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Yorodumi- PDB-1qlb: respiratory complex II-like fumarate reductase from Wolinella suc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qlb | |||||||||
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Title | respiratory complex II-like fumarate reductase from Wolinella succinogenes | |||||||||
Components | (FUMARATE REDUCTASE ...) x 3 | |||||||||
Keywords | OXIDOREDUCTASE / CITRIC ACID CYCLE / RESPIRATORY CHAIN IRON-SULPHUR PROTEIN | |||||||||
Function / homology | Function and homology information succinate dehydrogenase / succinate dehydrogenase (quinone) activity / oxidoreductase activity, acting on the CH-CH group of donors / anaerobic respiration / 3 iron, 4 sulfur cluster binding / : / tricarboxylic acid cycle / respiratory electron transport chain / electron transport chain / 2 iron, 2 sulfur cluster binding ...succinate dehydrogenase / succinate dehydrogenase (quinone) activity / oxidoreductase activity, acting on the CH-CH group of donors / anaerobic respiration / 3 iron, 4 sulfur cluster binding / : / tricarboxylic acid cycle / respiratory electron transport chain / electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | WOLINELLA SUCCINOGENES (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | |||||||||
Authors | Lancaster, C.R.D. / Kroeger, A. / Auer, M. / Michel, H. | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qlb.cif.gz | 484.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qlb.ent.gz | 385.3 KB | Display | PDB format |
PDBx/mmJSON format | 1qlb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qlb_validation.pdf.gz | 989.9 KB | Display | wwPDB validaton report |
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Full document | 1qlb_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1qlb_validation.xml.gz | 53.9 KB | Display | |
Data in CIF | 1qlb_validation.cif.gz | 80.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ql/1qlb ftp://data.pdbj.org/pub/pdb/validation_reports/ql/1qlb | HTTPS FTP |
-Related structure data
Related structure data | 1qla S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.97509, -0.00632, 0.22173), Vector: |
-Components
-FUMARATE REDUCTASE ... , 3 types, 6 molecules ADBECF
#1: Protein | 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 | 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 | 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 |
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-Non-polymers , 8 types, 520 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-HEM / #12: Water | ChemComp-HOH / | |
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-Details
Sequence details | FOR 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 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 65 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.00 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.4 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 275 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.996 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 26, 1999 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.996 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QLA 1qla 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
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Solvent computation | Bsol: 61.5 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.33→38.87 Å
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Refine LS restraints |
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Refine LS restraints NCS | Rms dev position: 0.009 Å / Weight position: 300 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.33→2.41 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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