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- PDB-3a38: Crystal structure of high-potential iron-sulfur protein from Ther... -

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Basic information

Entry
Database: PDB / ID: 3a38
TitleCrystal structure of high-potential iron-sulfur protein from Thermochromatium tepidum at 0.7 angstrom resolution
ComponentsHigh-potential iron-sulfur protein
KeywordsELECTRON TRANSPORT / IRON-SULFUR CLUSTER / Iron / Iron-sulfur / Metal-binding / Transport
Function / homology
Function and homology information


aerobic electron transport chain / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
High potential iron-sulphur protein / High-Potential Iron-Sulfur Protein; Chain A / High potential iron-sulfur protein / High potential iron-sulphur protein / High potential iron-sulphur protein superfamily / High potential iron-sulfur proteins family profile. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / High-potential iron-sulfur protein
Similarity search - Component
Biological speciesThermochromatium tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.7 Å
AuthorsTakeda, K. / Kusumoto, K. / Hirano, Y. / Miki, K.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Detailed assessment of X-ray induced structural perturbation in a crystalline state protein.
Authors: Takeda, K. / Kusumoto, K. / Hirano, Y. / Miki, K.
History
DepositionJun 10, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: High-potential iron-sulfur protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5266
Polymers8,7941
Non-polymers7325
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.509, 58.959, 23.415
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein High-potential iron-sulfur protein / HiPIP


Mass: 8793.851 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: P80176
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: 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: 1.51 Å3/Da / Density % sol: 32.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 1.9M ammonium sulfate, 10mM dithiothreitol, 100mM sodium citrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.71 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.71 Å / Relative weight: 1
ReflectionResolution: 0.7→50 Å / Num. obs: 96778 / % possible obs: 94.7 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 57.2
Reflection shellResolution: 0.7→0.73 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 8.9 / Num. unique all: 6229 / % possible all: 61.7

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IUA

1iua


Resolution: 0.7→50 Å / Num. parameters: 8703 / Num. restraintsaints: 413 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.074 8561 -RANDOM FROM 0.8 TO 0.7 ANGSTROM RESOLUTION
Rwork0.0658 ---
all0.0666 96693 --
obs0.0658 96693 94.7 %-
Refine analyzeNum. disordered residues: 38 / Occupancy sum hydrogen: 544.02 / Occupancy sum non hydrogen: 744.38
Refinement stepCycle: LAST / Resolution: 0.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms616 0 29 162 807
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.028
X-RAY DIFFRACTIONs_angle_d2.8
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0
X-RAY DIFFRACTIONs_approx_iso_adps0

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