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- PDB-1sb3: Structure of 4-hydroxybenzoyl-CoA reductase from Thauera aromatica -

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Basic information

Entry
Database: PDB / ID: 1sb3
TitleStructure of 4-hydroxybenzoyl-CoA reductase from Thauera aromatica
Components(4-hydroxybenzoyl-CoA reductase ...) x 3
KeywordsOXIDOREDUCTASE / XANTHINE OXIDASE FAMILY / dimer of heterotrimers / (A / B / C)2
Function / homology
Function and homology information


4-hydroxybenzoyl-CoA reductase / 4-hydroxybenzoyl-CoA reductase activity / FAD binding / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / iron ion binding / metal ion binding
Similarity search - Function
4-hydroxybenzoyl-CoA reductase, gamma subunit / 4-hydroxybenzoyl-CoA reductase, alpha subunit / 4-hydroxybenzoyl-CoA reductase, beta subunit / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / CO dehydrogenase flavoprotein, C-terminal domain / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / [2Fe-2S]-binding domain / Molybdopterin dehydrogenase, FAD-binding ...4-hydroxybenzoyl-CoA reductase, gamma subunit / 4-hydroxybenzoyl-CoA reductase, alpha subunit / 4-hydroxybenzoyl-CoA reductase, beta subunit / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / CO dehydrogenase flavoprotein, C-terminal domain / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / [2Fe-2S]-binding domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal / CO dehydrogenase flavoprotein, C-terminal domain superfamily / FAD binding domain in molybdopterin dehydrogenase / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde oxidase/xanthine dehydrogenase / Aldehyde oxidase/xanthine dehydrogenase, second molybdopterin binding domain / Molybdopterin cofactor-binding domain / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding / Aldehyde oxidase/xanthine dehydrogenase, first molybdopterin binding domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily / [2Fe-2S]-binding domain superfamily / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain superfamily / [2Fe-2S] binding domain / Molybdopterin cofactor-binding domain / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / FAD-binding, type PCMH, subdomain 1 / Aldehyde Oxidoreductase; domain 3 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / Beta-grasp domain / FAD-binding, type PCMH, subdomain 2 / 2Fe-2S iron-sulfur cluster binding domain / FAD-binding, type PCMH-like superfamily / Beta-grasp domain superfamily / Enolase-like; domain 1 / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) / DNA polymerase; domain 1 / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / Chem-PCD / IRON/SULFUR CLUSTER / 4-hydroxybenzoyl-CoA reductase subunit gamma / 4-hydroxybenzoyl-CoA reductase subunit alpha / 4-hydroxybenzoyl-CoA reductase subunit beta
Similarity search - Component
Biological speciesThauera aromatica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsUnciuleac, M. / Warkentin, E. / Page, C.C. / Boll, M. / Ermler, U.
Citation
Journal: Structure / Year: 2004
Title: Structure of a Xanthine Oxidase-Related 4-Hydroxybenzoyl-CoA Reductase with an Additional [4Fe-4S] Cluster and an Inverted Electron Flow.
Authors: Unciuleac, M. / Warkentin, E. / Page, C.C. / Boll, M. / Ermler, U.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization of 4-Hydroxybenzoyl-CoA Reductase and the structure of its Electron Donor Ferredoxin
Authors: Unciuleac, M. / Boll, M. / Warkentin, E. / Ermler, U.
History
DepositionFeb 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_asym_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_seq_id / _struct_conn.ptnr1_label_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The authors state that the observed electron density clearly identifies residue 251 ...SEQUENCE The authors state that the observed electron density clearly identifies residue 251 (chains A and D) as ALA and residues 142, 143, and 144 (chains C and F) as LYS, ILE and ILE respectively, in contrast to the reference sequence data.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxybenzoyl-CoA reductase alpha subunit
B: 4-hydroxybenzoyl-CoA reductase beta subunit
C: 4-hydroxybenzoyl-CoA reductase gamma subunit
D: 4-hydroxybenzoyl-CoA reductase alpha subunit
E: 4-hydroxybenzoyl-CoA reductase beta subunit
F: 4-hydroxybenzoyl-CoA reductase gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,09619
Polymers267,9996
Non-polymers5,09713
Water18,7721042
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32580 Å2
ΔGint-251 kcal/mol
Surface area75620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.620, 150.200, 175.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
/ NCS ensembles :
ID
1
2
3
4
5
6
DetailsThe biological assembly is the heterohexamer given by the asymmetric unit

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Components

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4-hydroxybenzoyl-CoA reductase ... , 3 types, 6 molecules ADBECF

#1: Protein 4-hydroxybenzoyl-CoA reductase alpha subunit


Mass: 82378.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thauera aromatica (bacteria) / Strain: strain K, DSMZ 6984 / References: UniProt: O33819, EC: 1.3.99.20
#2: Protein 4-hydroxybenzoyl-CoA reductase beta subunit


Mass: 34416.250 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thauera aromatica (bacteria) / Strain: strain K, DSMZ 6984 / References: UniProt: O33820, EC: 1.3.99.20
#3: Protein 4-hydroxybenzoyl-CoA reductase gamma subunit


Mass: 17204.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thauera aromatica (bacteria) / Strain: strain K, DSMZ 6984 / References: UniProt: O33818, EC: 1.3.99.20

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Non-polymers , 7 types, 1055 molecules

#4: Chemical ChemComp-PCD / (MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V) / MOLYBDENUM COFACTOR / MOCO / Molybdenum cofactor


Mass: 844.471 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H26MoN8O16P2S2
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#7: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#8: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#9: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1042 / 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: 2.91 Å3/Da / Density % sol: 57.37 %
Crystal growTemperature: 303 K / pH: 7.5
Details: TRIETHANOLAMINE, MGCL2, DITHIONITE, PEG 4000, HEPES, MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 8, 2002 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 149325 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 20.9 Å2 / Rsym value: 0.058 / Net I/σ(I): 15
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.22 / % possible all: 93.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QJ2

1qj2
PDB Unreleased entry


Resolution: 2.2→19.9 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3824133.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: IN THE NCS RESTRAINTS, GROUPS 1-3 ARE MAIN-CHAIN ATOMS PLUS CB OF THE THREE SUBUNITS, RESPECTIVELY, GROUPS 4-6 CORRESPONDINGLY THE REMAINING SIDE-CHAIN ATOMS
RfactorNum. reflection% reflectionSelection details
Rfree0.205 7543 5.1 %RANDOM
Rwork0.171 ---
obs0.171 149240 96.1 %-
all-149240 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.63 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 33.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.51 Å20 Å20 Å2
2---5.55 Å20 Å2
3---11.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18596 0 259 1042 19897
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCS
Ens-IDDom-IDRefine-IDRms dev position (Å)Weight Biso Weight position
11X-RAY DIFFRACTION0.0662100
22X-RAY DIFFRACTION0.0692100
33X-RAY DIFFRACTION0.0682100
44X-RAY DIFFRACTION0.21270
55X-RAY DIFFRACTION0.17270
66X-RAY DIFFRACTION0.18270
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.268 1153 5 %
Rwork0.222 22092 -
obs--90.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TO
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4ALL.PAR_MALL.TOP_M
X-RAY DIFFRACTION54OH_CIS.PAR

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