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- PDB-6fd1: 7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII LOW TEMPERATURE, 1.35 A -

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Basic information

Entry
Database: PDB / ID: 6fd1
Title7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII LOW TEMPERATURE, 1.35 A
Components7-FE FERREDOXIN I (FD1)
KeywordsELECTRON TRANSPORT / IRON-SULFUR
Function / homology
Function and homology information


3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / DNA binding / metal ion binding
Similarity search - Function
Ferredoxin, C-terminal / : / Domain of unknown function (DUF3470) / 7Fe ferredoxin / : / Alpha-Beta Plaits - #20 / 4Fe-4S binding domain / 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. ...Ferredoxin, C-terminal / : / Domain of unknown function (DUF3470) / 7Fe ferredoxin / : / Alpha-Beta Plaits - #20 / 4Fe-4S binding domain / 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-1
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsStout, C.D. / Stura, E.A. / Mcree, D.E.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Structure of Azotobacter vinelandii 7Fe ferredoxin at 1.35 A resolution and determination of the [Fe-S] bonds with 0.01 A accuracy.
Authors: Stout, C.D. / Stura, E.A. / McRee, D.E.
History
DepositionSep 17, 1997Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 7-FE FERREDOXIN I (FD1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7073
Polymers12,0601
Non-polymers6472
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.840, 54.840, 92.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein 7-FE FERREDOXIN I (FD1) / FD1


Mass: 12059.530 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P00214
#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.: 162 / 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: 2.89 Å3/Da / Density % sol: 57.38 %
Description: ALL DATA INCLUDING NEGATIVE I'S WERE USED WERE PROCESSED IN POINT GROUP 422 - PRESERVE BIJVOET PAIRS
Crystal growpH: 7.8
Details: PROTEIN CRYSTALLIZED FROM 4.8M AMMONIUM SULFATE, 0.45M TRIS-HCL, PH 7.8
Crystal grow
*PLUS
Method: batch method
Details: anaerobic conditions, Martin, A.E., (1990) Proc. Natl. Acad. Sci. USA., 87, 598.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MTris-HCl11
25.1 Mammonium sulfate11
31.0 mMprotein11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.35→100 Å / Num. obs: 57315 / % possible obs: 96.5 % / Redundancy: 3.3 % / Rsym value: 0.057 / Net I/σ(I): 21.3
Reflection shellResolution: 1.35→1.38 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.747 / % possible all: 72
Reflection
*PLUS
Lowest resolution: 50 Å / Rmerge(I) obs: 0.057

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Processing

Software
NameVersionClassification
TRIVIALCASEmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
TRIVIALCASEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FD1

5fd1


Resolution: 1.35→100 Å / Num. parameters: 9211 / Num. restraintsaints: 10844 / Cross valid method: R-FREE / σ(F): 0 / StereochEM target val spec case: FE CLUSTERS NOT RESTRAINED / Stereochemistry target values: ENGH & HUBER
Details: FREE R USED UNTIL LAST CYCLE WHEN ALL DATA WAS INCLUDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1544 5 %EVERY 20TH REFLECTION
all0.15 30880 --
obs0.153 -96.5 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 776 / Occupancy sum non hydrogen: 1011.5
Refinement stepCycle: LAST / Resolution: 1.35→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms846 0 15 162 1023
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.04
X-RAY DIFFRACTIONs_similar_dist0.02
X-RAY DIFFRACTIONs_from_restr_planes0.2
X-RAY DIFFRACTIONs_zero_chiral_vol0.2
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.2
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.02
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.3
X-RAY DIFFRACTIONs_approx_iso_adps0.2
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 9999 Å / Rfactor all: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS

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