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- PDB-2xld: Cytochrome c prime from Alcaligenes xylosoxidans: Ferrous R124Q v... -

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Basic information

Entry
Database: PDB / ID: 2xld
TitleCytochrome c prime from Alcaligenes xylosoxidans: Ferrous R124Q variant
ComponentsCYTOCHROME C'
KeywordsELECTRON TRANSPORT / HAEMOPROTEIN / 4-HELIX BUNDLE
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: 1.4 Å
AuthorsHough, M.A. / Antonyuk, S.V. / Hasnain, S.S.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Distal-to-Proximal No Conversion in Hemoproteins: The Role of the Proximal Pocket.
Authors: Hough, M.A. / Antonyuk, S.V. / Barbieri, S. / Rustage, N. / Mckay, A.L. / Servid, A.E. / Eady, R.R. / Andrew, C.R. / Hasnain, S.S.
History
DepositionJul 20, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 11, 2020Group: Derived calculations / Other / Polymer sequence / Category: entity_poly / pdbx_database_status / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4134
Polymers13,6021
Non-polymers8113
Water2,486138
1
A: CYTOCHROME C'
hetero molecules

A: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8268
Polymers27,2052
Non-polymers1,6216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area4030 Å2
ΔGint-86.9 kcal/mol
Surface area12080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.230, 53.230, 181.510
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-2017-

HOH

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Components

#1: Protein CYTOCHROME C'


Mass: 13602.377 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACHROMOBACTER XYLOSOXIDANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / 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.: 138 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 124 TO GLN
Has protein modificationY
Sequence detailsR124Q MUTATION

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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: 2.73 Å3/Da / Density % sol: 54.9 % / Description: NONE
Crystal growpH: 7.4 / Details: AMMONIUM SULPHATE, HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.8
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.4→45 Å / Num. obs: 31045 / % possible obs: 95 % / Redundancy: 7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 19
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 3 / % possible all: 84.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0106refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→44.68 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.628 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21966 1242 4 %RANDOM
Rwork0.18681 ---
obs0.18813 29802 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.836 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å2-0.51 Å20 Å2
2---1.01 Å20 Å2
3---1.52 Å2
Refinement stepCycle: LAST / Resolution: 1.4→44.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms916 0 53 138 1107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221033
X-RAY DIFFRACTIONr_bond_other_d0.0030.02670
X-RAY DIFFRACTIONr_angle_refined_deg2.1072.0891427
X-RAY DIFFRACTIONr_angle_other_deg1.11231630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4655136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.62725.12839
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97915148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.982153
X-RAY DIFFRACTIONr_chiral_restr0.1230.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211195
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02198
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_it2.4371.5646
X-RAY DIFFRACTIONr_mcbond_other1.0151.5262
X-RAY DIFFRACTIONr_mcangle_it3.47821026
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.8443387
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.5154.5397
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.9431703
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 89 -
Rwork0.29 2141 -
obs--100 %

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