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- PDB-3fop: A Triangular Cytochrome b562 Superstructure Mediated by Ni Coordi... -

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Basic information

Entry
Database: PDB / ID: 3fop
TitleA Triangular Cytochrome b562 Superstructure Mediated by Ni Coordination - Hexagonal Form
ComponentsSoluble cytochrome b562
KeywordsELECTRON TRANSPORT / Four Helix Bundle / 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 / N-1,10-phenanthrolin-5-ylacetamide / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsTezcan, F.A. / Radford, R.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: A superprotein triangle driven by nickel(II) coordination: exploiting non-natural metal ligands in protein self-assembly.
Authors: Radford, R.J. / Tezcan, F.A.
History
DepositionDec 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 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_comp_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.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_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.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Soluble cytochrome b562
B: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,01810
Polymers23,0762
Non-polymers1,9428
Water36020
1
A: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5095
Polymers11,5381
Non-polymers9714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5095
Polymers11,5381
Non-polymers9714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Soluble cytochrome b562
hetero molecules

A: Soluble cytochrome b562
B: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,52715
Polymers34,6143
Non-polymers2,91312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
Unit cell
Length a, b, c (Å)104.897, 104.897, 107.925
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 2 / Auth seq-ID: 1 - 106 / Label seq-ID: 1 - 106

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 11537.963 Da / Num. of mol.: 2 / Mutation: K59C, R62A, H63A, 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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-PXX / N-1,10-phenanthrolin-5-ylacetamide


Mass: 237.257 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H11N3O
#4: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.54 Å3/Da / Density % sol: 65.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG2000, 0.2 M MgCl2, 0.1 M TRIS, 3.3 mM NiCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97607 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2008
Details: Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing)
RadiationMonochromator: Side-scattering cuberoot I-beam bent single crystal; asymetric cut 12.2 degs.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97607 Å / Relative weight: 1
ReflectionResolution: 3→107.833 Å / Num. all: 7479 / Num. obs: 7479 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.1 % / Rmerge(I) obs: 0.151 / Rsym value: 0.151 / Net I/σ(I): 4.7
Reflection shellResolution: 3→3.16 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.2 / Num. measured all: 17168 / Num. unique all: 1053 / Rsym value: 0.6 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QLA

2qla


Resolution: 3→90.91 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.851 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.807 / SU B: 17.171 / SU ML: 0.313 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.428 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 519 7 %RANDOM
Rwork0.221 ---
all0.225 7569 --
obs0.225 7461 99.89 %-
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 max: 63.22 Å2 / Biso mean: 43.31 Å2 / Biso min: 11.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 3→90.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1608 0 126 20 1754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221780
X-RAY DIFFRACTIONr_angle_refined_deg1.4412.1472414
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0645210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.20327.43678
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.52915300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.209154
X-RAY DIFFRACTIONr_chiral_restr0.0890.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021352
X-RAY DIFFRACTIONr_nbd_refined0.2320.2769
X-RAY DIFFRACTIONr_nbtor_refined0.2910.21205
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.251
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.26
X-RAY DIFFRACTIONr_mcbond_it0.5211.51082
X-RAY DIFFRACTIONr_mcangle_it0.93221686
X-RAY DIFFRACTIONr_scbond_it1.2353908
X-RAY DIFFRACTIONr_scangle_it2.1544.5724
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
424TIGHT POSITIONAL0.040.05
380MEDIUM POSITIONAL0.370.5
424TIGHT THERMAL0.070.5
380MEDIUM THERMAL0.552
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 37 -
Rwork0.269 499 -
all-536 -
obs--99.81 %

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