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- PDB-2xle: Cytochrome c prime from Alcaligenes xylosoxidans: Ferrous R124K v... -

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Basic information

Entry
Database: PDB / ID: 2xle
TitleCytochrome c prime from Alcaligenes xylosoxidans: Ferrous R124K variant with bound NO
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 / NITRIC OXIDE / Cytochrome c'
Similarity search - Component
Biological speciesACHROMOBACTER XYLOSOXIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 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 1.3Jul 24, 2019Group: Data collection / Derived calculations
Category: diffrn_source / pdbx_struct_special_symmetry / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Mar 11, 2020Group: Other / Polymer sequence / Category: entity_poly / pdbx_database_status
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf
Revision 2.1Oct 16, 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 / _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)14,3484
Polymers13,6031
Non-polymers7453
Water5,080282
1
A: CYTOCHROME C'
hetero molecules

A: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6968
Polymers27,2072
Non-polymers1,4896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area4310 Å2
ΔGint-86.5 kcal/mol
Surface area13220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.082, 54.082, 181.019
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-2042-

HOH

21A-2122-

HOH

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Components

#1: Protein CYTOCHROME C'


Mass: 13603.429 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-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.81 Å3/Da / Density % sol: 56.2 % / Description: NONE
Crystal growpH: 7.5 / Details: AMMONIUM SULPHATE, HEPES PH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 23, 2007 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.12→37 Å / Num. obs: 57744 / % possible obs: 94.3 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 15.53 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 30.8
Reflection shellResolution: 1.12→1.16 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 7.1 / % possible all: 66.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.12→37 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.133 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.18135 2904 5 %RANDOM
Rwork0.1517 ---
obs0.15319 54614 94.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.729 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0.21 Å20 Å2
2---0.41 Å20 Å2
3---0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.12→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms956 0 50 282 1288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221338
X-RAY DIFFRACTIONr_bond_other_d0.0010.02904
X-RAY DIFFRACTIONr_angle_refined_deg1.8962.0491859
X-RAY DIFFRACTIONr_angle_other_deg1.04232231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4755190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54325.25459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6615221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.284156
X-RAY DIFFRACTIONr_chiral_restr0.1130.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211612
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02270
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_it1.5351.5816
X-RAY DIFFRACTIONr_mcbond_other0.6951.5328
X-RAY DIFFRACTIONr_mcangle_it2.2621315
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8693522
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8274.5529
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.24432242
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.122→1.151 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 165 -
Rwork0.21 2687 -
obs--64.83 %

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