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- PDB-3tu6: The Structure of a Pseudoazurin From Sinorhizobium meliltoi -

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Basic information

Entry
Database: PDB / ID: 3tu6
TitleThe Structure of a Pseudoazurin From Sinorhizobium meliltoi
ComponentsPseudoazurin (Blue copper protein)
KeywordsELECTRON TRANSPORT / cupredoxins / beta barrel / electron transfer / redox
Function / homology
Function and homology information


periplasmic space / electron transfer activity / copper ion binding
Similarity search - Function
Pseudoazurin / Amicyanin/Pseudoazurin / Blue (type 1) copper protein, plastocyanin-type / 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 ...Pseudoazurin / Amicyanin/Pseudoazurin / Blue (type 1) copper protein, plastocyanin-type / 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 / Pseudoazurin
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLaming, E.M. / McGrath, A.P. / Guss, J.M. / Maher, M.J.
CitationJournal: J.Inorg.Biochem. / Year: 2012
Title: The X-ray crystal structure of a pseudoazurin from Sinorhizobium meliloti.
Authors: Laming, E.M. / McGrath, A.P. / Guss, J.M. / Kappler, U. / Maher, M.J.
History
DepositionSep 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Dec 19, 2012Group: Database references
Revision 1.3Feb 28, 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_ref_seq_dif / 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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _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: Pseudoazurin (Blue copper protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6133
Polymers13,4581
Non-polymers1562
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.627, 53.494, 59.921
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pseudoazurin (Blue copper protein)


Mass: 13457.520 Da / Num. of mol.: 1 / Fragment: UNP residues 22-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: RM1021 / Gene: azu2, AZU2T, R02830, SMc04047 / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92M26
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG MME 2000, potassium bromide, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2011
RadiationMonochromator: SI VORTEX-ES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 8214 / Num. obs: 8214 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.181 / Χ2: 0.95 / Net I/σ(I): 4.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.077.20.9177880.911100
2.07-2.157.20.6547970.9531100
2.15-2.257.20.6358060.9091100
2.25-2.377.20.5038110.8751100
2.37-2.527.20.48000.9141100
2.52-2.717.10.3098131.0381100
2.71-2.997.10.2128300.9411100
2.99-3.427.10.1378121.0651100
3.42-4.316.90.1078460.9761100
4.31-506.40.0679110.9221100

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30.62 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.905 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.051 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2613 783 9.6 %RANDOM
Rwork0.2019 7346 --
obs0.2075 8129 99.36 %-
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 max: 75.21 Å2 / Biso mean: 28.1554 Å2 / Biso min: 7.02 Å2
Baniso -1Baniso -2Baniso -3
1-4.04 Å20 Å20 Å2
2---2.16 Å20 Å2
3----1.88 Å2
Refinement stepCycle: LAST / Resolution: 2→30.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms931 0 7 63 1001
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.022960
X-RAY DIFFRACTIONr_bond_other_d0.0010.02653
X-RAY DIFFRACTIONr_angle_refined_deg0.811.9761294
X-RAY DIFFRACTIONr_angle_other_deg0.70531609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7915128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.14425.55636
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.41215164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.874153
X-RAY DIFFRACTIONr_chiral_restr0.0480.2140
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211078
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02172
X-RAY DIFFRACTIONr_mcbond_it1.2872628
X-RAY DIFFRACTIONr_mcbond_other0.3162263
X-RAY DIFFRACTIONr_mcangle_it2.1723997
X-RAY DIFFRACTIONr_scbond_it4.8416.5332
X-RAY DIFFRACTIONr_scangle_it7.2848.5296
LS refinement shellResolution: 1.998→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 53 -
Rwork0.282 520 -
all-573 -
obs--99.31 %
Refinement TLS params.Method: refined / Origin x: 0.669 Å / Origin y: 2.397 Å / Origin z: 17.584 Å
111213212223313233
T0.0072 Å20.0097 Å20.0179 Å2-0.0898 Å2-0.0058 Å2--0.0354 Å2
L0.1084 °20.1983 °20.3539 °2-2.6148 °2-0.5337 °2--1.1308 °2
S0.0198 Å °0.0634 Å °0.0182 Å °0.111 Å °0.0136 Å °0.0726 Å °-0.0261 Å °0.0371 Å °-0.0334 Å °

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