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- PDB-3de9: Crystal Structure of a Trimeric Cytochrome cb562 Assembly Induced... -

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Basic information

Entry
Database: PDB / ID: 3de9
TitleCrystal Structure of a Trimeric Cytochrome cb562 Assembly Induced by Nickel Coordination
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / Ni-stabilized trimeric superstructure / Electron transport / Heme / Iron / Metal-binding / Periplasm / Transport
Function / homology
Function and homology information


electron transfer activity / periplasmic space / iron ion binding / heme binding
Similarity search - Function
Cytochrome c/b562 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NICKEL (II) ION / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsSalgado, E.N. / Lewis, R.A. / Rheingold, A.L. / Tezcan, F.A.
CitationJournal: Inorg.Chem. / Year: 2009
Title: Control of protein oligomerization symmetry by metal coordination: C2 and C3 symmetrical assemblies through Cu(II) and Ni(II) coordination.
Authors: Salgado, E.N. / Lewis, R.A. / Mossin, S. / Rheingold, A.L. / Tezcan, F.A.
History
DepositionJun 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 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: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5195
Polymers11,7261
Non-polymers7934
Water99155
1
A: Soluble cytochrome b562
hetero molecules

A: Soluble cytochrome b562
hetero molecules

A: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,55615
Polymers35,1783
Non-polymers2,37812
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area6110 Å2
ΔGint-140 kcal/mol
Surface area15660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.042, 51.042, 121.971
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-107-

NI

21A-108-

NI

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Components

#1: Protein Soluble cytochrome b562 / Cytochrome b-562


Mass: 11726.153 Da / Num. of mol.: 1 / Mutation: K59H, D73H, K77H, R98C, Y101C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABE7
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.61 Å3/Da / Density % sol: 52.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris, 23% PEG 4000, 4.16 mM NiSO4, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å
DetectorType: Bruker Apex II / Detector: CCD / Date: Mar 2, 2008
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 7513 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rsym value: 0.065
Reflection shellResolution: 2.04→2.14 Å / Redundancy: 3.1 % / Num. unique all: 970 / Rsym value: 0.492 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
APEXdata collection
SAINTdata reduction
SADABSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→25.52 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.903 / SU B: 6.385 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27806 519 7 %RANDOM
Rwork0.21735 ---
obs0.22172 6918 99.11 %-
all-7499 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.472 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.05 Å20 Å2
2--0.09 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.04→25.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms819 0 46 55 920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.022884
X-RAY DIFFRACTIONr_bond_other_d0.0010.02763
X-RAY DIFFRACTIONr_angle_refined_deg1.9182.1141201
X-RAY DIFFRACTIONr_angle_other_deg1.00231791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8485105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.56526.66742
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.88515154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.339153
X-RAY DIFFRACTIONr_chiral_restr0.1180.2125
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02978
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02137
X-RAY DIFFRACTIONr_nbd_refined0.2390.2248
X-RAY DIFFRACTIONr_nbd_other0.1760.2790
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2417
X-RAY DIFFRACTIONr_nbtor_other0.0960.2479
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.235
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3120.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.24
X-RAY DIFFRACTIONr_mcbond_it1.3111.5681
X-RAY DIFFRACTIONr_mcbond_other0.2651.5213
X-RAY DIFFRACTIONr_mcangle_it1.5472845
X-RAY DIFFRACTIONr_scbond_it2.8293404
X-RAY DIFFRACTIONr_scangle_it3.8984.5354
LS refinement shellResolution: 2.04→2.096 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 38 -
Rwork0.259 513 -
obs--99.28 %

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