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- PDB-1qlb: respiratory complex II-like fumarate reductase from Wolinella suc... -

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Basic information

Entry
Database: PDB / ID: 1qlb
Titlerespiratory complex II-like fumarate reductase from Wolinella succinogenes
Components(FUMARATE REDUCTASE ...) x 3
KeywordsOXIDOREDUCTASE / CITRIC ACID CYCLE / RESPIRATORY CHAIN IRON-SULPHUR PROTEIN
Function / homology
Function and homology information


: / succinate dehydrogenase / oxidoreductase activity, acting on the CH-CH group of donors / 3 iron, 4 sulfur cluster binding / electron transport chain / respirasome / tricarboxylic acid cycle / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding ...: / succinate dehydrogenase / oxidoreductase activity, acting on the CH-CH group of donors / 3 iron, 4 sulfur cluster binding / electron transport chain / respirasome / tricarboxylic acid cycle / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding / plasma membrane
Similarity search - Function
Ubiquitin-like (UB roll) - #820 / Fumarate reductase type B, transmembrane subunit / 4Fe-4S dicluster domain / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain / Alpha-helical ferredoxin / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / Fumarate reductase/succinate dehydrogenase, transmembrane subunit ...Ubiquitin-like (UB roll) - #820 / Fumarate reductase type B, transmembrane subunit / 4Fe-4S dicluster domain / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain / Alpha-helical ferredoxin / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / FAD-dependent oxidoreductase SdhA/FrdA/AprA / Fumarate reductase / succinate dehydrogenase FAD-binding site. / 3 helical TM bundles of succinate and fumarate reductases / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / Succinate dehydogenase/fumarate reductase N-terminal / 2Fe-2S iron-sulfur cluster binding domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Fumarate reductase flavoprotein C-term / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / Alpha-helical ferredoxin / FAD binding domain / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / FAD/NAD(P)-binding domain / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / FAD/NAD(P)-binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Ubiquitin-like (UB roll) / Roll / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / FUMARIC ACID / PROTOPORPHYRIN IX CONTAINING FE / IRON/SULFUR CLUSTER / Fumarate reductase flavoprotein subunit / Fumarate reductase cytochrome b subunit / Fumarate reductase iron-sulfur subunit
Similarity search - Component
Biological speciesWOLINELLA SUCCINOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsLancaster, C.R.D. / Kroeger, A. / Auer, M. / Michel, H.
CitationJournal: Nature / Year: 1999
Title: Structure of Fumarate Reductase from Wolinella Succinogenes at 2.2 Angstroms Resolution
Authors: Lancaster, C.R.D. / Kroeger, A. / Auer, M. / Michel, H.
History
DepositionAug 25, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 1999Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2012Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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.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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FUMARATE REDUCTASE FLAVOPROTEIN SUBUNIT
B: FUMARATE REDUCTASE IRON-SULFUR PROTEIN
C: FUMARATE REDUCTASE CYTOCHROME B SUBUNIT
D: FUMARATE REDUCTASE FLAVOPROTEIN SUBUNIT
E: FUMARATE REDUCTASE IRON-SULFUR PROTEIN
F: FUMARATE REDUCTASE CYTOCHROME B SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,81324
Polymers259,7956
Non-polymers7,01718
Water9,080504
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33070 Å2
ΔGint-196.1 kcal/mol
Surface area100860 Å2
MethodPQS
Unit cell
Length a, b, c (Å)118.400, 85.050, 188.850
Angle α, β, γ (deg.)90.00, 96.46, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.97509, -0.00632, 0.22173), (-0.00665, -0.99998, 0.00072), (0.22172, -0.00217, -0.97511)
Vector: -10.38753, 42.64769, 93.91269)

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Components

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FUMARATE REDUCTASE ... , 3 types, 6 molecules ADBECF

