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- PDB-1hlq: CRYSTAL STRUCTURE OF RHODOFERAX FERMENTANS HIGH POTENTIAL IRON-SU... -

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Basic information

Entry
Database: PDB / ID: 1hlq
TitleCRYSTAL STRUCTURE OF RHODOFERAX FERMENTANS HIGH POTENTIAL IRON-SULFUR PROTEIN REFINED TO 1.45 A
ComponentsHIGH-POTENTIAL IRON-SULFUR PROTEIN
KeywordsELECTRON TRANSPORT / Iron sulfur cluster
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 speciesRhodoferax fermentans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsGonzalez, A. / Ciurli, S. / Benini, S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of Rhodoferax fermentans high-potential iron-sulfur protein solved by MAD.
Authors: Gonzalez, A. / Benini, S. / Ciurli, S.
#1: Journal: Eur.J.Biochem. / Year: 1997
Title: The primary structure of Rhodoferax fermentans high potential iron-sulfur protein, an electron donor to the photosynthetic reaction center
Authors: Van Driesche, G. / Ciurli, S. / Hochkoeppler, A. / Van Beeumen, J.J.
#2: Journal: FEBS Lett. / Year: 1995
Title: The high-potential iron-sulfur protein (HIPIP) from Rhodoferax fermentans is competent in photosynthetic electron transfer
Authors: Hochkoeppler, A. / Ciurli, S. / Venturoli, G. / Zannoni, D.
#3: Journal: Arch.Biochem.Biophys. / Year: 1995
Title: Isolation, characterization, and functional role of the high potentialiron-sulfur protein (HIPIP) from Rhodopherax fermentans
Authors: Hochkoeppler, A. / Kofod, P. / Ferro, G. / Ciurli, S.
#4: Journal: Eur.J.Biochem. / Year: 1996
Title: 1H NMR of high potential iron-sulfur protein from the purple non-sulfur bacterium Rhodoferax fermentans
Authors: Ciurli, S. / Cremonini, M.A. / Kofod, P. / Luchinat, C.
#5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Kinetics of photoinduced electron transfer from high potential iron-sulfur protein (HIPIP) to the photosynthetic reaction center of the purple phototroph Rhodoferax fermentans
Authors: Hochkoeppler, A. / Zannoni, D. / Ciurli, S. / Meyer, T.E. / Cusanovich, M.A. / Tolin, G.
History
DepositionDec 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIGH-POTENTIAL IRON-SULFUR PROTEIN
B: HIGH-POTENTIAL IRON-SULFUR PROTEIN
C: HIGH-POTENTIAL IRON-SULFUR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,11811
Polymers23,5833
Non-polymers1,5358
Water4,684260
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.312, 88.312, 61.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

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Components

#1: Protein HIGH-POTENTIAL IRON-SULFUR PROTEIN / HIPIP


Mass: 7860.968 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rhodoferax fermentans (bacteria) / References: UniProt: P80882
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


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


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: HiPIP (20mg/ml, 20mM Tris pH 8, 2mM Beta-mercaptoethanol, 3.2M (NH4)2SO4 in 100mM Tris buffer, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
220 mMTris-HCl1droppH8.
32 mMbeta-mercaptoethanol1drop
43.2 Mammonium sulfate1reservoir
5100 mMTris-HCl1reservoirpH8.

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONEMBL/DESY, HAMBURG BW7B11.105
SYNCHROTRONEMBL/DESY, HAMBURG BW7A21.738, 1.742, 0.995
Detector
TypeIDDetectorDateDetails
MARRESEARCH1IMAGE PLATEApr 23, 1997mirrors
MARRESEARCH2IMAGE PLATEJun 9, 1997mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Asymmetric cut Si(111)SINGLE WAVELENGTHMx-ray1
2Channel cut Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.1051
21.7381
31.7421
40.9951
ReflectionResolution: 1.45→22.09 Å / Num. all: 42975 / Num. obs: 42975 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 17.254 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 6.9
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 0.6 / Num. unique all: 5912 / % possible all: 95.4
Reflection
*PLUS
Highest resolution: 1.45 Å / Lowest resolution: 22.09 Å / Num. obs: 42770 / % possible obs: 99 % / Num. measured all: 239390
Reflection shell
*PLUS
% possible obs: 95.4 % / Num. unique obs: 41858 / Num. measured obs: 238478

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.45→22 Å / SU B: 0.83862 / SU ML: 0.03238 / Isotropic thermal model: Anisotropic / Cross valid method: FREE R-VALUE / σ(F): 0 / σ(I): 0 / ESU R: 0.07766 / Stereochemistry target values: Engh & Huber
Details: Used conjugate direction method with maximum likelihood NCS and MAD phases were used as restrains
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2151 5 %random
Rwork0.187 ---
all0.186 42733 --
obs0.186 42733 99.6 %-
Refine analyze
FreeObs
Luzzati coordinate error0.0766 Å0.0777 Å
Luzzati d res low-22 Å
Refinement stepCycle: LAST / Resolution: 1.45→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1688 0 54 281 2023
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0080.02
X-RAY DIFFRACTIONp_angle_d0.0260.04
X-RAY DIFFRACTIONp_planar_d0.0680.05
X-RAY DIFFRACTIONp_mcbond_it1.3112
X-RAY DIFFRACTIONp_mcangle_it1.9083
X-RAY DIFFRACTIONp_scbond_it1.5082
X-RAY DIFFRACTIONp_scangle_it2.0793
X-RAY DIFFRACTIONp_plane_restr8.47
X-RAY DIFFRACTIONp_chiral_restr0.0980.15
X-RAY DIFFRACTIONp_singtor_nbd0.1570.3
X-RAY DIFFRACTIONp_multtor_nbd0.2590.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.1240.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor8.47
X-RAY DIFFRACTIONp_staggered_tor13.915
X-RAY DIFFRACTIONp_transverse_tor15.820
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_special_tor
LS refinement shellResolution: 1.453→1.604 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rwork0.19 -
obs-10629
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg78.4
X-RAY DIFFRACTIONp_planar_d0.05
X-RAY DIFFRACTIONp_plane_restr0.030.023
X-RAY DIFFRACTIONp_chiral_restr0.15

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