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- PDB-1js2: Crystal structure of C77S HiPIP: a serine ligated [4Fe-4S] cluster -

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Basic information

Entry
Database: PDB / ID: 1js2
TitleCrystal structure of C77S HiPIP: a serine ligated [4Fe-4S] cluster
Componentshigh-potential iron protein
KeywordsELECTRON TRANSPORT / serine ligated [4Fe-4S] cluster
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMansy, S.S. / Xiong, Y. / Hemann, C. / Hille, R. / Sundaralingam, M. / Cowan, J.A.
CitationJournal: Biochemistry / Year: 2002
Title: Crystal structure and stability studies of C77S HiPIP: a serine ligated [4Fe-4S] cluster.
Authors: Mansy, S.S. / Xiong, Y. / Hemann, C. / Hille, R. / Sundaralingam, M. / Cowan, J.A.
History
DepositionAug 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 17, 2013Group: Structure summary
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_comp_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_comp_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.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: high-potential iron protein
B: high-potential iron protein
C: high-potential iron protein
D: high-potential iron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1498
Polymers37,7424
Non-polymers1,4074
Water3,387188
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.059, 30.182, 68.738
Angle α, β, γ (deg.)90.00, 111.27, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein
high-potential iron protein / HIGH POTENTIAL IRON-SULFUR PROTEIN / HIPIP


Mass: 9435.540 Da / Num. of mol.: 4 / Fragment: residues 38-122 of P00260 / Mutation: C77S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Allochromatium vinosum (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P00260
#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


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


Mass: 18.015 Da / Num. of mol.: 188 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: VAPOR DIFFUSION, HANGING DROP at pH 8.0, 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMTris-HCl1droppH8.0
21.1 mMC77S HiPIP1drop
345.5 %(v/v)saturatedammonium sulfate1reservoir
449.8 mM1reservoirKCl
550 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1.653 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.653 Å / Relative weight: 1
ReflectionResolution: 1.9→27.302 Å / Num. obs: 35617 / % possible obs: 90.4 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.094
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 2 / % possible all: 78.6

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→15 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1795 5 %Random
Rwork0.193 ---
obs-35613 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.527 Å20 Å2-4.086 Å2
2--3.152 Å20 Å2
3---1.375 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2640 0 32 188 2860
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.096
X-RAY DIFFRACTIONc_angle_deg1.328
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.01

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