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- PDB-3d89: Crystal Structure of a Soluble Rieske Ferredoxin from Mus musculus -

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Basic information

Entry
Database: PDB / ID: 3d89
TitleCrystal Structure of a Soluble Rieske Ferredoxin from Mus musculus
ComponentsRieske domain-containing protein
KeywordsELECTRON TRANSPORT / CASP Target / Rieske ferredoxin / [2Fe-2S] cluster / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG / Iron / Iron-sulfur / Metal-binding
Function / homology
Function and homology information


: / 2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
Rieske-like [2Fe-2S] domain / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Mainly Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Rieske domain-containing protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.071 Å
AuthorsLevin, E.J. / McCoy, J.G. / Elsen, N.L. / Seder, K.D. / Bingman, C.A. / Wesenberg, G.E. / Fox, B.G. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: X-ray structure of a soluble Rieske-type ferredoxin from Mus musculus.
Authors: Levin, E.J. / Elsen, N.L. / Seder, K.D. / McCoy, J.G. / Fox, B.G. / Phillips, G.N.
History
DepositionMay 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rieske domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1893
Polymers17,9511
Non-polymers2382
Water86548
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.413, 52.413, 108.808
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Detailsauthors state that Gel-filtration data has shown that in solution the protein is a monomer and the PISA calculated asymmetric dimer is elieved to be an artifact of the lattice packing.

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Components

#1: Protein Rieske domain-containing protein


Mass: 17951.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rfesd / Plasmid: PVP 16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8K2P6
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS STRUCTURE WAS SUBMITTED AS CASP8 ID T0391.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Protein Solution (~15 mg/ml native protein, 0.025 M NaCl, 0.005 M MOPS pH 7.0) mixed in a 1:1 ratio with Well Solution ( 25% MEPEG 5K, 0.12 M Trisodium citrate, 0.10 M MES ph 6.0) ...Details: Protein Solution (~15 mg/ml native protein, 0.025 M NaCl, 0.005 M MOPS pH 7.0) mixed in a 1:1 ratio with Well Solution ( 25% MEPEG 5K, 0.12 M Trisodium citrate, 0.10 M MES ph 6.0) Cryoprotected with 15% ethylene glycol; Mercury derivative crystal soaked overnight in in mother liquor containing 0.002 M thimersol, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-B10.96419
SYNCHROTRONAPS 22-BM21
Detector
TypeIDDetectorDateDetails
MARMOSAIC 300 mm CCD1CCDJul 6, 2007Adjustable focus K-B pair Si plus Pt, Rh coatings
MARMOSAIC 225 mm CCD2CCDJun 11, 2007Rosenbaum-Rock vertical focusing mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal cryo-cooled Si(111)SINGLE WAVELENGTHMx-ray1
2Rosenbaum-Rock monochromator high-resolution double-crystal Si (111) sagittal focusing, water cooledSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.964191
211
ReflectionResolution: 2.07→50 Å / Num. obs: 9806 / % possible obs: 99.4 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.057 / Χ2: 0.907 / Net I/σ(I): 18.354
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.07-2.147.10.6211.8459000.76695.5
2.14-2.2310.20.5289620.8799.9
2.23-2.3312.90.439590.694100
2.33-2.45140.2939600.96100
2.45-2.6114.20.2239690.944100
2.61-2.8114.20.1429780.873100
2.81-3.0914.10.0939840.974100
3.09-3.54140.0629881.018100
3.54-4.4613.60.05310070.99100
4.46-5012.30.03810990.86998.7

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Phasing

PhasingMethod: SAD
Phasing MAD set

R cullis centric: 0 / Highest resolution: 1.69 Å / Lowest resolution: 30.66 Å / Power centric: 0

IDR cullis acentricPower acentricReflection acentricReflection centric
ISO_100146062908
ANO_10.8331.077143060
Phasing MAD set shell

