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- PDB-1lfm: CRYSTAL STRUCTURE OF COBALT(III)-SUBSTITUTED CYTOCHROME C (TUNA) -

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Basic information

Entry
Database: PDB / ID: 1lfm
TitleCRYSTAL STRUCTURE OF COBALT(III)-SUBSTITUTED CYTOCHROME C (TUNA)
ComponentsCYTOCHROME C
KeywordsELECTRON TRANSPORT / CYTOCHROME C / Folding / Intermediates
Function / homology
Function and homology information


respirasome / mitochondrial intermembrane space / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome c, class IA/ IB / 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
PROTOPORPHYRIN IX CONTAINING CO / Cytochrome c
Similarity search - Component
Biological speciesThunnus thynnus (Atlantic bluefin tuna)
MethodX-RAY DIFFRACTION / rigid body refinement / Resolution: 1.5 Å
AuthorsTezcan, F.A. / Findley, W.M. / Crane, B.R. / Ross, S.A. / Lyubovitsky, J.G. / Gray, H.B. / Winkler, J.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Using deeply trapped intermediates to map the cytochrome c folding landscape.
Authors: Tezcan, F.A. / Findley, W.M. / Crane, B.R. / Ross, S.A. / Lyubovitsky, J.G. / Gray, H.B. / Winkler, J.R.
History
DepositionApr 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,0194
Polymers22,7802
Non-polymers1,2392
Water6,738374
1
A: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0102
Polymers11,3901
Non-polymers6201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0102
Polymers11,3901
Non-polymers6201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.175, 74.175, 35.561
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Cell settingtetragonal
Space group name H-MP43

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Components

#1: Protein CYTOCHROME C /


Mass: 11390.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thunnus thynnus (Atlantic bluefin tuna) / Organelle: mitochondriaMitochondrion / References: UniProt: P81459
#2: Chemical ChemComp-COH / PROTOPORPHYRIN IX CONTAINING CO


Mass: 619.575 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32CoN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: (NH4)2SO4, NaCl, Na3PO4, pH 6.4, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal grow
*PLUS
pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
150 mg/mlprotein1drop
270-75 %satammonium sulfate1reservoir
30.75 M1reservoirNaCl
40.1 MNaPi1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 25, 1999 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→15.69 Å / Num. all: 31317 / Num. obs: 27926 / % possible obs: 89.2 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 18.2 Å2 / Rsym value: 0.073 / Net I/σ(I): 17.3
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 2738 / Rsym value: 0.242 / % possible all: 88.4
Reflection
*PLUS
Highest resolution: 1.5 Å / Rmerge(I) obs: 0.073

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Processing

Software
NameClassification
XFITdata reduction
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: rigid body refinement
Starting model: 3CYT

3cyt


Resolution: 1.5→15.69 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2224 8 %RANDOM
Rwork0.183 ---
all0.183 31317 --
obs0.183 27926 89.2 %-
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.5→15.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1600 0 86 374 2060
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d1.36
LS refinement shellResolution: 1.5→1.55 Å / Rfactor Rfree error: 0.024
RfactorNum. reflection% reflection
Rfree0.366 225 -
Rwork0.361 --
obs-2762 88.4 %
Refinement
*PLUS
Highest resolution: 1.5 Å / Rfactor obs: 0.183 / Rfactor Rfree: 0.22 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.36
LS refinement shell
*PLUS
Rfactor Rfree: 0.366 / Rfactor Rwork: 0.361

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