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- PDB-2wlb: Adrenodoxin-like ferredoxin Etp1fd(516-618) of Schizosaccharomyce... -

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Basic information

Entry
Database: PDB / ID: 2wlb
TitleAdrenodoxin-like ferredoxin Etp1fd(516-618) of Schizosaccharomyces pombe mitochondria
ComponentsELECTRON TRANSFER PROTEIN 1, MITOCHONDRIAL
KeywordsELECTRON TRANSPORT / IRON-SULFUR / MITOCHONDRIA / IRON / TRANSPORT / FERREDOXIN / ADRENODOXIN-LIKE / METAL-BINDING
Function / homology
Function and homology information


Heme biosynthesis / heme a synthase / oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / heme A biosynthetic process / P450-containing electron transport chain / NADPH-hemoprotein reductase activity / mitochondrial [2Fe-2S] assembly complex / [2Fe-2S] cluster assembly / oxidoreductase activity, acting on NAD(P)H / iron-sulfur cluster binding ...Heme biosynthesis / heme a synthase / oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / heme A biosynthetic process / P450-containing electron transport chain / NADPH-hemoprotein reductase activity / mitochondrial [2Fe-2S] assembly complex / [2Fe-2S] cluster assembly / oxidoreductase activity, acting on NAD(P)H / iron-sulfur cluster binding / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / mitochondrial matrix / mitochondrion / metal ion binding
Similarity search - Function
Heme A synthase, type 2 / COX15/CtaA family / Cytochrome oxidase assembly protein / Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain ...Heme A synthase, type 2 / COX15/CtaA family / Cytochrome oxidase assembly protein / Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Heme A synthase-mitochondrial ferredoxin fusion protein
Similarity search - Component
Biological speciesSCHIZOSACCHAROMYCES POMBE (fission yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMueller, J.J. / Hannemann, F. / Schiffler, B. / Bernhardt, R. / Heinemann, U.
CitationJournal: J.Inorg.Biochem. / Year: 2011
Title: Structural and Thermodynamic Characterization of the Adrenodoxin-Like Domain of the Electron-Transfer Protein Etp1 from Schizosaccharomyces Pombe.
Authors: Mueller, J.J. / Hannemann, F. / Schiffler, B. / Ewen, K.M. / Kappl, R. / Heinemann, U. / Bernhardt, R.
History
DepositionJun 23, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1May 19, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Apr 3, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Oct 9, 2019Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_database_status.status_code_sf
Revision 1.6Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: ELECTRON TRANSFER PROTEIN 1, MITOCHONDRIAL
B: ELECTRON TRANSFER PROTEIN 1, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9654
Polymers22,6132
Non-polymers3522
Water362
1
A: ELECTRON TRANSFER PROTEIN 1, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4822
Polymers11,3071
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ELECTRON TRANSFER PROTEIN 1, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4822
Polymers11,3071
Non-polymers1761
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.965, 81.965, 68.289
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A29 - 45
2111B29 - 45
1211A56 - 81
2211B56 - 81
1311A89 - 104
2311B89 - 104
1411A111 - 114
2411B111 - 114

NCS oper:
IDCodeMatrixVector
1given(-0.6512, 0.2999, 0.6972), (-0.3867, 0.6593, -0.6448), (-0.653, -0.6895, -0.3133)-41.78, 12.68, -11.17
2given(-0.6512, 0.2999, 0.6972), (-0.3867, 0.6593, -0.6448), (-0.653, -0.6895, -0.3133)-41.78, 12.68, -11.17
3given(-0.6512, 0.2999, 0.6972), (-0.3867, 0.6593, -0.6448), (-0.653, -0.6895, -0.3133)-41.78, 12.68, -11.17
4given(-0.6512, 0.2999, 0.6972), (-0.3867, 0.6593, -0.6448), (-0.653, -0.6895, -0.3133)-41.78, 12.68, -11.17

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Components

#1: Protein ELECTRON TRANSFER PROTEIN 1, MITOCHONDRIAL / ETP1-FD


Mass: 11306.626 Da / Num. of mol.: 2 / Fragment: ADRENODOXIN-LIKE DOMAIN, RESIDUES 516-618
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHIZOSACCHAROMYCES POMBE (fission yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q10361
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.6 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: VAPOUR DIFFUSION, SITTING DROP, 4 DEGR. CENTIGRADE. RESERVOIR: 0.04M HEPES,1.8M NA-CITRATE, 3% GLYCEROL,PH7.0. PROTEIN SOLUTION: 18.4MG/ML PROTEIN, 20MM POTASSIUMPHOSPHATE,PH7.4. 0.3 PLUS 0.3 MICROLITER DROPLET.

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU H2B / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 6, 2004
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 8006 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 56.1 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.5
Reflection shellResolution: 2.6→2.78 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.4 / % possible all: 92.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
SWISS-MODELLERphasing
PHASERphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1E6E,1AYF,1L6V,2BT6

1e6e

1ayf

1l6v

2bt6


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / SU B: 10.626 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.463 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 390 4.6 %RANDOM
Rwork0.182 ---
obs0.184 8006 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.16 Å20 Å2
2--0.31 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1567 0 8 2 1577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221597
X-RAY DIFFRACTIONr_bond_other_d0.0020.021056
X-RAY DIFFRACTIONr_angle_refined_deg1.4532.0022161
X-RAY DIFFRACTIONr_angle_other_deg0.91532597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5935202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.13225.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.90315275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7951510
X-RAY DIFFRACTIONr_chiral_restr0.0770.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021800
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02282
X-RAY DIFFRACTIONr_nbd_refined0.2150.2365
X-RAY DIFFRACTIONr_nbd_other0.2020.21138
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2823
X-RAY DIFFRACTIONr_nbtor_other0.090.2901
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.237
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.310.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2321300
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.9331630
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.764.5619
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.2926527
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 812 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.040.05
2Btight positional0.040.05
1Atight thermal0.10.5
2Btight thermal0.10.5
LS refinement shellResolution: 2.6→2.69 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.389 47
Rwork0.348 745

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