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- PDB-2v2k: THE CRYSTAL STRUCTURE OF FDXA, A 7FE FERREDOXIN FROM MYCOBACTERIU... -

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Basic information

Entry
Database: PDB / ID: 2v2k
TitleTHE CRYSTAL STRUCTURE OF FDXA, A 7FE FERREDOXIN FROM MYCOBACTERIUM SMEGMATIS
ComponentsFERREDOXIN
KeywordsELECTRON TRANSPORT / IRON / TRANSPORT / IRON-SULFUR / MYCOBACTERIUM TUBERCULOSIS / FE-S CLUSTER / METAL-BINDING / 7FE FERREDOXIN / ELECTRON TRANSFER / MYCOBACTERIUM SMEGMATIS / 4FE-4S CLUSTER INSTABILITY
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
ACETATE ION / FE3-S4 CLUSTER / Ferredoxin
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRicagno, S. / de Rosa, M. / Aliverti, A. / Zanetti, G. / Bolognesi, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: The Crystal Structure of Fdxa, a 7Fe Ferredoxin from Mycobacterium Smegmatis.
Authors: Ricagno, S. / De Rosa, M. / Aliverti, A. / Zanetti, G. / Bolognesi, M.
History
DepositionJun 6, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_seq_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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
B: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1077
Polymers22,8652
Non-polymers1,2425
Water2,126118
1
A: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0243
Polymers11,4331
Non-polymers5922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0834
Polymers11,4331
Non-polymers6513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)54.581, 54.526, 135.382
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2005-

HOH

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Components

#1: Protein FERREDOXIN / / 7-IRON FERREDOXIN


Mass: 11432.598 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-105 / Source method: isolated from a natural source / Source: (natural) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC2 / References: UniProt: P00215
#2: Chemical
ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe3S4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFERREDOXINS ARE IRON-SULFUR PROTEINS THAT TRANSFER ELECTRONS IN A WIDE VARIETY OF METABOLIC REACTIONS.

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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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growpH: 5.5 / Details: AMMONIUM SULPHATE, MPD, SODIUM ACETATE, pH 5.50

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 26, 2007
RadiationMonochromator: DIAMONDS CRYSTALS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 26692 / % possible obs: 93.9 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.9
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
MOSFLMdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H98

1h98


Resolution: 1.6→67.73 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.047 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY CONTAINS SOME ATOMS REFINED WITH ZERO OCCUPANCY FOR WHICH B-FACTORS HAVE BEEN REFINED.
RfactorNum. reflection% reflectionSelection details
Rfree0.202 1344 5 %RANDOM
Rwork0.165 ---
obs0.167 25306 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20 Å2
2--2.49 Å20 Å2
3----1.82 Å2
Refinement stepCycle: LAST / Resolution: 1.6→67.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1569 0 32 118 1719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221676
X-RAY DIFFRACTIONr_bond_other_d0.0180.021062
X-RAY DIFFRACTIONr_angle_refined_deg1.5282.0052293
X-RAY DIFFRACTIONr_angle_other_deg1.22332633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0645212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.87626.88377
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51215239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.664152
X-RAY DIFFRACTIONr_chiral_restr0.7070.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021867
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02277
X-RAY DIFFRACTIONr_nbd_refined0.2980.2393
X-RAY DIFFRACTIONr_nbd_other0.1840.21086
X-RAY DIFFRACTIONr_nbtor_refined0.1670.2814
X-RAY DIFFRACTIONr_nbtor_other0.0860.2650
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1920.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.131.51356
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.12821716
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2233718
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1644.5552
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
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.289 105
Rwork0.261 1839
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.93540.9577-0.70510.8802-0.50774.5215-0.0195-0.1101-0.02550.0621-0.0552-0.06480.01880.02490.0746-0.06030.0043-0.0058-0.05210.0153-0.072720.056211.908722.1878
24.23140.7602-1.07071.1494-0.7233.7401-0.193-0.1445-0.4257-0.05250.0423-0.10320.4335-0.26170.1507-0.0103-0.04410.0265-0.06480.016-0.051315.55085.044821.6034
32.294-0.50511.06582.1459-2.07077.40290.1685-0.3750.0707-0.029-0.1229-0.08750.2385-0.4538-0.0456-0.0707-0.0310.02880.10450.0279-0.088810.82648.695932.5961
40.089-0.605-0.32684.14682.19261.2225-0.15020.07150.13540.0271-0.1534-0.18240.1432-0.22360.30360.0116-0.0089-0.00280.02490.01540.032321.48311.597514.631
516.5168-5.2046-9.8012.03424.837913.5818-0.1277-0.33310.1226-0.06230.0754-0.0102-0.12330.22330.05220.0192-0.0141-0.01490.03150.0054-0.001222.264714.301526.3929
61.9592-0.1871-0.37331.019-0.44772.4068-0.02330.0315-0.0755-0.04810.00970.00160.0789-0.07790.0136-0.0446-0.00380.0019-0.0701-0.0091-0.036219.565813.6859-7.5864
73.05210.3036-1.23270.931-0.3852.1650.08020.03270.25080.06590.0250.0035-0.2328-0.1169-0.1052-0.03460.02430.0102-0.0670.0068-0.026518.824622.4069-6.9487
80.66461.281-0.86362.5734-2.33545.4371-0.00210.1759-0.0292-0.12090.04330.1093-0.1045-0.224-0.0412-0.06710.0215-0.02020.04930.0246-0.036211.072519.9256-15.8261
98.6508-3.43840.2437.87260.58060.0773-0.10170.1135-0.12830.1129-0.0906-0.0185-0.07350.04290.19240.0174-0.00490.0130.00080.01650.034421.401313.2401-0.1249
1028.9756-7.798619.62072.356-3.823621.54590.10740.2632-0.39620.2189-0.0099-0.05770.0211-0.0345-0.09740.0094-0.00850.0065-0.0614-0.02310.023420.329510.7948-11.8632
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 55
2X-RAY DIFFRACTION2A56 - 86
3X-RAY DIFFRACTION3A87 - 104
4X-RAY DIFFRACTION4A107
5X-RAY DIFFRACTION5A108
6X-RAY DIFFRACTION6B1 - 55
7X-RAY DIFFRACTION7B56 - 85
8X-RAY DIFFRACTION8B86 - 103
9X-RAY DIFFRACTION9B107
10X-RAY DIFFRACTION10B108

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