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- PDB-3h31: Structure of Rhodothermus marinus HiPIP at 1.0 A resolution -

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Basic information

Entry
Database: PDB / ID: 3h31
TitleStructure of Rhodothermus marinus HiPIP at 1.0 A resolution
ComponentsHigh potential iron-sulfur protein
KeywordsELECTRON TRANSPORT / Iron-sulfur protein / Iron / 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 / membrane
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. / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Few Secondary Structures ...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. / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Few Secondary Structures / Irregular / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / High potential iron-sulfur protein
Similarity search - Component
Biological speciesRhodothermus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1 Å
AuthorsStelter, M. / Melo, A.M.P. / Saraiva, L. / Teixeira, M. / Archer, M.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2010
Title: Structure at 1.0 A resolution of a high-potential iron-sulfur protein involved in the aerobic respiratory chain of Rhodothermus marinus
Authors: Stelter, M. / Melo, A.M.P. / Hreggvidsson, G.O. / Hjorleifsdottir, S. / Saraiva, L.M. / Teixeira, M. / Archer, M.
History
DepositionApr 15, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Database references
Revision 1.3Jan 24, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Nov 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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)8,4522
Polymers8,1001
Non-polymers3521
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.267, 43.343, 46.787
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


Mass: 8100.005 Da / Num. of mol.: 1 / Fragment: UNP residues 54-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodothermus marinus (bacteria) / Strain: ITI-378 / Gene: hip / Plasmid: pET12a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD(DE3) / References: UniProt: C4P582
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.71 Å3/Da / Density % sol: 27.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: ammonium sulfate, dioxane, sodium citrate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONSLS X06SA10.918
ROTATING ANODEENRAF-NONIUS FR57121.541
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDJan 16, 2007
MARRESEARCH2IMAGE PLATEAug 6, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1si 111SINGLE WAVELENGTHMx-ray1
2MirrorsSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9181
21.5411
ReflectionResolution: 1→46.8 Å / Num. obs: 30715 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Biso Wilson estimate: 5.05 Å2 / Rmerge(I) obs: 0.128 / Rsym value: 0.128 / Net I/σ(I): 9.2
Reflection shellResolution: 1→1.05 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 2.9 / Num. unique all: 4410 / Rsym value: 0.396 / % possible all: 100

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Processing

Software
NameClassification
MAR345dtbdata collection
SHELXmodel building
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1→10 Å / Num. parameters: 7289 / Num. restraintsaints: 9514 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.144 521 -RANDOM
Rwork0.1044 ---
obs0.1044 30715 100 %-
all-55765 --
Displacement parametersBiso mean: 10 Å2
Refine analyzeNum. disordered residues: 18 / Occupancy sum hydrogen: 482 / Occupancy sum non hydrogen: 690.59
Refinement stepCycle: LAST / Resolution: 1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms563 0 8 140 711
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.042
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0328
X-RAY DIFFRACTIONs_zero_chiral_vol0.12
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.111
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.053
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.051
X-RAY DIFFRACTIONs_approx_iso_adps0.095

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