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- PDB-2vkr: 3Fe-4S, 4Fe-4S plus Zn Acidianus ambivalens ferredoxin -

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Basic information

Entry
Database: PDB / ID: 2vkr
Title3Fe-4S, 4Fe-4S plus Zn Acidianus ambivalens ferredoxin
ComponentsZINC-CONTAINING FERREDOXIN
KeywordsELECTRON TRANSPORT / ZINC / IRON / 3FE-4S / 4FE-4S / TRANSPORT / ZN CENTER / HEMIHEDRIC TWINNIG / IRON-SULFUR PROTEIN / FERREDOXIN / METHYLATION / THERMOPHILE / IRON-SULFUR / THERMOSTABLE PROTEIN / METAL-BINDING / PROTEIN FOLDING
Function / homology
Function and homology information


3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / zinc ion binding
Similarity search - Function
Ferredoxin zinc-binding / 4Fe-4S dicluster 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 / Zinc-containing ferredoxin
Similarity search - Component
Biological speciesACIDIANUS AMBIVALENS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsFrazao, C. / Aragao, D. / Coelho, R. / Leal, S.S. / Gomes, C.M. / Teixeira, M. / Carrondo, M.A.
Citation
Journal: FEBS Lett. / Year: 2008
Title: Crystallographic analysis of the intact metal centres [3Fe-4S](1+/0) and [4Fe-4S](2+/1+) in a Zn(2+) -containing ferredoxin.
Authors: Frazao, C. / Aragao, D. / Coelho, R. / Leal, S.S. / Gomes, C.M. / Teixeira, M. / Carrondo, M.A.
#1: Journal: Biochemistry / Year: 2007
Title: A Spectroscopic Study of the Temperature Induced Modifications on Ferredoxin Folding and Iron-Sulfur Moieties
Authors: Todorovic, S. / Leal, S.S. / Salgueiro, C.A. / Zebger, I. / Hildebrandt, P. / Murgida, D.H. / Gomes, C.M.
#2: Journal: Proteins: Struct.,Funct., Genet. / Year: 2007
Title: Studies of the Molten Globule State of Ferredoxin: Structural Characterisation and Implications on Protein Folding and Iron-Sulfur Centre Assembly
Authors: Leal, S.S. / Gomes, C.M.
#3: Journal: Biochemistry / Year: 2006
Title: Natural Domain Design: Enhanced Thermal Stability of a Zinc Lacking Ferredoxin Isoform Shows that a Hydrophobic Core Efficiently Replaces the Structural Metal Site
Authors: Rocha, R. / Leal, S. / Teixeira, M. / Regalla, M. / Huber, H. / Baptista, A. / Soares, C.M. / Gomes, C.M.
#4: Journal: J.Biol.Inorg.Chem. / Year: 1998
Title: ,Di-Cluster, Seven-Iron Ferredoxins from Hyperthermophilic Sulfolobales
Authors: Gomes, C.M. / Faria, A. / Carita, J.C. / Mendes, J. / Regalla, M. / Chicau, P. / Huber, H. / Stetter, K.O. / Teixeira, M.
#5: Journal: Eur.J.Biochem. / Year: 1995
Title: A Seven Iron Ferredoxin from the Thermoacidophilic Archaeon Desulfurolobus Ambivalens
Authors: Teixeira, M. / Batista, R. / Campos, A. / Gomes, C. / Mendes, J. / Pacheco, I. / Anemuller, S. / Hagen, W.
History
DepositionDec 23, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Database references / Experimental preparation
Category: citation / exptl_crystal_grow
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5Mar 29, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: audit_author / database_2 ...audit_author / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _database_2.pdbx_DOI ..._audit_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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
Revision 1.6Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ZINC-CONTAINING FERREDOXIN
B: ZINC-CONTAINING FERREDOXIN
C: ZINC-CONTAINING FERREDOXIN
D: ZINC-CONTAINING FERREDOXIN
E: ZINC-CONTAINING FERREDOXIN
F: ZINC-CONTAINING FERREDOXIN
G: ZINC-CONTAINING FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,09228
Polymers77,1027
Non-polymers4,99021
Water1,964109
1
A: ZINC-CONTAINING FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7274
Polymers11,0151
Non-polymers7133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ZINC-CONTAINING FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7274
Polymers11,0151
Non-polymers7133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: ZINC-CONTAINING FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7274
Polymers11,0151
Non-polymers7133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: ZINC-CONTAINING FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7274
Polymers11,0151
Non-polymers7133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: ZINC-CONTAINING FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7274
Polymers11,0151
Non-polymers7133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: ZINC-CONTAINING FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7274
Polymers11,0151
Non-polymers7133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
7
G: ZINC-CONTAINING FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7274
Polymers11,0151
Non-polymers7133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)117.500, 117.500, 50.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.10909, -0.86413, 0.4913), (0.14898, 0.50288, 0.85142), (-0.98281, -0.01968, 0.18359)71.42393, 4.73281, 0.23226
2given(-0.46133, 0.88706, -0.01717), (0.88702, 0.4607, -0.03089), (-0.01949, -0.02948, -0.99938)-2.0864, 1.61628, 54.18728
3given(-0.81509, -0.32123, -0.48212), (0.36144, 0.36841, -0.85653), (0.45276, -0.8724, -0.18418)96.95162, 49.48711, 11.46147
4given(-0.40557, -0.91386, -0.01925), (0.91405, -0.40534, -0.01481), (0.00573, -0.02361, 0.9997)117.25011, 55.82421, -17.61574
5given(-0.83159, 0.24483, 0.49852), (0.41585, -0.32051, 0.85109), (0.36815, 0.91506, 0.16472)2.85829, 21.96861, -3.64962
6given(-0.52712, -0.64709, 0.55084), (-0.6344, -0.13164, -0.76171), (0.56541, -0.75097, -0.34112)61.41705, 145.93777, 64.36745

