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- PDB-6tjr: Structure of HdrA-like subunit from Hyphomicrobium denitrificans -

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Basic information

Entry
Database: PDB / ID: 6tjr
TitleStructure of HdrA-like subunit from Hyphomicrobium denitrificans
ComponentsFumarate reductase/succinate dehydrogenase flavoprotein domain protein
KeywordsFLAVOPROTEIN / heterodisulfide reductase / electron bifurcation / dissimilatory sulfur oxidation / FAD
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / oxidoreductase activity / nucleotide binding / metal ion binding
Similarity search - Function
: / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / IRON/SULFUR CLUSTER / Fumarate reductase/succinate dehydrogenase flavoprotein domain protein
Similarity search - Component
Biological speciesHyphomicrobium denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.43 Å
AuthorsKayastha, K. / Ermler, U. / Dahl, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationDa 351/8-1 Germany
CitationJournal: Febs J. / Year: 2021
Title: Structural and spectroscopic characterization of a HdrA-like subunit from Hyphomicrobium denitrificans.
Authors: Ernst, C. / Kayastha, K. / Koch, T. / Venceslau, S.S. / Pereira, I.A.C. / Demmer, U. / Ermler, U. / Dahl, C.
History
DepositionNov 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fumarate reductase/succinate dehydrogenase flavoprotein domain protein
B: Fumarate reductase/succinate dehydrogenase flavoprotein domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,83511
Polymers75,5842
Non-polymers3,2519
Water10,773598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10010 Å2
ΔGint-60 kcal/mol
Surface area24600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.620, 145.620, 64.100
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Fumarate reductase/succinate dehydrogenase flavoprotein domain protein


Mass: 37792.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hyphomicrobium denitrificans (bacteria)
Gene: Hden_0691 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): delta iscR / References: UniProt: D8JT26
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 598 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.6 Å3/Da / Density % sol: 52.61 % / Description: Yellow-Brownish in color
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: MES 0.1M, PEP 629 25% (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.43→47.67 Å / Num. obs: 138112 / % possible obs: 96.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 17.39 Å2 / CC1/2: 1 / Rrim(I) all: 0.049 / Rsym value: 0.045 / Net I/σ(I): 20.1
Reflection shellResolution: 1.43→1.481 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1 / Num. unique obs: 10500 / CC1/2: 0.403 / Rrim(I) all: 0.1241 / Rsym value: 0.1005 / % possible all: 74.02

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
PDB_EXTRACT3.25data extraction
ARP/wARPmodel building
XSCALEdata scaling
SHARPphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.43→47.67 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.056 / SU Rfree Blow DPI: 0.055 / SU Rfree Cruickshank DPI: 0.054
RfactorNum. reflection% reflectionSelection details
Rfree0.179 6799 4.92 %RANDOM
Rwork0.163 ---
obs0.164 138112 96.7 %-
Displacement parametersBiso max: 191.34 Å2 / Biso mean: 27.35 Å2 / Biso min: 8.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.1246 Å20 Å20 Å2
2--0.1246 Å20 Å2
3----0.2493 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: final / Resolution: 1.43→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5156 0 182 603 5941
Biso mean--42.33 34.01 -
Num. residues----680
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1982SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes108HARMONIC2
X-RAY DIFFRACTIONt_gen_planes899HARMONIC5
X-RAY DIFFRACTIONt_it5663HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion742SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7335SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5663HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7753HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion4.14
X-RAY DIFFRACTIONt_other_torsion16.41
LS refinement shellResolution: 1.43→1.47 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 349 4.82 %
Rwork0.298 6892 -
all0.299 7241 -
obs--69.12 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.38230.0294-0.04250.8315-0.07150.3433-0.0171-0.05440.05450.10560.0222-0.01-0.0456-0.0115-0.0051-0.01330.01-0.0066-0.0333-0.007-0.051426.774943.376134.0042
20.5086-0.0031-0.07061.0805-0.04260.44260.03880.0448-0.0182-0.1569-0.0778-0.26410.0270.06760.039-0.0560.03340.0394-0.05880.0237-0.0443.071327.343120.5005
30.77080.21670.29771.1816-0.41660.14450.0784-0.01280.0704-0.0830.0043-0.1398-0.03530.0417-0.08260.00290.0076-0.0091-0.00780.0172-0.033531.437631.892727.2383
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 341
2X-RAY DIFFRACTION2{ B|* }B2 - 341

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