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- PDB-1gy1: Crystal structures of Ser86Asp and Met148Leu Rusticyanin -

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Basic information

Entry
Database: PDB / ID: 1gy1
TitleCrystal structures of Ser86Asp and Met148Leu Rusticyanin
ComponentsRUSTICYANIN
KeywordsELECTRON TRANSPORT / S86D / M148L / RUSTICYANIN / MUTANT / METAL-BINDING / PERIPLASMIC
Function / homology
Function and homology information


periplasmic space / electron transfer activity / copper ion binding
Similarity search - Function
Rusticyanin / 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 ...Rusticyanin / 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 / Rusticyanin / Rusticyanin
Similarity search - Component
Biological speciesTHIOBACILLUS FERROOXIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsHough, M.A. / Kanbi, L.D. / Antonyuk, S. / Dodd, F. / Hasnain, S.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Crystal Structures of the met148Leu and Ser86Asp Mutants of Rusticyanin from Thiobacillus Ferrooxidans: Insights Into the Structural Relationship with the Cupredoxins and the Multi Copper Proteins
Authors: Kanbi, L.D. / Antonyuk, S. / Hough, M.A. / Hall, J. / Dodd, F. / Hasnain, S.
History
DepositionApr 16, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 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
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: RUSTICYANIN
B: RUSTICYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3174
Polymers33,1902
Non-polymers1272
Water3,909217
1
A: RUSTICYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6592
Polymers16,5951
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RUSTICYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6592
Polymers16,5951
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)43.098, 61.408, 53.346
Angle α, β, γ (deg.)90.00, 96.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RUSTICYANIN


Mass: 16594.977 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THIOBACILLUS FERROOXIDANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P24930, UniProt: P0C918*PLUS
#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.: 217 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B ENGINEERED MUTATION SER86ASP

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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: 2.11 Å3/Da / Density % sol: 41.84 %
Crystal growpH: 5 / Details: pH 5.00
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 3.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 mg/mlprotein1drop
210 mMsulphuric acid1droppH3.8
310 mM1reservoirNaCl
430 %PEG80001reservoir
550 mMcitric acid1reservoirpH5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.65→52.7 Å / Num. obs: 32189 / % possible obs: 95.7 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 22.5
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3 % / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 5 / % possible all: 72.9
Reflection
*PLUS
Num. measured all: 277815
Reflection shell
*PLUS
% possible obs: 72.9 % / Redundancy: 3 % / Mean I/σ(I) obs: 5

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1A8Z

1a8z


Resolution: 1.65→52.7 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.455 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19 1628 5.1 %RANDOM
Rwork0.166 ---
obs0.167 30543 95.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 1.65→52.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2332 0 2 217 2551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222397
X-RAY DIFFRACTIONr_bond_other_d0.0010.022122
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.9363284
X-RAY DIFFRACTIONr_angle_other_deg1.14634978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7273306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.36915386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.3390.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022662
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02466
X-RAY DIFFRACTIONr_nbd_refined0.2340.3455
X-RAY DIFFRACTIONr_nbd_other0.210.31910
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0560.52
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.5243
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1410.51
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3930.36
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2270.346
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.511
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8051.51535
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.47622508
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0343862
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3014.5776
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: 1.65→1.69 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.21 85
Rwork0.188 1635
Refinement
*PLUS
Lowest resolution: 52.7 Å / Rfactor obs: 0.165 / Rfactor Rfree: 0.189 / Rfactor Rwork: 0.165
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.5

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