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- PDB-1qhq: AURACYANIN, A BLUE COPPER PROTEIN FROM THE GREEN THERMOPHILIC PHO... -

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Basic information

Entry
Database: PDB / ID: 1qhq
TitleAURACYANIN, A BLUE COPPER PROTEIN FROM THE GREEN THERMOPHILIC PHOTOSYNTHETIC BACTERIUM CHLOROFLEXUS AURANTIACUS
ComponentsPROTEIN (AURACYANIN)
KeywordsELECTRON TRANSFER / CUPREDOXIN / BLUE COPPER PROTEIN / AZURIN-LIKE / THERMOPHILE
Function / homology
Function and homology information


photosynthetic electron transport chain / electron transfer activity / oxidoreductase activity / copper ion binding / plasma membrane
Similarity search - Function
Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Auracyanin-B
Similarity search - Component
Biological speciesChloroflexus aurantiacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsBond, C.S. / Blankenship, R.E. / Freeman, H.C. / Guss, J.M. / Maher, M. / Selvaraj, F. / Wilce, M.C.J. / Willingham, K.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of auracyanin, a "blue" copper protein from the green thermophilic photosynthetic bacterium Chloroflexus aurantiacus.
Authors: Bond, C.S. / Blankenship, R.E. / Freeman, H.C. / Guss, J.M. / Maher, M.J. / Selvaraj, F.M. / Wilce, M.C. / Willingham, K.M.
History
DepositionMay 25, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Mar 7, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (AURACYANIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7025
Polymers14,4111
Non-polymers2914
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PROTEIN (AURACYANIN)
hetero molecules

A: PROTEIN (AURACYANIN)
hetero molecules

A: PROTEIN (AURACYANIN)
hetero molecules

A: PROTEIN (AURACYANIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,80820
Polymers57,6444
Non-polymers1,16516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_554y,x,-z-2/31
crystal symmetry operation10_664-y+1,-x+1,-z-2/31
Buried area4770 Å2
ΔGint-129 kcal/mol
Surface area21310 Å2
MethodPISA
3
A: PROTEIN (AURACYANIN)
hetero molecules

A: PROTEIN (AURACYANIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,40410
Polymers28,8222
Non-polymers5828
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/31
MethodPQS
Unit cell
Length a, b, c (Å)115.739, 115.739, 54.549
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-142-

CL

21A-143-

SO4

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Components

#1: Protein PROTEIN (AURACYANIN)


Mass: 14410.964 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: GREEN GLIDING THERMOPHILIC PHOTOSYNTHETIC BACTERIUM
Source: (natural) Chloroflexus aurantiacus (bacteria) / Cellular location: PERIPHERAL MEMBRANE PROTEIN / References: UniProt: P27197
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsSO4 S 143 LIES ON A SPECIAL POSITION AND THUS HAS 0.25 OCCUPANCY CL 142 LIES ON A TWO-FOLD AXIS

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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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growpH: 7 / Details: HEPES PH 7.5, 2M LI2SO4, pH 7.0
Crystal grow
*PLUS
pH: 8.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16.5 mg/mlprotein1drop
220 mMTris1drop
310 mM1dropNaCl
4100 mMHEPES1reservoir
52 M1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.7817,1.3050,1.3779,1.3799,1.3876,1.5418
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Sep 1, 1997
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.78171
21.3051
31.37791
41.37991
51.38761
61.54181
ReflectionResolution: 1.55→20 Å / Num. obs: 29884 / % possible obs: 93.5 % / Redundancy: 3 % / Biso Wilson estimate: 15 Å2 / Rsym value: 9.3 / Net I/σ(I): 20
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 4 % / Mean I/σ(I) obs: 4 / Rsym value: 22.5 / % possible all: 98.3
Reflection
*PLUS
Num. measured all: 538869 / Rmerge(I) obs: 0.093
Reflection shell
*PLUS
% possible obs: 98.3 % / Rmerge(I) obs: 0.225

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Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.55→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.233 927 3 %RANDOM
Rwork0.198 ---
obs-28390 98 %-
Displacement parametersBiso mean: 20.5 Å2
Refinement stepCycle: LAST / Resolution: 1.55→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1011 0 12 247 1270
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0180.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0250.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 3 % / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20.5 Å2
LS refinement shell
*PLUS
Rfactor Rfree: 0.285 / Rfactor obs: 0.267

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