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- PDB-1e84: Cytochrome c' from Alcaligenes xylosoxidans - reduced structure -

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Basic information

Entry
Database: PDB / ID: 1.0E+84
TitleCytochrome c' from Alcaligenes xylosoxidans - reduced structure
ComponentsCYTOCHROME C'
KeywordsELECTRON TRANSPORT / CYTOCHROME / HEME / 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 speciesALCALIGENES XYLOSOXIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLawson, D.M. / Stevenson, C.E.M. / Andrew, C.R. / Eady, R.R.
Citation
Journal: Embo J. / Year: 2000
Title: Unprecedented Proximal Binding of Nitric Oxide to Heme: Implications for Guanylate Cyclase
Authors: Lawson, D.M. / Stevenson, C.E.M. / Andrew, C.R. / Eady, R.R.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Three-Dimensional Structure of Cytochrome C' from Two Alcaligenes Species and the Implications for Four-Helix Bundle Structures.
Authors: Dobbs, A.J. / Anderson, B.F. / Faber, H.R. / Baker, E.N.
History
DepositionSep 15, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2000Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 23, 2019Group: Data collection / Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_ref_seq_dif.details
Revision 2.0Mar 11, 2020Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Dec 13, 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
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)14,2502
Polymers13,6311
Non-polymers6191
Water2,414134
1
A: CYTOCHROME C'
hetero molecules

A: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5004
Polymers27,2632
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area2890 Å2
ΔGint-15.2 kcal/mol
Surface area14660 Å2
MethodPQS
Unit cell
Length a, b, c (Å)52.819, 52.819, 182.602
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein CYTOCHROME C'


Mass: 13631.442 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: FORMERLY KNOWN AS ALCALIGENES SP. / Source: (natural) ALCALIGENES XYLOSOXIDANS (bacteria) / Cellular location: PERIPLASM / Strain: NCIB 11015 / References: UniProt: P00138
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCYTOCHROME C' IS THE MOST WIDELY OCCURRING BACTERIAL C-TYPE CYTOCHROME. CYTOCHROMES C'
Has protein modificationY
Sequence detailsN-TERMINAL RESIDUE IS PYRROLIDONE CARBOXYLIC ACID (PCA)

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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: 2.71 Å3/Da / Density % sol: 54.3 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP VAPOUR DIFFUSION. PROTEIN AT CONCENTRATION 8 MG/ML WAS MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION CONSISTING OF 55-65% SATURATED AMMONIUM SULFATE IN 100 MM HEPES BUFFER AT PH 7. ...Details: HANGING DROP VAPOUR DIFFUSION. PROTEIN AT CONCENTRATION 8 MG/ML WAS MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION CONSISTING OF 55-65% SATURATED AMMONIUM SULFATE IN 100 MM HEPES BUFFER AT PH 7.5. REDUCED USING MOTHER LIQUOR CONTAINING 20 MM SODIUM DITHIONITE.
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
220 mMTris-HCl1drop
355-65 %satammonium sulfate1reservoir
4100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Jan 15, 2000 / Details: MIRRORS
RadiationMonochromator: DIAMOND C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 12387 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 31.6
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 8.3 / % possible all: 84.5
Reflection shell
*PLUS
% possible obs: 84.5 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CGO

1cgo


Resolution: 1.9→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.16
Details: FE ATOM OF HEME REFINED WITH ANISOTROPIC THERMAL PARAMETERS
RfactorNum. reflection% reflectionSelection details
Rfree0.273 597 5 %RANDOM
Rwork0.217 ---
obs-12387 97.1 %-
Displacement parametersBiso mean: 22 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms931 0 43 134 1108
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0330.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0370.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.043
X-RAY DIFFRACTIONp_mcangle_it3.2555
X-RAY DIFFRACTIONp_scbond_it5.5166
X-RAY DIFFRACTIONp_scangle_it6.1568
X-RAY DIFFRACTIONp_plane_restr0.03060.04
X-RAY DIFFRACTIONp_chiral_restr0.1270.15
X-RAY DIFFRACTIONp_singtor_nbd0.1720.3
X-RAY DIFFRACTIONp_multtor_nbd0.2660.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1740.3
X-RAY DIFFRACTIONp_planar_tor57
X-RAY DIFFRACTIONp_staggered_tor13.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor27.520
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS

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