#1: Protein FUMARATE REDUCTASE FLAVOPROTEIN SUBUNIT


Mass: 72941.195 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: 8-ALPHA-[-N-EPSILON-HISTIDYL] COVALENT BOND BETWEEN FLAVIN ADENINE DINUCLEOTIDE (FAD) AND HIS 43
Source: (natural) WOLINELLA SUCCINOGENES (bacteria) / References: UniProt: P17412, succinate dehydrogenase
#2: Protein FUMARATE REDUCTASE IRON-SULFUR PROTEIN


Mass: 27197.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) WOLINELLA SUCCINOGENES (bacteria) / References: UniProt: P17596, succinate dehydrogenase
#3: Protein FUMARATE REDUCTASE CYTOCHROME B SUBUNIT


Mass: 29759.059 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: HAEM AXIAL LIGANDS - HIS 44, HIS 93, HIS 143, HIS 182
Source: (natural) WOLINELLA SUCCINOGENES (bacteria) / References: UniProt: P17413

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Sugars , 1 types, 2 molecules

#11: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 8 types, 520 molecules

#4: 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
#5: Chemical ChemComp-FUM / FUMARIC ACID / Fumaric acid


Mass: 116.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4O4
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#8: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#9: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#10: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 504 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsFOR RESIDUES 281- 289 (CHAINS A AND D) THERE IS AN ERROR IN THE SEQUENCE REPORTED IN THE SWS ...FOR RESIDUES 281- 289 (CHAINS A AND D) THERE IS AN ERROR IN THE SEQUENCE REPORTED IN THE SWS DATABASE ENTRY P17412, REFERENCE, LAUTERBACH F., KOERTNER C., ALBRACHT S.P., UNDEN G., KROEGER A., ARCH. MICROBIOL. 154:386-393(1990). THE CORRECT SEQUENCE HAS JUST BEEN CONFIRMED TO BE: DVDGHRFMP (J. SIMON & A. KROEGER, UNPUBLISHED)

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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: 3.64 Å3/Da / Density % sol: 65 %
Crystal growpH: 6 / Details: pH 6.00
Crystal grow
*PLUS
pH: 6.4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
19.5 mg/mlprotein1drop
20.05 %dodecyl-beta-maltoside1drop
31 mM1dropK3FeCN6
40.20 %decylmaltoside1drop
52.4 %benzamidine1drop
610 %PEG33501drop
775 mM1dropNaCl
85 %DMF1drop
91 mMDMN1drop
101 mMmalonate1drop
1110 mMHEPES1drop
1210 mMcitrate1drop
13150 mM1reservoirNaCl
1410 %PEG33501reservoir
1520 mMcitrate1reservoir

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Data collection

DiffractionMean temperature: 275 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.996
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 26, 1999 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.996 Å / Relative weight: 1
ReflectionResolution: 2.33→38.87 Å / Num. obs: 152939 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 38 Å2 / Rsym value: 0.075 / Net I/σ(I): 9.5
Reflection shellResolution: 2.33→2.39 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.388 / % possible all: 99.7
Reflection
*PLUS
Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.388

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QLA

1qla
PDB Unreleased entry


Resolution: 2.33→38.87 Å / Rfactor Rfree error: 0.0045 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES (MLF)
Details: N(OBS)/N(PAR) = 2.01
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2499 1.6 %2499 THIN SHELLS
Rwork0.213 ---
obs0.213 152939 95.8 %-
Solvent computationBsol: 61.5 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 39 Å2
Baniso -1Baniso -2Baniso -3
1--3.593 Å20 Å2-3.353 Å2
2---0.903 Å20 Å2
3---4.496 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.33→38.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18148 0 404 504 19056
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_deg1.298
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.64
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.6551.5
X-RAY DIFFRACTIONc_mcangle_it1.1772
X-RAY DIFFRACTIONc_scbond_it0.772
X-RAY DIFFRACTIONc_scangle_it1.2212.5
Refine LS restraints NCSRms dev position: 0.009 Å / Weight position: 300
LS refinement shellResolution: 2.33→2.41 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.251 257 1.6 %
Rwork0.256 15460 -
obs--99.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4PARHEM.ROYTOPHEM.ROY
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.64

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