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- PDB-3ehb: A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytoc... -

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Basic information

Entry
Database: PDB / ID: 3ehb
TitleA D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome c Oxidase by Altering the side chain orientation of a distant, conserved Glutamate
Components
  • (Cytochrome c oxidase subunit ...) x 2
  • (FV fragment Chain ...) x 2
KeywordsOXIDOREDUCTASE/IMMUNE SYSTEM / proton pumping / water chain / electron transfer / Cell inner membrane / Cell membrane / Copper / Electron transport / Heme / Hydrogen ion transport / Ion transport / Iron / Membrane / Metal-binding / Oxidoreductase / Respiratory chain / Transmembrane / Transport / Pyrrolidone carboxylic acid / OXIDOREDUCTASE-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


respiratory chain complex IV / oxidative phosphorylation / cytochrome-c oxidase / cytochrome-c oxidase activity / immunoglobulin complex / electron transport coupled proton transport / immunoglobulin mediated immune response / : / antigen binding / respiratory electron transport chain ...respiratory chain complex IV / oxidative phosphorylation / cytochrome-c oxidase / cytochrome-c oxidase activity / immunoglobulin complex / electron transport coupled proton transport / immunoglobulin mediated immune response / : / antigen binding / respiratory electron transport chain / electron transport chain / adaptive immune response / immune response / copper ion binding / heme binding / extracellular space / metal ion binding / plasma membrane
Similarity search - Function
Cytochrome c oxidase, subunit I bacterial type / Helix Hairpins - #90 / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit II / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / : ...Cytochrome c oxidase, subunit I bacterial type / Helix Hairpins - #90 / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit II / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / : / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / : / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Helix Hairpins / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / HEME-A / PEROXIDE ION / Ig kappa chain V-V region MOPC 149 / Cytochrome c oxidase subunit 2 / Ig heavy chain V region 5-84 / Cytochrome c oxidase subunit 1-beta
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsKoepke, J. / Mueller, H. / Peng, G.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: A d-pathway mutation decouples the paracoccusdenitrificans cytochrome C oxidase by altering the side-chain orientation of a distant conserved glutamate
Authors: Durr, K.L. / Koepke, J. / Hellwig, P. / Muller, H. / Angerer, H. / Peng, G. / Olkhova, E. / Richter, O.-M.H. / Ludwig, B. / Michel, H.
History
DepositionSep 12, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / pdbx_validate_chiral
Revision 1.5Oct 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 oxidase subunit 1-beta
B: Cytochrome c oxidase subunit 2
C: FV fragment Chain H
D: FV fragment Chain L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,82233
Polymers122,6374
Non-polymers10,18529
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26240 Å2
ΔGint-154 kcal/mol
Surface area38390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.461, 151.332, 157.487
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Cytochrome c oxidase subunit ... , 2 types, 2 molecules AB

#1: Protein Cytochrome c oxidase subunit 1-beta / Cytochrome c oxidase polypeptide I-beta / Cytochrome aa3 subunit 1-beta


Mass: 62487.629 Da / Num. of mol.: 1 / Fragment: UNP residues 17-545 / Mutation: N131D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P98002, cytochrome-c oxidase
#2: Protein Cytochrome c oxidase subunit 2 / Cytochrome c oxidase polypeptide II / Cytochrome aa3 subunit 2 / Oxidase aa(3) subunit 2


Mass: 32563.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P08306, cytochrome-c oxidase

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Antibody , 2 types, 2 molecules CD

#3: Antibody FV fragment Chain H


Mass: 14324.923 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P18525*PLUS
#4: Antibody FV fragment Chain L


Mass: 13260.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P01636*PLUS

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Sugars , 1 types, 12 molecules

#10: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 7 types, 396 molecules

#5: Chemical ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#6: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#9: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#11: Chemical ChemComp-PER / PEROXIDE ION


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.1 Å3/Da / Density % sol: 70.03 %
Description: 25% (v/v) glycerol was used as cryoprotectant to flash freeze in a gaseous liquid nitrogen cooled stream
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: MPEG 2000 is contained in the crystallization buffer pH 5.5, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.92021 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 16, 2006
RadiationMonochromator: double mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92021 Å / Relative weight: 1
ReflectionResolution: 2.32→20 Å / Num. all: 87146 / Num. obs: 87146 / % possible obs: 98.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 51.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.14
Reflection shellResolution: 2.32→2.4 Å / Mean I/σ(I) obs: 3.93 / Num. unique all: 8161 / % possible all: 97

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
DMmodel building
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AR1

1ar1


Resolution: 2.32→19.69 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.594 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.208 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Due to a feature in the refinement program, the structure was refined with OXT on one or more residues that are not the terminal residues of the sequence. In all these instances the OXT was ...Details: Due to a feature in the refinement program, the structure was refined with OXT on one or more residues that are not the terminal residues of the sequence. In all these instances the OXT was changed to N of the next residue
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 2623 3 %RANDOM
Rwork0.20505 ---
all0.20618 86853 --
obs0.20618 84230 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 60.153 Å2
Refinement stepCycle: LAST / Resolution: 2.32→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7954 0 703 379 9036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0228944
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4882.0212142
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.70951003
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.70523.353343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.058151240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.4981526
X-RAY DIFFRACTIONr_chiral_restr0.1820.21348
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026376
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2510.24472
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3260.25956
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2465
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1840.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.050.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.38545189
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.88268089
X-RAY DIFFRACTIONr_scbond_it4.24345284
X-RAY DIFFRACTIONr_scangle_it5.77364049
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.318→2.377 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 157 -
Rwork0.224 5935 -
obs--100 %

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