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- PDB-1foc: Cytochrome C557: improperly folded thermus thermophilus C552 -

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Basic information

Entry
Database: PDB / ID: 1foc
TitleCytochrome C557: improperly folded thermus thermophilus C552
ComponentsCYTOCHROME RC557
KeywordsELECTRON TRANSPORT / cytochrome c / Thermus thermophilus / heme inversion
Function / homology
Function and homology information


electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Cytochrome c-552 / Cytochrome c-552
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsMcRee, D.E. / Williams, P.A. / Fee, J.A. / Bren, K.L.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Recombinant cytochrome rC557 obtained from Escherichia coli cells expressing a truncated Thermus thermophilus cycA gene. Heme inversion in an improperly matured protein
Authors: McRee, D.E. / Williams, P.A. / Sridhar, V. / Pastuszyn, A. / Bren, K.L. / Chen, Y. / Patel, K.M. / Todaro, T.R. / Sanders, D. / Luna, E. / Fee, J.A.
#1: Journal: To be published
Title: Integrity of thermus thermophilus cytochrome C552 synthesized by Escherichia coli cells expressing the host-specific cytochrome C maturation genes, CCMABCDEFGH: biochemical, spectral and ...Title: Integrity of thermus thermophilus cytochrome C552 synthesized by Escherichia coli cells expressing the host-specific cytochrome C maturation genes, CCMABCDEFGH: biochemical, spectral and structural characterization of the recombinant protein
Authors: Sridhar, V. / Pastuszyn, A. / Patel, K.M. / Chen, Y. / Todaro, T.R.
History
DepositionAug 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation / Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / Item: _exptl_crystal_grow.temp
Revision 2.0Mar 3, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME RC557
B: CYTOCHROME RC557
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7684
Polymers28,5312
Non-polymers1,2372
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-68 kcal/mol
Surface area12310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.720, 69.050, 36.582
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a dimer constructed from chains A and B

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Components

#1: Protein CYTOCHROME RC557


Mass: 14265.653 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: HEME INVERSION / Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: PET17B / Production host: Escherichia coli (E. coli) / References: UniProt: P04164, UniProt: Q5SME3*PLUS
#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4

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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: 2.18 Å3/Da / Density % sol: 43.71 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 42-46% MPEG 2K (w/v), 0.1M Na cacodylate pH 7.0, 50mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 24K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSSRL BL9-211.7389
SYNCHROTRONSSRL BL9-221.4586
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEJan 10, 2000
MARRESEARCH2IMAGE PLATEJan 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.73891
21.45861
ReflectionResolution: 3→40 Å / Num. all: 77124 / Num. obs: 5309 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 114 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 7.2
Reflection shellResolution: 3→3.08 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.526 / % possible all: 89.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
XTALVIEWrefinement
CNS0.9refinement
CCP4(SCALA)data scaling
RefinementResolution: 3→40 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection
Rfree0.4232 -
Rwork0.2728 -
all-5278
obs-5278
Refinement stepCycle: LAST / Resolution: 3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 86 0 2030

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