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- PDB-2ux6: Pseudoazurin with engineered amicyanin ligand loop, oxidized form... -

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Basic information

Entry
Database: PDB / ID: 2ux6
TitlePseudoazurin with engineered amicyanin ligand loop, oxidized form, pH 7.5
ComponentsPSEUDOAZURIN
KeywordsELECTRON TRANSPORT / TYPE-1 COPPER / METAL-BINDING / REDOX POTENTIAL / COPPER / TRANSPORT / CUPREDOXIN / PERIPLASMIC / SPECTROSCOPIC PROPERTIES / LOOP SHORTENING / PROTEIN SCAFFOLD / ELECTRON TRANSFER
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 speciesACHROMOBACTER CYCLOCLASTES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsVelarde, M. / Huber, R. / Yanagisawa, S. / Dennison, C. / Messerschmidt, A.
CitationJournal: Biochemistry / Year: 2007
Title: Influence of Loop Shortening on the Metal Binding Site of Cupredoxin Pseudoazurin.
Authors: Velarde, M. / Huber, R. / Yanagisawa, S. / Dennison, C. / Messerschmidt, A.
History
DepositionMar 27, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PSEUDOAZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0604
Polymers12,8691
Non-polymers1913
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)105.627, 105.626, 57.925
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein PSEUDOAZURIN / BLUE COPPER PROTEIN


Mass: 12868.755 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE C-TERMINAL LIGAND-BINDING LOOP BETWEEN H81 AND M86 HAS BEEN REPLACED BY THE RESPECTIVE SHORTER LOOP OF AMICYANIN
Source: (gene. exp.) ACHROMOBACTER CYCLOCLASTES (bacteria) / Organ: PERIPLASM / Plasmid: PTRCPAZAMI, PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P19567
#2: Chemical ChemComp-CU / COPPER (II) ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE CONTAINS THE SIGNAL PEPTIDE SEQUENCE. THE MATURE SEQUENCE STARTS AT A29 AND HAS 124 ...THIS SEQUENCE CONTAINS THE SIGNAL PEPTIDE SEQUENCE. THE MATURE SEQUENCE STARTS AT A29 AND HAS 124 AMINO ACID REDIDUES.

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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: 2.04 Å3/Da / Density % sol: 39.16 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP VAPOR DIFFUSION METHOD, MIXING 1MICRO-L OF PROTEIN (20 MG/ML IN 50 MM TRIS/HCL, PH 7.5 PLUS 30 MM NACL) WITH 1 MICRO-L RESERVOIR SOLUTION (10 MM TRIS/HCL, PH 7.5 PLUS 2 M ...Details: HANGING DROP VAPOR DIFFUSION METHOD, MIXING 1MICRO-L OF PROTEIN (20 MG/ML IN 50 MM TRIS/HCL, PH 7.5 PLUS 30 MM NACL) WITH 1 MICRO-L RESERVOIR SOLUTION (10 MM TRIS/HCL, PH 7.5 PLUS 2 M AMMONIUM SULFATE PLUS 2 M NACL).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 21, 2006 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 28824 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.3
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.1 / % possible all: 71.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BQK

1bqk


Resolution: 1.3→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.995 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. LOOP A10 TO A15 HAS BEEN MODELED WITH TWO MAIN CHAIN CONFORMATIONS. SOME SIDE CHAINS HAVE BEEN MODELED WITH TWO ALTERNATE SIDE CHAIN ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. LOOP A10 TO A15 HAS BEEN MODELED WITH TWO MAIN CHAIN CONFORMATIONS. SOME SIDE CHAINS HAVE BEEN MODELED WITH TWO ALTERNATE SIDE CHAIN CONFORMATIONS. THE COPPER AND SULFUR ATOMS HAVE BEEN REFINED ANISOTROPICALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1467 5.1 %RANDOM
Rwork0.193 ---
obs0.195 27344 94.5 %-
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: 26.14 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å2-0.59 Å20 Å2
2---1.19 Å20 Å2
3---1.78 Å2
Refinement stepCycle: LAST / Resolution: 1.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms903 0 8 115 1026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022993
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.221.981342
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1595131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.9926.48637
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7315173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.573151
X-RAY DIFFRACTIONr_chiral_restr0.0790.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02745
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.2466
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2647
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.283
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3480.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6471.5664
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.97921043
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7363359
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.514.5299
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.33 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.295 63
Rwork0.238 1513
Refinement TLS params.Method: refined / Origin x: 18.851 Å / Origin y: 64.02 Å / Origin z: 26.184 Å
111213212223313233
T-0.0891 Å20.0262 Å20.0689 Å2--0.0937 Å20.0259 Å2---0.1055 Å2
L2.9096 °2-2.6009 °20.1317 °2-4.4142 °2-0.2895 °2--0.6137 °2
S0.1978 Å °0.2388 Å °0.4533 Å °-0.3515 Å °-0.2272 Å °-0.7145 Å °-0.0238 Å °-0.055 Å °0.0294 Å °

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