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- PDB-3hip: HIGH-POTENTIAL IRON-SULFUR PROTEIN FROM CHROMATIUM PURPURATUM -

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Basic information

Entry
Database: PDB / ID: 3hip
TitleHIGH-POTENTIAL IRON-SULFUR PROTEIN FROM CHROMATIUM PURPURATUM
ComponentsHIGH-POTENTIAL IRON-SULFUR PROTEIN
KeywordsELECTRON TRANSFER / PHOTOSYNTHESIS / 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. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / High-potential iron-sulfur protein
Similarity search - Component
Biological speciesMarichromatium purpuratum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKerfeld, C.A. / Salmeen, A.E. / Yeates, T.O.
Citation
Journal: Biochemistry / Year: 1998
Title: Crystal structure and possible dimerization of the high-potential iron-sulfur protein from Chromatium purpuratum.
Authors: Kerfeld, C.A. / Salmeen, A.E. / Yeates, T.O.
#1: Journal: Biochemistry / Year: 1996
Title: Isolation and Characterization of Soluble Electron Transfer Proteins from Chromatium Purpuratum
Authors: Kerfeld, C.A. / Chan, C. / Hirasawa, M. / Kleis-Sanfrancisco, S. / Yeates, T.O. / Knaff, D.B.
History
DepositionJun 15, 1998Processing site: BNL
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_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_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)27,3406
Polymers26,2853
Non-polymers1,0553
Water00
1
A: HIGH-POTENTIAL IRON-SULFUR PROTEIN
hetero molecules

A: HIGH-POTENTIAL IRON-SULFUR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2274
Polymers17,5242
Non-polymers7032
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
2
B: HIGH-POTENTIAL IRON-SULFUR PROTEIN
C: HIGH-POTENTIAL IRON-SULFUR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2274
Polymers17,5242
Non-polymers7032
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.500, 108.800, 37.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.204136, -0.427515, -0.880611), (0.958463, 0.095695, -0.268638), (0.199163, -0.898919, 0.390257)77.6146, 18.7748, 9.1577
2given(0.073, 0.997237, -0.014505), (-0.996845, 0.072304, -0.032869), (-0.031673, 0.016896, 0.999389)23.1564, 60.8267, -16.9554
DetailsMOLECULES B AND C ARE RELATED BY A NONCRYSTALLOGRAPHIC TWO-FOLD SYMMETRY AXIS.

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Components

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


Mass: 8761.788 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Marichromatium purpuratum (bacteria) / Cellular location: PERIPLASM / References: UniProt: P59860
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
Sequence detailsTHE FIRST 25 AMINO ACIDS OF C. PURPURATUM HIPIP WERE DETERMINED BY AUTOMATED EDMAN DEGRADATION (REF. ...THE FIRST 25 AMINO ACIDS OF C. PURPURATUM HIPIP WERE DETERMINED BY AUTOMATED EDMAN DEGRADATION (REF. 1, ABOVE). THE REST OF THE PRIMARY STRUCTURE WAS ASSIGNED FROM THE ELECTRON DENSITY WITH CONSIDERATION OF HOMOLOGY TO THE PRIMARY STRUCTURES OF OTHER HIPIPS. DISCREPANCY BETWEEN IDENTITY DETERMINED BY EDMAN DEGRADATION AND CRYSTAL STRUCTURE AT RESIDUE 110 (S) FOR D. SIDECHAINS FOR THE FOLLOWING RESIDUES ARE INCOMPLETE DUE TO INSUFFICIENT ELECTRON DENSITY: 102, 118, 125 (MOL A AND B), 147 (MOL B). LIKELY INCOMPLETE: 144, 152, 154-157, 167.

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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: 1.9 Å3/Da / Density % sol: 34 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.4
Details: CRYSTALLIZED BY VAPOR DIFFUSION OVER A RESERVOIR CONTAINING 100 MM CITRATE BUFFER, PH 5.4 AND 3.2 M AMMONIUM SULFATE PROTEIN CONCENTRATION = 8.0 MG/ML, vapor diffusion - hanging drop
Crystal
*PLUS
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18.0 mg/mlprotein1drop
25 mMTris1drop
33 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.7 Å / Num. obs: 6568 / % possible obs: 94.1 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 6.9
Reflection shellResolution: 2.8→2.91 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 3.3 / % possible all: 93
Reflection
*PLUS
Lowest resolution: 8 Å / Num. measured all: 13850

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HIP

1hip


Resolution: 2.8→8 Å / Data cutoff high absF: 1000000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
Details: STRICT NCS RELEASED ONLY FOR LAST CYCLE OF REFINEMENT RESIDUE 127 HAS SIGNIFICANT ELECTRON DENSITY FOR THE SIDE-CHAIN BUT HAS A LARGE B FACTOR.
RfactorNum. reflection% reflectionSelection details
Rfree0.288 710 10.5 %RANDOM
Rwork0.224 ---
obs0.224 5767 98.5 %-
Displacement parametersBiso mean: 18.2 Å2
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1839 0 24 0 1863
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.21
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.8→2.9 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.357 94 13.4 %
Rwork0.316 591 -
obs--97.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2TOPHCSDX.PRO
X-RAY DIFFRACTION3PARHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.21

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