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- PDB-2jkw: Pseudoazurin M16F -

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Basic information

Entry
Database: PDB / ID: 2jkw
TitlePseudoazurin M16F
ComponentsPSEUDOAZURIN
KeywordsELECTRON TRANSPORT / COPPER / PERIPLASM / TRANSPORT / CUPREDOXIN / ELECTRON TRANSFER / PSEUDOAZURIN / METAL-BINDING / PI- INTERACTIONS
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: 1.6 Å
AuthorsYanagisawa, S. / Crowley, P.B. / Firbank, S.J. / Lawler, A.T. / Hunter, D.M. / McFarlane, W. / Li, C. / Kohzuma, T. / Banfield, M.J. / Dennison, C.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: Pi-Interaction Tuning of the Active Site Properties of Metalloproteins.
Authors: Yanagisawa, S. / Crowley, P.B. / Firbank, S.J. / Lawler, A.T. / Hunter, D.M. / Mcfarlane, W. / Li, C. / Kohzuma, T. / Banfield, M.J. / Dennison, C.
History
DepositionSep 1, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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 / struct_site
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 / _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
B: PSEUDOAZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2254
Polymers26,0982
Non-polymers1272
Water8,215456
1
A: PSEUDOAZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1122
Polymers13,0491
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PSEUDOAZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1122
Polymers13,0491
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)34.930, 90.540, 35.220
Angle α, β, γ (deg.)90.00, 98.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PSEUDOAZURIN / PSEUDOAZURIN M16F / BLUE COPPER PROTEIN


Mass: 13048.918 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACHROMOBACTER CYCLOCLASTES (bacteria) / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / References: UniProt: P19567
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, MET 44 TO PHE ENGINEERED RESIDUE IN CHAIN B, MET 44 TO PHE
Sequence detailsPOINT MUTATION MET16PHE

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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: 1.97 Å3/Da / Density % sol: 37.5 % / Description: NONE
Crystal growpH: 7.5 / Details: 5 MM TRIS PH 7.5, 35 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.283
DetectorType: MARRESEARCH / Detector: CCD / Details: RH COATED COLLIMATING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 1.6→25.5 Å / Num. obs: 28533 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.7
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.4.0067refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BQK

1bqk


Resolution: 1.6→45.27 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.252 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18 1442 5.1 %RANDOM
Rwork0.131 ---
obs0.134 27053 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20.22 Å2
2---0.12 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1812 0 2 456 2270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221880
X-RAY DIFFRACTIONr_bond_other_d0.0010.021236
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.9652557
X-RAY DIFFRACTIONr_angle_other_deg0.9433062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2175256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12926.05671
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.86215300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.413152
X-RAY DIFFRACTIONr_chiral_restr0.0850.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212146
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02340
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1861.51246
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.87921999
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7443634
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1354.5554
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: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.269 107
Rwork0.158 1979

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