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- PDB-3c62: Tetrameric Cytochrome cb562 (H59/D62/H63/H73/A74/H77) Assembly St... -

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Basic information

Entry
Database: PDB / ID: 3c62
TitleTetrameric Cytochrome cb562 (H59/D62/H63/H73/A74/H77) Assembly Stabilized by Interprotein Zinc Coordination
ComponentsSoluble cytochrome b562
KeywordsELECTRON TRANSPORT / 16-helix bundle / interfacial Zn-coordination / Heme / Iron / Metal-binding / 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 / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.87 Å
AuthorsTezcan, F.A. / Salgado, E.N. / Lewis, R.A. / Faraone-Mennella, J.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: Metal-mediated self-assembly of protein superstructures: influence of secondary interactions on protein oligomerization and aggregation.
Authors: Salgado, E.N. / Lewis, R.A. / Faraone-Mennella, J. / Tezcan, F.A.
History
DepositionFeb 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: Soluble cytochrome b562
D: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,48817
Polymers46,5604
Non-polymers2,92813
Water9,116506
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10080 Å2
ΔGint-272 kcal/mol
Surface area19360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)47.968, 90.133, 49.357
Angle α, β, γ (deg.)90.000, 109.640, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 11640.037 Da / Num. of mol.: 4 / Mutation: K59H, R62D, D73H, D74A, 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


Mass: 18.015 Da / Num. of mol.: 506 / 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: 2.16 Å3/Da / Density % sol: 43.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 11% PEG 400, 100 mM CaCl2, 100 mM TRIS, 2 mM ZnCl2, pH 7.5, 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: APEX II CCD / Detector: CCD / Date: Sep 14, 2007 / Details: microcapillary collimator
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 38708 / Num. obs: 36614 / % possible obs: 94.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.46 % / Biso Wilson estimate: 10.7 Å2 / Rmerge(I) obs: 0.168 / Rsym value: 0.168 / Net I/σ(I): 6.95
Reflection shellResolution: 1.85→1.89 Å / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.56 / Rsym value: 0.63 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
APEXdata collection
SAINTdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2BC5

2bc5


Resolution: 1.87→25.23 Å / FOM work R set: 0.83 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.273 2273 7 %random
Rwork0.231 ---
obs0.273 32566 99.6 %-
all-32689 --
Solvent computationBsol: 61.549 Å2
Displacement parametersBiso mean: 12.52 Å2
Baniso -1Baniso -2Baniso -3
1-2.015 Å20 Å2-1.24 Å2
2--1.987 Å20 Å2
3----4.002 Å2
Refinement stepCycle: LAST / Resolution: 1.87→25.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3252 0 181 506 3939
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it0.8942
X-RAY DIFFRACTIONc_scbond_it1.6563
X-RAY DIFFRACTIONc_mcangle_it1.3312.5
X-RAY DIFFRACTIONc_scangle_it2.3133.5
LS refinement shellResolution: 1.87→1.88 Å /
RfactorNum. reflection
Rfree0.312 48
Rwork0.231 -
obs-709
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3param19x.heme
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param

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