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- PDB-4tpu: CRYSTAL STRUCTURE OF FERREDOXIN-DEPENDENT DISULFIDE REDUCTASE FRO... -

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Basic information

Entry
Database: PDB / ID: 4tpu
TitleCRYSTAL STRUCTURE OF FERREDOXIN-DEPENDENT DISULFIDE REDUCTASE FROM METHANOSARCINA ACETIVORANS
ComponentsRubredoxin
KeywordsELECTRON TRANSPORT / FTR-LIKE PROTEIN / DISULFIDE REDUCTASE
Function / homology
Function and homology information


ferredoxin-thioredoxin reductase activity / ferredoxin:thioredoxin reductase / oxidoreductase activity, acting on iron-sulfur proteins as donors / 4 iron, 4 sulfur cluster binding / iron ion binding
Similarity search - Function
Ferredoxin thioredoxin reductase catalytic beta subunit / Ferredoxin thioredoxin reductase catalytic beta subunit superfamily / Ferredoxin thioredoxin reductase catalytic beta chain / Rubrerythrin, domain 2 - #10 / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rubrerythrin, domain 2 / Single Sheet / Mainly Beta
Similarity search - Domain/homology
BROMIDE ION / : / IRON/SULFUR CLUSTER / UREA / Ferredoxin-thioredoxin reductase subunit B
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.355 Å
AuthorsKumar, A.K. / Yennawar, H.P. / Yennawar, N.H. / Ferry, J.G.
CitationJournal: Biochemistry / Year: 2015
Title: Structural and Biochemical Characterization of a Ferredoxin:Thioredoxin Reductase-like Enzyme from Methanosarcina acetivorans.
Authors: Kumar, A.K. / Kumar, R.S. / Yennawar, N.H. / Yennawar, H.P. / Ferry, J.G.
History
DepositionJun 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / entity_src_gen / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,63517
Polymers20,3601
Non-polymers1,27516
Water84747
1
A: Rubredoxin
hetero molecules

A: Rubredoxin
hetero molecules

A: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,90651
Polymers61,0813
Non-polymers3,82548
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation11_555y,-z,-x1
Buried area9430 Å2
ΔGint-197 kcal/mol
Surface area31210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.181, 93.181, 93.181
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23
Components on special symmetry positions
IDModelComponents
11A-412-

HOH

21A-426-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Rubredoxin /


Mass: 20360.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans (archaea) / Strain: ATCC 35395 / DSM 2834 / JCM 12185 / C2A / Gene: MA_1659 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TQ92

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Non-polymers , 7 types, 63 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-URE / UREA / Urea


Mass: 60.055 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH4N2O
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Br
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.31 Å3/Da / Density % sol: 62.86 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2M AMMONIUM SULFATE, 0.1M HEPES BUFFER, 0.1M UREA, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 3, 2011
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.355→50 Å / Num. all: 11465 / Num. obs: 11465 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 18.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 23.9
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 18.6 % / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(PHENIX.REFINE: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.355→29.47 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1086 9.89 %Random selection
Rwork0.202 ---
obs0.208 10978 95.8 %-
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.69 Å2 / ksol: 0.41 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.355→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1358 0 33 47 1438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121418
X-RAY DIFFRACTIONf_angle_d1.4551914
X-RAY DIFFRACTIONf_dihedral_angle_d16.458542
X-RAY DIFFRACTIONf_chiral_restr0.084189
X-RAY DIFFRACTIONf_plane_restr0.007251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3547-2.46180.31471280.23321168X-RAY DIFFRACTION91
2.4618-2.59150.33121330.2461164X-RAY DIFFRACTION93
2.5915-2.75380.28471320.24161200X-RAY DIFFRACTION94
2.7538-2.96620.30461270.22441202X-RAY DIFFRACTION95
2.9662-3.26440.27371360.21341270X-RAY DIFFRACTION99
3.2644-3.73590.28581410.21541245X-RAY DIFFRACTION97
3.7359-4.70380.24621440.161284X-RAY DIFFRACTION98
4.7038-29.46870.24171450.19711359X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 22.2073 Å / Origin y: 18.3517 Å / Origin z: 4.8343 Å
111213212223313233
T0.2808 Å20.0188 Å20.1075 Å2-0.3371 Å2-0.0132 Å2--0.3245 Å2
L5.124 °2-0.5028 °21.2345 °2-0.1196 °2-0.0119 °2--0.6385 °2
S-0.0164 Å °-0.137 Å °0.1801 Å °-0.0166 Å °-0.0035 Å °-0.0803 Å °0.1037 Å °0.1648 Å °0.0157 Å °
Refinement TLS groupSelection details: all

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