R cullis centric: 0 / Power centric: 0

IDResolution (Å)R cullis acentricPower acentricReflection acentricReflection centric
ISO_17.35-30.6600124139
ISO_15.27-7.3500265139
ISO_14.33-5.2700358153
ISO_13.76-4.3300436142
ISO_13.37-3.7600506151
ISO_13.08-3.3700560153
ISO_12.85-3.0800625149
ISO_12.67-2.8500673145
ISO_12.51-2.6700715147
ISO_12.39-2.5100768156
ISO_12.28-2.3900807152
ISO_12.18-2.2800837150
ISO_12.09-2.1800899149
ISO_12.02-2.0900915150
ISO_11.95-2.0200959149
ISO_11.89-1.95001001149
ISO_11.83-1.89001034154
ISO_11.78-1.83001045139
ISO_11.73-1.78001032128
ISO_11.69-1.73001047114
ANO_17.35-30.660.7990.7961240
ANO_15.27-7.350.6971.4142650
ANO_14.33-5.270.8471.2133580
ANO_13.76-4.330.8591.3954360
ANO_13.37-3.760.7871.4775060
ANO_13.08-3.370.811.4345600
ANO_12.85-3.080.7531.4556250
ANO_12.67-2.850.7451.4436730
ANO_12.51-2.670.7711.2537150
ANO_12.39-2.510.7821.2317680
ANO_12.28-2.390.8121.1338070
ANO_12.18-2.280.8261.028370
ANO_12.09-2.180.860.9288990
ANO_12.02-2.090.8670.8619150
ANO_11.95-2.020.8760.7529590
ANO_11.89-1.950.9080.67210010
ANO_11.83-1.890.9340.64710260
ANO_11.78-1.830.9420.58410100
ANO_11.73-1.780.9660.5689590
ANO_11.69-1.730.9810.5458630
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-0.1095.60970.253HG19.290.67
26.48439.077101.378HG36.570.49
33.12139.8940.465HG19.960.42
44.7432.39135.752HG23.650.22
58.2112.00149.89HG29.620.28
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 17514
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.83-10071.90.755504
4.58-5.8364.40.91501
3.97-4.5863.10.904502
3.59-3.9764.30.898512
3.31-3.5967.60.891510
3.1-3.3167.90.893506
2.94-3.165.70.868524
2.8-2.9461.40.864542
2.68-2.858.70.839563
2.57-2.6858.40.854584
2.47-2.5761.70.858610
2.39-2.4762.50.857628
2.31-2.3959.10.859642
2.24-2.3163.20.847683
2.18-2.2463.60.871678
2.12-2.1868.10.878699
2.06-2.1265.10.861728
2.01-2.0668.80.864734
1.97-2.0165.90.861752
1.92-1.9768.80.854786
1.88-1.9266.10.851767
1.84-1.8871.30.811822
1.81-1.8471.10.803795
1.77-1.8176.50.812804
1.74-1.7778.50.776807
1.69-1.7476.70.761331

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM5phasing
REFMAC5.2.0005refinement
PDB_EXTRACT3data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.071→37.75 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.245 / WRfactor Rwork: 0.218 / SU B: 7.655 / SU ML: 0.124 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.213 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 472 4.839 %RANDOM
Rwork0.199 ---
obs0.2 9754 99.399 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 46.027 Å2
Baniso -1Baniso -2Baniso -3
1-0.148 Å20 Å20 Å2
2--0.148 Å20 Å2
3----0.295 Å2
Refinement stepCycle: LAST / Resolution: 2.071→37.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1099 0 8 48 1155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221159
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.9441563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5285140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56623.57156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86315206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14157
X-RAY DIFFRACTIONr_chiral_restr0.1090.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02881
X-RAY DIFFRACTIONr_nbd_refined0.2150.2453
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2757
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.260
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.26
X-RAY DIFFRACTIONr_mcbond_it1.0181.5706
X-RAY DIFFRACTIONr_mcangle_it1.48621114
X-RAY DIFFRACTIONr_scbond_it2.1693523
X-RAY DIFFRACTIONr_scangle_it3.124.5445
LS refinement shellResolution: 2.071→2.125 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 24 -
Rwork0.295 643 -
all-707 -
obs--94.342 %
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)
180.9735-41.32612.421787.7722-26.13814.06270.62050.6405-4.5263-3.7394-0.4616-1.65323.04920.9092-0.15890.41110.09190.12340.6839-0.25830.393617.1736-23.3367-5.3402
27.2761.62860.96437.9249-1.568512.2897-0.12961.67020.9406-0.21230.23430.9811-0.9165-0.3876-0.1047-0.22980.0121-0.06420.53320.2340.01966.4897-8.43350.8772
35.70930.13270.43821.84660.64577.1449-0.0370.6010.2396-0.00560.07250.0034-0.24290.3816-0.0355-0.06840.0060.0370.20380.05610.089917.5359-11.366612.7765
49.34563.5648-4.23815.9282-2.847820.0657-0.20160.8653-1.2974-0.41750.0954-0.01592.34310.49180.10620.25650.1697-0.01180.0153-0.08010.21518.51-25.372413.4182
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA14 - 1814 - 18
2X-RAY DIFFRACTION2AA19 - 3519 - 35
3X-RAY DIFFRACTION3AA36 - 13336 - 133
4X-RAY DIFFRACTION4AA134 - 154134 - 154

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