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- PDB-4cda: Spectroscopically-validated structure of ferric cytochrome c prim... -

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Basic information

Entry
Database: PDB / ID: 4cda
TitleSpectroscopically-validated structure of ferric cytochrome c prime from Alcaligenes xylosoxidans
ComponentsCYTOCHROME C'
KeywordsELECTRON TRANSPORT / RESONANCE RAMAN / VALIDATION / GAS SENSOR / LIGAND DISCRIMINATION / HAEM / HEME
Function / homology
Function and homology information


electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c prime, subgroup / Cytochrome c, class II / Cytochrome c prime / Cytochrome C' / Cytochrome c class II profile. / Cytochrome c/b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Cytochrome c'
Similarity search - Component
Biological speciesACHROMOBACTER XYLOSOXIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKekilli, D. / Dworkowski, F. / Antonyuk, S. / Hough, M.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Fingerprinting Redox and Ligand States in Haemprotein Crystal Structures Using Resonance Raman Spectroscopy.
Authors: Kekilli, D. / Dworkowski, F.S. / Pompidor, G. / Fuchs, M.R. / Andrew, C.R. / Antonyuk, S. / Strange, R.W. / Eady, R.R. / Hasnain, S.S. / Hough, M.A.
History
DepositionOct 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 2.0Mar 11, 2020Group: Advisory / Derived calculations ...Advisory / Derived calculations / Other / Polymer sequence
Category: entity_poly / pdbx_database_status ...entity_poly / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Dec 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4424
Polymers13,6311
Non-polymers8113
Water4,666259
1
A: CYTOCHROME C'
hetero molecules

A: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8848
Polymers27,2632
Non-polymers1,6216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area1820 Å2
ΔGint-49.3 kcal/mol
Surface area13470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.354, 53.354, 180.992
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-2041-

HOH

21A-2117-

HOH

31A-2121-

HOH

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Components

#1: Protein CYTOCHROME C' / CYTOCHROME C PRIME


Mass: 13631.442 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACHROMOBACTER XYLOSOXIDANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00138
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 7.5 / Details: AMMONIUM SULFATE, HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.8
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2012 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.3→46.21 Å / Num. obs: 38076 / % possible obs: 99.1 % / Redundancy: 4.2 % / Biso Wilson estimate: 9.3 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.1 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YLI

2yli


Resolution: 1.3→46.21 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.691 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17935 1932 5.1 %RANDOM
Rwork0.1544 ---
obs0.15567 36137 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.206 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0.35 Å20 Å2
2---0.35 Å20 Å2
3---1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.3→46.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms958 0 53 259 1270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021073
X-RAY DIFFRACTIONr_bond_other_d0.0010.021005
X-RAY DIFFRACTIONr_angle_refined_deg2.0782.0591476
X-RAY DIFFRACTIONr_angle_other_deg0.94132318
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.015141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17124.31844
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65215167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.271156
X-RAY DIFFRACTIONr_chiral_restr0.090.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211300
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02238
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3250.952523
X-RAY DIFFRACTIONr_mcbond_other1.3150.944522
X-RAY DIFFRACTIONr_mcangle_it1.4741.434656
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4230.997550
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr11.38332076
X-RAY DIFFRACTIONr_sphericity_free43.98541
X-RAY DIFFRACTIONr_sphericity_bonded10.28452264
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 153 -
Rwork0.251 2612 -
obs--98.93 %

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