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- PDB-3hb3: High resolution crystal structure of Paracoccus denitrificans cyt... -

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Basic information

Entry
Database: PDB / ID: 3hb3
TitleHigh resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase
Components
  • (ANTIBODY FV FRAGMENT) x 2
  • (Cytochrome c oxidase subunit ...) x 2
KeywordsOXIDOREDUCTASE / Electron transfer / Proton transfer / Proton pumping / Membrane protein / Cell inner membrane / Cell membrane / Copper / Disulfide bond / Electron transport / Heme / Hydrogen ion transport / Ion transport / Iron / Membrane / Metal-binding / Respiratory chain / Transmembrane / Transport / Pyrrolidone carboxylic acid
Function / homology
Function and homology information


respiratory chain complex IV / cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / immunoglobulin complex / electron transport coupled proton transport / immunoglobulin mediated immune response / antigen binding / ATP synthesis coupled electron transport / respiratory electron transport chain ...respiratory chain complex IV / cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / immunoglobulin complex / electron transport coupled proton transport / immunoglobulin mediated immune response / antigen binding / ATP synthesis coupled electron transport / respiratory electron transport chain / adaptive immune response / immune response / copper ion binding / heme binding / extracellular region / 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 / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / 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 / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COPPER (I) ION / HEME-A / : / HYDROGEN PEROXIDE / 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: 2.25 Å
AuthorsKoepke, J. / Angerer, H. / Peng, G.
CitationJournal: Biochim.Biophys.Acta / Year: 2009
Title: High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase: New insights into the active site and the proton transfer pathways
Authors: Koepke, J. / Olkhova, E. / Angerer, H. / Muller, H. / Peng, G. / Michel, H.
History
DepositionMay 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 27, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / pdbx_entry_details ...chem_comp_atom / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_chiral
Item: _chem_comp_atom.pdbx_stereo_config

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c oxidase subunit 1-beta
B: Cytochrome c oxidase subunit 2
C: ANTIBODY FV FRAGMENT
D: ANTIBODY FV FRAGMENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,10436
Polymers122,6364
Non-polymers11,46832
Water9,980554
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28690 Å2
ΔGint-146 kcal/mol
Surface area37820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.403, 150.473, 157.185
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: 62486.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Gene: ctaDII / 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) / Gene: ctaC, coiI, ctaB / Production host: Escherichia coli (E. coli) / References: UniProt: P08306, cytochrome-c oxidase

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Antibody , 2 types, 2 molecules CD

#3: Antibody ANTIBODY FV FRAGMENT


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 ANTIBODY FV FRAGMENT


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, 14 molecules

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


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 7 types, 572 molecules

#5: Chemical ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#6: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#7: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#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.: 10 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#11: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / 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: 4.02 Å3/Da / Density % sol: 69.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5.5
Details: 25% glycerol, pH 5.5, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9198 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 4, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 2.25→111.8 Å / Num. all: 90709 / Num. obs: 90709 / % possible obs: 99.04 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 14.2
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 3.2 / % possible all: 98.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
EPMRphasing
REFMAC5.1.24refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AR1

1ar1


Resolution: 2.25→19.98 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.89 / SU B: 7.585 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.209 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27996 2819 3 %RANDOM
Rwork0.21836 ---
all0.22024 90709 --
obs0.22024 90709 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.272 Å2
Refinement stepCycle: LAST / Resolution: 2.25→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7956 0 883 554 9393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0219217
X-RAY DIFFRACTIONr_angle_refined_deg2.6831.95612425
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.79551003
X-RAY DIFFRACTIONr_chiral_restr0.230.21419
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.026381
X-RAY DIFFRACTIONr_nbd_refined0.2640.25033
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2340.2598
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3230.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3130.28
X-RAY DIFFRACTIONr_mcbond_it1.3811.55040
X-RAY DIFFRACTIONr_mcangle_it2.40728088
X-RAY DIFFRACTIONr_scbond_it3.53834134
X-RAY DIFFRACTIONr_scangle_it5.1664.54331
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.427 194
Rwork0.369 6525
obs-6525

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