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- PDB-1ov8: Auracyanin B structure in space group, P65 -

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Basic information

Entry
Database: PDB / ID: 1ov8
TitleAuracyanin B structure in space group, P65
ComponentsAuracyanin B
KeywordsELECTRON TRANSPORT
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLee, M. / Maher, M.J. / Freeman, H.C. / Guss, J.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Auracyanin B structure in space group P6(5).
Authors: Lee, M. / Maher, M.J. / Freeman, H.C. / Guss, J.M.
History
DepositionMar 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Aug 16, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Auracyanin B
B: Auracyanin B
C: Auracyanin B
D: Auracyanin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,44915
Polymers57,6444
Non-polymers80511
Water10,070559
1
A: Auracyanin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6064
Polymers14,4111
Non-polymers1953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Auracyanin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6674
Polymers14,4111
Non-polymers2563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: Auracyanin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6064
Polymers14,4111
Non-polymers1953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: Auracyanin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5713
Polymers14,4111
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
C: Auracyanin B
D: Auracyanin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1777
Polymers28,8222
Non-polymers3555
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-46 kcal/mol
Surface area11270 Å2
MethodPISA
6
A: Auracyanin B
B: Auracyanin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2738
Polymers28,8222
Non-polymers4516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-50 kcal/mol
Surface area11390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.885, 115.885, 108.149
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
Auracyanin B / Ac-B


Mass: 14410.964 Da / Num. of mol.: 4 / Fragment: N-terminal soluble domain / Source method: isolated from a natural source / Details: Thermophilic green photosynthetic bacterium / Source: (natural) Chloroflexus aurantiacus (bacteria) / References: UniProt: P27197
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 559 / 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: 3.21 Å3/Da / Density % sol: 61.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.25 M Lithium sulfate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
19 mg/mlprotein1drop
20.1 MHEPES1reservoirpH7.5
32.25 M1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 64839 / Num. obs: 64839 / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 16.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 2.5 / % possible all: 96.8
Reflection
*PLUS
Num. obs: 63349 / % possible obs: 97.7 % / Num. measured all: 458718
Reflection shell
*PLUS
% possible obs: 96.8 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QHQ

1qhq


Resolution: 1.9→26.13 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.369 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21916 3227 5.1 %RANDOM
Rwork0.19189 ---
obs0.19327 60113 97.74 %-
all-64834 --
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: 15.424 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20.19 Å20 Å2
2--0.38 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.9→26.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4040 0 31 559 4630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0214168
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.9355758
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1373552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.81115612
X-RAY DIFFRACTIONr_chiral_restr0.1020.2676
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023288
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2390.32047
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.5642
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2630.377
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.558
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.3661.52780
X-RAY DIFFRACTIONr_mcangle_it1.82524480
X-RAY DIFFRACTIONr_scbond_it3.3631388
X-RAY DIFFRACTIONr_scangle_it4.5664.51278
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.296 235
Rwork0.275 4332
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0998-2.8322-0.05366.97610.29641.80590.55010.60870.1886-0.6917-0.5284-0.3358-0.03510.1951-0.02160.23970.16790.02580.19130.08420.109313.953792.77140.0101
23.0529-1.6568-0.09052.84560.42512.9842-0.0868-0.02430.10490.04180.05670.0399-0.18050.08550.03010.13250.081-0.05840.06850.00720.12330.180465.59155.119
33.531-2.9972-0.19686.25920.0531.6672-0.267-0.19990.18371.0560.283-0.3083-0.14970.144-0.0160.3530.1011-0.07920.08740.01420.103529.400366.030759.6191
41.5836-0.7304-0.33864.3780.26622.86570.0207-0.0219-0.0852-0.0799-0.0581-0.06550.01140.21160.03730.15430.06490.02660.05060.04690.117713.966593.668154.5087
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1402 - 140
2X-RAY DIFFRACTION2BB2 - 1402 - 140
3X-RAY DIFFRACTION3CC2 - 1402 - 140
4X-RAY DIFFRACTION4DD2 - 1402 - 140
Software
*PLUS
Version: 5.1.24 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.219 / Rfactor Rwork: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.58

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