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- PDB-1wtf: Crystal structure of Bacillus thermoproteolyticus Ferredoxin Vari... -

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Basic information

Entry
Database: PDB / ID: 1wtf
TitleCrystal structure of Bacillus thermoproteolyticus Ferredoxin Variants Containing Unexpected [3Fe-4S] Cluster that is linked to Coenzyme A at 1.6 A Resolution
ComponentsFerredoxin
KeywordsELECTRON TRANSPORT / 3Fe-4S cluster / Coenzyme A / Ferredoxin / Complex
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / electron transfer activity / iron ion binding
Similarity search - Function
: / 3Fe-4S ferredoxin / 4Fe-4S single cluster domain of Ferredoxin I / Alpha-Beta Plaits - #20 / 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
COENZYME A / FE3-S4 CLUSTER / Ferredoxin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsShirakawa, T. / Takahashi, Y. / Wada, K. / Hirota, J. / Takao, T. / Ohmori, D. / Fukuyama, K.
CitationJournal: Biochemistry / Year: 2005
Title: Identification of variant molecules of Bacillus thermoproteolyticus ferredoxin: crystal structure reveals bound coenzyme A and an unexpected [3Fe-4S] cluster associated with a canonical [4Fe-4S] ligand motif
Authors: Shirakawa, T. / Takahashi, Y. / Wada, K. / Hirota, J. / Takao, T. / Ohmori, D. / Fukuyama, K.
History
DepositionNov 22, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_asym_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_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_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_asym_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_seq_id / _struct_conn.ptnr1_label_asym_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_type.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
C: Ferredoxin
D: Ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,33312
Polymers35,0944
Non-polymers2,2398
Water13,691760
1
A: Ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0295
Polymers8,7741
Non-polymers1,2554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1653
Polymers8,7741
Non-polymers3922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0692
Polymers8,7741
Non-polymers2961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0692
Polymers8,7741
Non-polymers2961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.461, 63.387, 56.857
Angle α, β, γ (deg.)90.00, 95.06, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer.

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Components

#1: Protein
Ferredoxin


Mass: 8773.595 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thermoproteolyticus (bacteria)
Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: P10245
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical
ChemComp-F3S / FE3-S4 CLUSTER


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


Mass: 18.015 Da / Num. of mol.: 760 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.68 Å3/Da / Density % sol: 54.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Ammonium sulfate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11
SYNCHROTRONSPring-8 BL41XU21.5
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 29, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.51
ReflectionResolution: 1.6→50 Å / Num. obs: 49210 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 7.5
Reflection shellResolution: 1.6→1.68 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.062 / Mean I/σ(I) obs: 7.5 / Num. unique all: 49210 / % possible all: 98.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→31.84 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 763977.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 4844 10.1 %RANDOM
Rwork0.182 ---
all0.185 ---
obs0.182 48081 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.4307 Å2 / ksol: 0.390685 e/Å3
Displacement parametersBiso mean: 16.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.74 Å20 Å2-0.01 Å2
2--5.48 Å20 Å2
3----3.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.04 Å-0.04 Å
Refinement stepCycle: LAST / Resolution: 1.6→31.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2448 0 91 760 3299
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d3.75
X-RAY DIFFRACTIONc_mcbond_it1.751.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it3.112
X-RAY DIFFRACTIONc_scangle_it4.152.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.246 752 9.7 %
Rwork0.202 6996 -
obs--95.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2FS3_PAR&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3COA_XPLOR_PAR.TXT&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4SO4_XPLOR_PAR.TXT&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5WATER_REP.PARAM&_1_TOPOLOGY_INFILE_5

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