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- PDB-1h98: New Insights into Thermostability of Bacterial Ferredoxins: High ... -

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Basic information

Entry
Database: PDB / ID: 1h98
TitleNew Insights into Thermostability of Bacterial Ferredoxins: High Resolution Crystal Structure of the Seven-Iron Ferredoxin from Thermus thermophilus
ComponentsFERREDOXIN
KeywordsELECTRON TRANSPORT / THERMOPHILIC / IRON-SULFUR / AZOTOBACTER / HYDROGEN BONDS / STABILITY / HIGH RESOLUTION
Function / homology
Function and homology information


3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
7Fe ferredoxin / : / 4Fe-4S binding domain / Alpha-Beta Plaits - #20 / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FE3-S4 CLUSTER / IRON/SULFUR CLUSTER / Ferredoxin
Similarity search - Component
Biological speciesTHERMUS AQUATICUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsMacedo-Ribeiro, S. / Martins, B.M. / Pereira, P.J.B. / Buse, G. / Huber, R. / Soulimane, T.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2001
Title: New Insights Into the Thermostability of Bacterial Ferredoxins: High-Resolution Crystal Structure of the Seven-Iron Ferredoxin from Thermus Thermophilus
Authors: Macedo-Ribeiro, S. / Martins, B.M. / Pereira, P.J.B. / Buse, G. / Huber, R. / Soulimane, T.
History
DepositionMar 5, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3413
Polymers8,6941
Non-polymers6472
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)29.700, 42.120, 62.990
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 / [3FE-4S][4FE-4S] FERREDOXIN / SEVEN-IRON FERREDOXIN


Mass: 8693.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS AQUATICUS (bacteria) / References: UniProt: P03942
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTRANSFER ELECTRONS IN A WIDE VARIETY OF METABOLIC REACTIONS
Sequence detailsLEU 69 A GLY 97 ARE COVALENTLY LINKED. THE RESIDUES 70 TO 96 FROM SWISSPROT ENTRY P03942 ARE NOT ...LEU 69 A GLY 97 ARE COVALENTLY LINKED. THE RESIDUES 70 TO 96 FROM SWISSPROT ENTRY P03942 ARE NOT PRESENT IN THE SEQUENCE THE PRESENT CRYSTAL STRUCTURE, TOGETHER WITH AMINOACID SEQUENCING (MACEDO-RIBEIRO ET AL, JBIC IN PRESS)AND GEL FILTRATION CLEARLY SHOW THAT FDTT HAS ONLY 78 AMINOACIDS AND THAT THE AMINOACID AT POSITION 6 IS A GLU INSTEAD OF GLN

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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: 2.27 Å3/Da / Density % sol: 46 %
Crystal growpH: 5.4
Details: 2.2 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE PH 5.0-5.4, 5-10% GLYCEROL
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
25 mMHEPES1droppH7.0
32.2 Mammonium sulfate1reservoir
40.1 Msodium acetate1reservoirpH5.2

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.64→13.4 Å / Num. obs: 9579 / % possible obs: 96.3 % / Redundancy: 19.2 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 5
Reflection shellResolution: 1.64→1.73 Å / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 2.4 / % possible all: 98.8
Reflection
*PLUS
Lowest resolution: 13.4 Å / Num. measured all: 183792
Reflection shell
*PLUS
% possible obs: 98.8 %

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Processing

Software
NameClassification
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FD1

6fd1


Resolution: 1.64→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.189 -5 %
Rwork0.159 --
obs0.159 183792 96.3 %
Displacement parametersBiso mean: 19.6 Å2
Refinement stepCycle: LAST / Resolution: 1.64→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms595 0 15 58 668
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.874
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.177
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.435
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Refinement
*PLUS
Lowest resolution: 8 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.177
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.435

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