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- PDB-2aan: Auracyanin A: A "blue" copper protein from the green thermophilic... -

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Basic information

Entry
Database: PDB / ID: 2aan
TitleAuracyanin A: A "blue" copper protein from the green thermophilic photosynthetic bacterium,chloroflexus aurantiacus
Componentsauracyanin A
KeywordsELECTRON TRANSPORT / CUPREDOXIN fold
Function / homology
Function and homology information


photosynthetic electron transport chain / electron transfer activity / oxidoreductase activity / copper ion binding / plasma membrane
Similarity search - Function
: / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Auracyanin-A
Similarity search - Component
Biological speciesChloroflexus aurantiacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLee, M. / Guss, J.M. / Freeman, H.C.
CitationJournal: to be published
Title: The Crystal Structure of Auracyanin A at 1.85 A Resolution: Why the Photosynthetic Bacterium Chloroflexus Needs Two Almost Identical 'Blue' Copper Proteins
Authors: Lee, M. / Guss, J.M. / Freeman, H.C.
History
DepositionJul 13, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 11, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 23, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.5Mar 13, 2024Group: 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
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: auracyanin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1714
Polymers13,9151
Non-polymers2563
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: auracyanin A
hetero molecules

A: auracyanin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3428
Polymers27,8312
Non-polymers5116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area1580 Å2
ΔGint-53 kcal/mol
Surface area10580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.578, 70.578, 45.665
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-149-

HOH

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Components

#1: Protein auracyanin A


Mass: 13915.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloroflexus aurantiacus (bacteria) / Plasmid: pRSETA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8RMH6
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 38.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: Lithium sulfate, sodium citrate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 0.96868 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 7, 2004
RadiationMonochromator: Sillicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96868 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 9667 / Num. obs: 9667 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.8 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.086
Reflection shellResolution: 1.85→1.898 Å / Redundancy: 10 % / Rmerge(I) obs: 0.32 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: auracyanin B

Resolution: 1.85→18 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.253 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20703 465 4.8 %RANDOM
Rwork0.16217 ---
all0.16436 9667 --
obs0.16436 9202 93.85 %-
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: 16.993 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20 Å2
2--0.49 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.85→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms901 0 11 92 1004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022926
X-RAY DIFFRACTIONr_bond_other_d0.0010.02826
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.9651266
X-RAY DIFFRACTIONr_angle_other_deg0.79231932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0175122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71626.66736
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.95915139
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.031151
X-RAY DIFFRACTIONr_chiral_restr0.10.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021041
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02159
X-RAY DIFFRACTIONr_nbd_refined0.1970.2170
X-RAY DIFFRACTIONr_nbd_other0.1680.2778
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2462
X-RAY DIFFRACTIONr_nbtor_other0.0860.2571
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.258
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1040.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.226
X-RAY DIFFRACTIONr_mcbond_it4.3934768
X-RAY DIFFRACTIONr_mcbond_other1.384253
X-RAY DIFFRACTIONr_mcangle_it4.5026977
X-RAY DIFFRACTIONr_scbond_it5.1244364
X-RAY DIFFRACTIONr_scangle_it7.4876289
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 32 -
Rwork0.196 709 -
obs--99.33 %
Refinement TLS params.Method: refined / Origin x: 14.8724 Å / Origin y: 43.8968 Å / Origin z: 2.2029 Å
111213212223313233
T-0.0315 Å2-0.0169 Å2-0.0002 Å2--0.013 Å2-0.0173 Å2---0.0102 Å2
L0.6365 °20.152 °2-0.0371 °2-0.4497 °20.2101 °2--0.9222 °2
S0.0094 Å °-0.026 Å °-0.0071 Å °0.0163 Å °0.0593 Å °-0.0628 Å °-0.0512 Å °0.0563 Å °-0.0687 Å °

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