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- PDB-2cua: THE CUA DOMAIN OF CYTOCHROME BA3 FROM THERMUS THERMOPHILUS -

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Basic information

Entry
Database: PDB / ID: 2cua
TitleTHE CUA DOMAIN OF CYTOCHROME BA3 FROM THERMUS THERMOPHILUS
ComponentsPROTEIN (CUA)
KeywordsELECTRON TRANSPORT / CUA CENTER
Function / homology
Function and homology information


cytochrome-c oxidase / cytochrome-c oxidase activity / respirasome / copper ion binding / plasma membrane
Similarity search - Function
Ba3-like heme-copper oxidase subunit II, C-terminal / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / 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-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DINUCLEAR COPPER ION / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsWilliams, P.A. / Blackburn, N.J. / Sanders, D. / Bellamy, H. / Stura, E.A. / Fee, J.A. / Mcree, D.E.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: The CuA domain of Thermus thermophilus ba3-type cytochrome c oxidase at 1.6 A resolution.
Authors: Williams, P.A. / Blackburn, N.J. / Sanders, D. / Bellamy, H. / Stura, E.A. / Fee, J.A. / McRee, D.E.
History
DepositionFeb 18, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 28, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (CUA)
B: PROTEIN (CUA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0186
Polymers29,6332
Non-polymers3854
Water3,351186
1
A: PROTEIN (CUA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0093
Polymers14,8171
Non-polymers1932
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (CUA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0093
Polymers14,8171
Non-polymers1932
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.900, 70.600, 53.500
Angle α, β, γ (deg.)90.00, 98.12, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.0579, -0.444, -0.8942), (0.1911, -0.8742, 0.4465), (-0.9799, -0.1967, 0.0342)
Vector: 10.766, 11.205, 39.655)

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Components

#1: Protein PROTEIN (CUA)


Mass: 14816.730 Da / Num. of mol.: 2 / Fragment: SOLUBLE CUA-CONTAINING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Species (production host): Escherichia coli / Cellular location (production host): PERIPLASM / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P98052, cytochrome-c oxidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE CUA CENTER COMPRISES TWO CU ATOMS DIRECTLY BONDED, ONE IS FORMALLY 1+ AND THE OTHER 2+ ZINC ...THE CUA CENTER COMPRISES TWO CU ATOMS DIRECTLY BONDED, ONE IS FORMALLY 1+ AND THE OTHER 2+ ZINC AIDED CRYSTALLISATION
Sequence detailsTHE PROTEIN CRYSTALLISED COMPRISED RESIDUES 34-168 ALONE.

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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: 2.33 Å3/Da / Density % sol: 46 %
Crystal growpH: 6.5
Details: 0.2-20% MPEG 5K 100MM NA CACODYLATE PH 6.5 1MM ZNCL2
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.UnitCommon nameCrystal-IDSol-IDChemical formula
10.2-20 %mPEG500011
2100 mMsodium cacodylate11
3mM11ZnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.5498,1.3799,1.3780,1.3050,1.0
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54981
21.37991
31.3781
41.3051
511
ReflectionResolution: 1.6→20 Å / Num. obs: 30110 / % possible obs: 92.4 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 10.2
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.093 / Mean I/σ(I) obs: 8.8 / Rsym value: 0.093 / % possible all: 73.2
Reflection
*PLUS
Num. measured all: 119934
Reflection shell
*PLUS
% possible obs: 73.2 %

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Processing

Software
NameVersionClassification
SHELXL-97refinement
XTALVIEWrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.6→50 Å / Num. parameters: 8752 / Cross valid method: THROUGHOUT / σ(F): 0
Details: N TERMINUS MAY BE IN A NON-NATIVE CONFORMATION DETERMINED BY THE CRYSTAL PACKING.
RfactorNum. reflection% reflectionSelection details
Rfree0.2965 -5 %5%
all0.2264 28069 --
obs0.2265 -88.7 %-
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1978 0 6 186 2170
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.338
X-RAY DIFFRACTIONs_zero_chiral_vol0.037
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.046
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.09
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.083
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.226 / Rfactor Rfree: 0.296
Solvent computation
*PLUS
Displacement parameters
*PLUS

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