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- PDB-4cdv: Spectroscopically-validated structure of cytochrome c prime from ... -

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Basic information

Entry
Database: PDB / ID: 4cdv
TitleSpectroscopically-validated structure of cytochrome c prime from Alcaligenes xylosoxidans, reduced by X-ray irradiation at 100K
ComponentsCYTOCHROME C'
KeywordsELECTRON TRANSPORT / RESONANCE RAMAN / VALIDATION / GAS SENSOR / LIGAND DISCRIMINATION / FERRIC / HAEM / HEME / RADIOLYSIS
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: 1.17 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
DepositionNov 6, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3463
Polymers13,6311
Non-polymers7152
Water4,270237
1
A: CYTOCHROME C'
hetero molecules

A: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6926
Polymers27,2632
Non-polymers1,4294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area3970 Å2
ΔGint-72.2 kcal/mol
Surface area12870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.281, 53.281, 180.751
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-2029-

HOH

21A-2031-

HOH

31A-2093-

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.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.58 Å3/Da / Density % sol: 52.4 % / 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 14, 2013 / 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: 1.17→46.1 Å / Num. obs: 49558 / % possible obs: 95 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.1
Reflection shellResolution: 1.17→1.24 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 2.6 / % possible all: 69.7

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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: 1.17→46.14 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.849 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.15998 2500 5.1 %RANDOM
Rwork0.13958 ---
obs0.14061 46928 94.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.939 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0.3 Å20 Å2
2---0.3 Å20 Å2
3---0.97 Å2
Refinement stepCycle: LAST / Resolution: 1.17→46.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms949 0 48 237 1234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021134
X-RAY DIFFRACTIONr_bond_other_d0.0010.021052
X-RAY DIFFRACTIONr_angle_refined_deg2.0742.0521568
X-RAY DIFFRACTIONr_angle_other_deg1.25432438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0625152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45224.89849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2315181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.364156
X-RAY DIFFRACTIONr_chiral_restr0.0950.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211355
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02250
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_it0.8770.793553
X-RAY DIFFRACTIONr_mcbond_other0.8610.789552
X-RAY DIFFRACTIONr_mcangle_it1.0641.195703
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.20.885581
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_restr15.81532184
X-RAY DIFFRACTIONr_sphericity_free26.754535
X-RAY DIFFRACTIONr_sphericity_bonded8.00352354
LS refinement shellResolution: 1.173→1.203 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.152 104 -
Rwork0.131 1781 -
obs--50.6 %

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