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- PDB-1qoa: FERREDOXIN MUTATION C49S -

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Basic information

Entry
Database: PDB / ID: 1qoa
TitleFERREDOXIN MUTATION C49S
ComponentsFERREDOXIN
KeywordsELECTRON TRANSPORT / IRON-SULFUR / FERREDOXIN
Function / homology
Function and homology information


electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
Ferredoxin [2Fe-2S], plant / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) ...Ferredoxin [2Fe-2S], plant / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 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 / Ferredoxin-1
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 1.7 Å
AuthorsHolden, H.M. / Benning, M.M.
CitationJournal: Biochemistry / Year: 1997
Title: Iron-sulfur cluster cysteine-to-serine mutants of Anabaena -2Fe-2S- ferredoxin exhibit unexpected redox properties and are competent in electron transfer to ferredoxin:NADP+ reductase.
Authors: Hurley, J.K. / Weber-Main, A.M. / Hodges, A.E. / Stankovich, M.T. / Benning, M.M. / Holden, H.M. / Cheng, H. / Xia, B. / Markley, J.L. / Genzor, C. / Gomez-Moreno, C. / Hafezi, R. / Tollin, G.
History
DepositionAug 14, 1997Processing site: BNL
Revision 1.0Jan 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FERREDOXIN
B: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7314
Polymers21,3792
Non-polymers3522
Water2,054114
1
A: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8652
Polymers10,6901
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8652
Polymers10,6901
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.730, 38.230, 148.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FERREDOXIN


Mass: 10689.559 Da / Num. of mol.: 2 / Mutation: C49S
Source method: isolated from a genetically manipulated source
Details: 2FE-2S FERREDOXIN / Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Plasmid: PAN662 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P0A3C7
#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.: 114 / 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: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growpH: 5.5 / Details: pH 5.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.6 Mammonium sulfate1reservoir
250 mMpotassium succinate1reservoir
31 %MPD1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→25 Å / Num. obs: 20715 / % possible obs: 84.7 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.029 / Net I/σ(I): 27.8
Reflection shellResolution: 1.7→1.78 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.105 / Mean I/σ(I) obs: 4.2 / % possible all: 66
Reflection
*PLUS
Num. obs: 21258 / % possible obs: 85 % / Num. measured all: 58282
Reflection shell
*PLUS
% possible obs: 66 % / Num. unique obs: 2175 / Num. measured obs: 3478

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Processing

Software
NameClassification
TNTrefinement
XDSdata reduction
XSCALIBREdata scaling
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: WILD TYPE

Resolution: 1.7→25 Å
RfactorNum. reflection% reflection
Rwork0.182 --
obs-20715 84 %
Refinement stepCycle: LAST / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1500 0 8 114 1622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg2.2
X-RAY DIFFRACTIONt_dihedral_angle_d17.6
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.005
X-RAY DIFFRACTIONt_gen_planes0.008
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.05712
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 20713 / Rfactor obs: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.25
X-RAY DIFFRACTIONt_plane_restr0.008

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