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- PDB-1cku: AB INITIO SOLUTION AND REFINEMENT OF TWO HIGH POTENTIAL IRON PROT... -

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Basic information

Entry
Database: PDB / ID: 1cku
TitleAB INITIO SOLUTION AND REFINEMENT OF TWO HIGH POTENTIAL IRON PROTEIN STRUCTURES AT ATOMIC RESOLUTION
ComponentsPROTEIN (HIPIP)
KeywordsELECTRON TRANSFER PROTEIN / ATOMIC RESOLUTION / DIRECT METHODS / IRON-SULPHUR CLUSTER / METALLOPROTEIN
Function / homology
Function and homology information


aerobic electron transport chain / 4 iron, 4 sulfur cluster binding / periplasmic space / 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. / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Few Secondary Structures / Irregular
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / High-potential iron-sulfur protein
Similarity search - Component
Biological speciesAllochromatium vinosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1.2 Å
AuthorsParisini, E. / Capozzi, F. / Lubini, P. / Lamzin, V. / Luchinat, C. / Sheldrick, G.M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Ab initio solution and refinement of two high-potential iron protein structures at atomic resolution.
Authors: Parisini, E. / Capozzi, F. / Lubini, P. / Lamzin, V. / Luchinat, C. / Sheldrick, G.M.
#1: Journal: J.Biol.Chem. / Year: 1974
Title: Two-Angstrom Crystal Structure of Oxidized Chromatium High Potential Iron Protein
Authors: Carter, C.W. / Kraut, J. / Freer, S.T. / Xuong, N.-H. / Alden, R.A. / Bartsch, R.G.
History
DepositionApr 24, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (HIPIP)
B: PROTEIN (HIPIP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5294
Polymers17,8262
Non-polymers7032
Water6,017334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.067, 51.389, 92.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.75271, 0.64149, -0.14805), (0.65695, 0.71718, -0.23253), (-0.04298, -0.27229, -0.96125)
Vector: 12.3334, -7.0584, 34.58648)

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Components

#1: Protein PROTEIN (HIPIP)


Mass: 8912.928 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Allochromatium vinosum (bacteria) / Strain: XL1BLUE / Plasmid: PLEHP20 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1BLUE / References: UniProt: P00260
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.25 Å3/Da / Density % sol: 45 %
Crystal growpH: 5.3
Details: 1.3 M AMMONIUM SULPHATE, 40 MM TRIS 180 MM KCL, pH 5.3
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
220 mMTris-HCl1drop
390 mM1dropKCl
41 Mammonium sulfate1drop
52 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9091
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 11, 1997 / Details: BENT CRYSTAL
RadiationMonochromator: GE SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9091 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. obs: 50551 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 12.5 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 9
Reflection shellResolution: 1.2→1.25 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 5.4 / % possible all: 94.4
Reflection
*PLUS
Num. measured all: 636238
Reflection shell
*PLUS
Rmerge(I) obs: 0.21

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 1.2→20 Å / Num. parameters: 14394 / Num. restraintsaints: 17533 / Cross valid method: FREE R / σ(F): 0
StereochEM target val spec case: NO RESTRAINTS ON PROSTHETIC GROUPS (RESIDUE 87 IN CHAINS A AND B)
Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.178 1321 2.5 %THIN SHELLS
all0.1275 51872 --
obs0.1315 -97.4 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 1182 / Occupancy sum non hydrogen: 1562.5
Refinement stepCycle: LAST / Resolution: 1.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1249 0 16 334 1599
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0.126
X-RAY DIFFRACTIONs_from_restr_planes0.03
X-RAY DIFFRACTIONs_zero_chiral_vol0.07
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.076
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.057
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.031
X-RAY DIFFRACTIONs_approx_iso_adps0.083
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 2.5 % / Rfactor Rwork: 0.132
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.03

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