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Components

#1: Protein
ZINC-CONTAINING FERREDOXIN / SEVEN-IRON FERREDOXIN / FERREDOXIN


Mass: 11014.585 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) ACIDIANUS AMBIVALENS (archaea) / References: UniProt: P49949
#2: Chemical
ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Fe3S4
#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 1.85 Å3/Da / Density % sol: 33.6 % / Description: HEMIHEDRIC TWINNED CRYSTAL
Crystal growMethod: vapor diffusion
Details: VAPOR DIFFUSION METHOD USING 2 MICROL DROPS OF FRESHLY PURIFIED PROTEIN AT 4.7 MG/ML IN 40 MM POTASSIUM PHOSPHATE PH 6.5 AND 150 NACL, PLUS 2 MICROL OF WELL SOLUTION, 2.4-3.0 M AMMONIUM ...Details: VAPOR DIFFUSION METHOD USING 2 MICROL DROPS OF FRESHLY PURIFIED PROTEIN AT 4.7 MG/ML IN 40 MM POTASSIUM PHOSPHATE PH 6.5 AND 150 NACL, PLUS 2 MICROL OF WELL SOLUTION, 2.4-3.0 M AMMONIUM SULPHATE BUFFERED WITH TRIS-HCL 0.1 M PH 8 AND 0.5 MICROL LAURYLDIMETHYLAMINE-OXIDE (LDAO) 7% (W/V).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 23, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.01→19.48 Å / Num. obs: 52106 / % possible obs: 99.2 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.9
Reflection shellResolution: 2.01→2.07 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.5 / % possible all: 99.6

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XER

1xer


Resolution: 2.01→19.48 Å / Num. parameters: 22469 / Num. restraintsaints: 52080 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: HEMIHEDRIC TWIN LAW 1 0 0, -1 -1 0, 0 0 -1, TWIN RATIO 0.39/0.61. NO INTER-MOLECULES TRANSFORMATION MATRICES WERE EVER USED FOR NCS RESTRAINTS. INSTEAD, NCS SIMILARITIES RESTRAINTS WERE ...Details: HEMIHEDRIC TWIN LAW 1 0 0, -1 -1 0, 0 0 -1, TWIN RATIO 0.39/0.61. NO INTER-MOLECULES TRANSFORMATION MATRICES WERE EVER USED FOR NCS RESTRAINTS. INSTEAD, NCS SIMILARITIES RESTRAINTS WERE APPLIED: 1. ATOMIC 1 TO 4 DISTANCES (DIHEDRALS) AND 2. ATOMIC DISPLACEMENT DISPLACEMENT PARAMETERS BETWEEN HOMOLOGOUS ATOMS, AMONG THE SEVEN MOLECULES IN THE ASYMMETRIC UNIT, WERE RESTRAINED TO THEIR COMMON VALUES. 3. THE STEREOCHEMISTRY OF THE METAL CENTERS AND THEIR LIGANDS WERE RESTRAINED TO THEIR COMMON GEOMETRY WITHOUT TARGET VALUES.
RfactorNum. reflection% reflectionSelection details
Rfree0.2729 2491 4.8 %THIN SHELLS
all0.2148 52097 --
obs0.2196 -99.6 %-
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5395
Refinement stepCycle: LAST / Resolution: 2.01→19.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5390 0 112 109 5611
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.018
X-RAY DIFFRACTIONs_similar_dist0.004
X-RAY DIFFRACTIONs_from_restr_planes0.024
X-RAY DIFFRACTIONs_zero_chiral_vol0.036
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.032
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.007
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.05
X-RAY DIFFRACTIONs_approx_iso_adps0

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