v/v Jeffamine ED-2003

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.55→40 Å / Num. obs: 319062 / % possible obs: 97.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.06 / Rrim(I) all: 0.159 / Χ2: 1.247 / Net I/σ(I): 7.4 / Num. measured all: 2104789
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.55-1.615.90.693316300.8940.2930.7540.60497.4
1.61-1.676.50.569315870.8790.2350.6170.68897.4
1.67-1.756.60.471317690.9460.1930.510.81897.8
1.75-1.846.40.345318870.9580.1440.3741.02598.1
1.84-1.956.40.254312550.970.1060.2751.38896.2
1.95-2.170.187321800.9850.0750.2011.35298.9
2.1-2.326.90.202322930.9870.0850.221.66699.1
2.32-2.656.40.143316020.9860.0590.1551.58196.7
2.65-3.3470.136323680.9770.0550.1461.72198.9
3.34-406.80.106324910.9920.0430.1151.46297.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U8V

1u8v


Resolution: 1.55→34.88 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.521 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15773 1998 6 %RANDOM
Rwork0.12642 ---
obs0.12662 316603 97.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.589 Å2
Baniso -1Baniso -2Baniso -3
1-2.79 Å20 Å20.14 Å2
2--0.13 Å20 Å2
3----2.83 Å2
Refinement stepCycle: 1 / Resolution: 1.55→34.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15706 0 298 1566 17570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01216788
X-RAY DIFFRACTIONr_bond_other_d0.0010.01615761
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.82722771
X-RAY DIFFRACTIONr_angle_other_deg0.6751.78136410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18152119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.9235116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.518103006
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1160.22501
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0219954
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023770
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_it4.5971.7528293
X-RAY DIFFRACTIONr_mcbond_other4.5861.7528293
X-RAY DIFFRACTIONr_mcangle_it6.1233.16210458
X-RAY DIFFRACTIONr_mcangle_other6.1233.16310459
X-RAY DIFFRACTIONr_scbond_it7.7122.1248495
X-RAY DIFFRACTIONr_scbond_other7.7112.1248496
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.4393.74712261
X-RAY DIFFRACTIONr_long_range_B_refined10.97119629
X-RAY DIFFRACTIONr_long_range_B_other10.97219537
X-RAY DIFFRACTIONr_rigid_bond_restr4.172332549
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 146 -
Rwork0.185 23111 -
obs--96.9 %

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