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- PDB-6n56: Crystal structure of fumarate reductase, flavo protein subunit, f... -

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Basic information

Entry
Database: PDB / ID: 6n56
TitleCrystal structure of fumarate reductase, flavo protein subunit, from Helicobacter pylori G27
ComponentsFumarate reductase, flavo protein subunit
KeywordsOXIDOREDUCTASE / SSGCID / Structural Genomics / Helicobacter pylori / Fumarate reductase / flavo protein subunit / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Fumarate reductase/succinate dehydrogenase, FAD-binding site / Fumarate reductase / succinate dehydrogenase FAD-binding site. / 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 / FAD binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Fumarate reductase. flavo protein subunit
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of fumarate reductase, flavo protein subunit, from Helicobacter pylori G27
Authors: Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionNov 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fumarate reductase, flavo protein subunit


Theoretical massNumber of molelcules
Total (without water)81,3141
Polymers81,3141
Non-polymers00
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area24890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.890, 63.890, 354.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Fumarate reductase, flavo protein subunit


Mass: 81313.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain G27) (bacteria)
Strain: G27 / Gene: frdA, HPG27_176 / Plasmid: HepyC.18004.a.B1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B5Z9W3, Oxidoreductases; Acting on the CH-CH group of donors
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20.9 mg/mL HepyC.18004.a.B1.PS38425 against Molecular dimensions Morpheus screen, D9 (10% PEG20000, 20% PEG550 MME, 20 mM 1,6-hexanediol, 20 mM 1-butanol, 20 mM (RS)-1,2- propanediol 2- ...Details: 20.9 mg/mL HepyC.18004.a.B1.PS38425 against Molecular dimensions Morpheus screen, D9 (10% PEG20000, 20% PEG550 MME, 20 mM 1,6-hexanediol, 20 mM 1-butanol, 20 mM (RS)-1,2- propanediol 2-propanol, 20 nM 1,4-butanediol, 20 mM 1,3-propanediol, 100 mM Bicine/Trizma base, pH 8.5), direct cryoprotection, tray 300244d9, puck ipi5-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 28, 2018
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.35→47.464 Å / Num. obs: 31955 / % possible obs: 99.4 % / Redundancy: 12.087 % / Biso Wilson estimate: 51.147 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.073 / Χ2: 1.049 / Net I/σ(I): 23.75 / Num. measured all: 386236 / Scaling rejects: 193
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.35-2.4112.4750.5954.7722890.9490.619100
2.41-2.4812.4880.4845.7722560.9660.504100
2.48-2.5512.5090.4196.5822310.9710.437100
2.55-2.6312.4380.3398.0921020.980.353100
2.63-2.7112.3880.2859.5420710.9890.297100
2.71-2.8112.4480.22811.8420250.9910.237100
2.81-2.9112.4150.18514.0619630.9940.19399.7
2.91-3.0312.3080.13818.0518630.9960.14499.7
3.03-3.1712.2950.10922.5817770.9970.11499.7
3.17-3.3212.160.08527.7917450.9980.08999.7
3.32-3.512.0450.0732.8516500.9980.07399.6
3.5-3.7211.8630.06235.6715560.9990.06599.6
3.72-3.9711.810.05240.7514930.9990.05499.6
3.97-4.2911.6520.04347.0413900.9990.04599
4.29-4.711.540.04148.1412660.9990.04398.9
4.7-5.2511.680.03949.2511740.9990.04198.7
5.25-6.0711.590.0447.6110350.9990.04298.3
6.07-7.4311.3090.03949.849050.9990.04197.4
7.43-10.5110.5560.03653.747270.9990.03896.8
10.51-47.4648.7830.03749.664370.9980.0490.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
MoRDaphasing
ARP/wARPmodel building
BUCCANEERmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2BS2 as per MoRDa
Resolution: 2.35→47.464 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.74
RfactorNum. reflection% reflectionSelection details
Rfree0.2224 2028 6.35 %0
Rwork0.1711 ---
obs0.1744 31914 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 134.2 Å2 / Biso mean: 52.5503 Å2 / Biso min: 3.2 Å2
Refinement stepCycle: final / Resolution: 2.35→47.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4812 0 0 215 5027
Biso mean---44.76 -
Num. residues----632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074917
X-RAY DIFFRACTIONf_angle_d0.8146652
X-RAY DIFFRACTIONf_dihedral_angle_d14.582951
X-RAY DIFFRACTIONf_chiral_restr0.048732
X-RAY DIFFRACTIONf_plane_restr0.005874
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3501-2.40890.24751420.185320572199100
2.4089-2.4740.27611320.194521162248100
2.474-2.54680.26181660.197420692235100
2.5468-2.6290.23681180.192920932211100
2.629-2.7230.26951390.197720932232100
2.723-2.8320.28741540.205121092263100
2.832-2.96090.2941470.211421002247100
2.9609-3.11690.28051350.19721242259100
3.1169-3.31220.24291500.190521162266100
3.3122-3.56780.21381460.17921592305100
3.5678-3.92670.22591460.157821412287100
3.9267-4.49460.15381430.12972171231499
4.4946-5.66120.17151360.14932209234599
5.6612-47.47390.2261740.1742329250398
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.5315-0.2761.4714.2203-0.41745.38930.142-0.7383-0.58080.62840.2106-0.20770.8423-0.1514-0.32280.49810.0230.00260.48380.05640.41440.5540.0259136.821
22.73280.33680.91410.7619-0.09613.3332-0.06030.2342-0.0911-0.10120.08340.0570.0704-0.3946-0.02710.35640.00990.0050.2719-0.06210.289-3.2967.1527109.2631
33.4518-0.18370.27460.9439-0.32442.9569-0.03880.3614-0.1249-0.36760.115-0.02930.2770.16330.01830.3914-0.0378-0.00140.2718-0.03960.27610.09579.6341103.5786
42.5933-0.7061-0.05563.37940.72671.64510.0641-0.0028-1.0471-0.3559-0.0062-0.25430.37160.3676-0.03460.46110.03090.09650.36160.01440.699724.7451-10.2633111.5165
51.45220.1926-0.21130.88350.01822.1215-0.08640.01260.1308-0.12660.1049-0.108-0.1280.1116-0.01380.3752-0.0119-0.01330.2614-0.02840.352913.375616.3727111.1999
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 653 through 707 )A653 - 707
2X-RAY DIFFRACTION2chain 'A' and (resid 1 through 198 )A1 - 198
3X-RAY DIFFRACTION3chain 'A' and (resid 199 through 277 )A199 - 277
4X-RAY DIFFRACTION4chain 'A' and (resid 278 through 408 )A278 - 408
5X-RAY DIFFRACTION5chain 'A' and (resid 409 through 652 )A409 - 652

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