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- PDB-5abr: Structure of FeSI protein from Azotobacter vinelandii -

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Basic information

Entry
Database: PDB / ID: 5abr
TitleStructure of FeSI protein from Azotobacter vinelandii
ComponentsFERREDOXIN, 2FE-2S
KeywordsELECTRON TRANSPORT / FERREDOXIN
Function / homology
Function and homology information


nitrogen fixation / 2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
: / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Ferredoxin, 2Fe-2s
Similarity search - Component
Biological speciesAZOTOBACTER VINELANDII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.11 Å
AuthorsKabasakal, B. / Murray, J.W.
CitationJournal: To be Published
Title: Structure of Fesi Protein from Azotobacter Vinelandii
Authors: Kabasakal, B. / Cotton, C.A.R. / Murray, J.W.
History
DepositionAug 7, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _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

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Assembly

Deposited unit
A: FERREDOXIN, 2FE-2S
B: FERREDOXIN, 2FE-2S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2284
Polymers26,8772
Non-polymers3522
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-41.1 kcal/mol
Surface area9930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.040, 60.100, 45.510
Angle α, β, γ (deg.)90.00, 109.37, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116B1 - 500
2116A1 - 500

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.5201, 0.005422, -0.8541), (0.000693, -1, -0.005926), (-0.8541, 0.002489, -0.5201)-12.03, 35.21, -21.51
3given(0.518989, 0.004513, -0.854769), (-0.00029, -0.999985, -0.005456), (-0.854781, 0.00308, -0.51898)-12.00103, 35.21083, -21.50599

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Components

#1: Protein FERREDOXIN, 2FE-2S / FESI PROTEIN / 2FEAVFDI / IRON-SULFUR PROTEIN I / SHETHNA PROTE


Mass: 13438.304 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AZOTOBACTER VINELANDII (bacteria) / Strain: DSM-2289 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Plasmid: PRSETA / Production host: ESCHERICHIA COLI KRX (bacteria) / References: UniProt: P82802
#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.: 128 / 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: 2.09 Å3/Da / Density % sol: 41.24 % / Description: NONE
Crystal growpH: 7.5 / Details: 100 MM HEPES PH 7.5, 77% V/V MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.73404
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Feb 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.73404 Å / Relative weight: 1
ReflectionResolution: 2.11→42.93 Å / Num. obs: 11386 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.1
Reflection shellResolution: 2.11→2.16 Å / Redundancy: 3 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.4 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XDSdata reduction
Aimlessdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.11→42.934 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.929 / SU B: 12.183 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.247 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2307 545 4.82 %RANDOM
Rwork0.1774 ---
obs0.18 11386 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.585 Å20 Å20.044 Å2
2---0.647 Å20 Å2
3----0.776 Å2
Refinement stepCycle: LAST / Resolution: 2.11→42.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1558 0 8 128 1694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0191616
X-RAY DIFFRACTIONr_bond_other_d0.0020.021516
X-RAY DIFFRACTIONr_angle_refined_deg2.3731.9512194
X-RAY DIFFRACTIONr_angle_other_deg1.1933.0053472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1335206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.18624.54566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71815228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.942156
X-RAY DIFFRACTIONr_chiral_restr0.1290.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211860
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02366
X-RAY DIFFRACTIONr_nbd_refined0.2520.2870
X-RAY DIFFRACTIONr_nbd_other0.1760.22894
X-RAY DIFFRACTIONr_nbtor_refined0.181518
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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

Dom-ID: 2 / Auth asym-ID: A / Ens-ID: 1 / Number: 1541 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.245
loose thermal1.810
LS refinement shellResolution: 2.11→2.165 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 29 -
Rwork0.218 827 -
obs--97.717 %
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)
126.294712.3485-3.31798.3744-1.81234.1134-0.0272-0.5215-0.1018-0.0385-0.13480.0251-0.14550.36370.1620.2781-0.0147-0.13120.0410.01890.0659-0.14517.221-7.766
28.27927.72032.03548.14932.13941.33280.1929-0.20240.33810.4956-0.18760.17910.1163-0.1203-0.00540.36350.0142-0.18250.0127-0.01350.1209-2.83113.804-0.329
33.3888-0.48942.29740.17890.10423.31320.03160.21110.0790.0368-0.0162-0.02930.18290.1946-0.01540.3917-0.0258-0.21770.01740.02110.12390.84911.58-8.255
418.69833.293-5.47694.1432-1.76537.0317-0.21370.2481-0.3088-0.03960.0171-0.2326-0.3621-0.07910.19660.2787-0.0168-0.15810.00440.00670.1169.84112.591-0.912
516.83740.0046.24162.74491.31779.5298-0.06420.7346-1.3514-0.48260.2673-0.29230.5530.3564-0.20310.4448-0.0703-0.07610.1029-0.10360.32786.8493.473-8.822
66.1961-4.9394-2.79686.67254.24513.7508-0.10.1198-0.28680.1921-0.02290.32170.2792-0.07210.12290.327-0.0175-0.15210.00970.00690.1001-9.02822.593-13.007
72.0022-1.9137-0.899810.70429.54679.853-0.0472-0.0018-0.1431-0.1635-0.16050.4488-0.0506-0.22740.20770.3829-0.0286-0.19090.00950.01670.1242-12.39619.071-22.083
81.901-0.18141.06540.0301-0.23923.4762-0.0780.10550.0697-0.00840.0072-0.0086-0.01240.14040.07080.4283-0.0018-0.19230.0406-0.01390.097-4.45423.648-17.928
917.6895-7.1674-10.143110.40587.307513.64090.20430.29360.1191-0.4910.1465-0.1178-0.07790.1222-0.35080.3419-0.0006-0.14050.0192-0.00940.0721-6.11722.608-29.466
108.97720.29373.34433.3876-4.2613.6486-0.0776-0.21380.3269-0.25110.1121-0.6356-1.26130.7915-0.03440.8693-0.28270.08510.2939-0.17830.4068-0.92531.762-22.859
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 14
2X-RAY DIFFRACTION2A15 - 47
3X-RAY DIFFRACTION3A48 - 78
4X-RAY DIFFRACTION4A79 - 94
5X-RAY DIFFRACTION5A95 - 107
6X-RAY DIFFRACTION6B4 - 20
7X-RAY DIFFRACTION7B21 - 47
8X-RAY DIFFRACTION8B48 - 78
9X-RAY DIFFRACTION9B79 - 94
10X-RAY DIFFRACTION10B95 - 107

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