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- PDB-1gy2: Crystal structure of Met148Leu rusticyanin -

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Basic information

Entry
Database: PDB / ID: 1gy2
TitleCrystal structure of 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: 1.82 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.F. / Dodd, F. / Hasnain, S.
History
DepositionApr 16, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Dec 13, 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 / 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_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

Downloads & links

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Assembly

Deposited unit
A: RUSTICYANIN
B: RUSTICYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3215
Polymers33,1022
Non-polymers2193
Water2,450136
1
A: RUSTICYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7073
Polymers16,5511
Non-polymers1562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RUSTICYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6142
Polymers16,5511
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.450, 61.430, 53.470
Angle α, β, γ (deg.)90.00, 96.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RUSTICYANIN


Mass: 16550.898 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: B7JAQ0, 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: 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B ENGINEERED MUTATION MET180LEU

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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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growpH: 5 / Details: 30% PEG 8000, 50 MM CITRIC ACID PH 5.0
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 3.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
210 mMsulphuric acid1droppH3.8
330 %PEG80001reservoir
450 mMcitric acid1reservoirpH5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→53.4 Å / Num. obs: 25330 / % possible obs: 92.2 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.1
Reflection shellResolution: 1.82→1.84 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 3 / % possible all: 94
Reflection
*PLUS
Num. measured all: 206007
Reflection shell
*PLUS
% possible obs: 94 % / Mean I/σ(I) obs: 2.96

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RCY

1rcy


Resolution: 1.82→53.4 Å / Cross valid method: THROUGHOUT / Details: NONE
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2359 9 %RANDOM
Rwork0.183 ---
obs0.184 25330 92.2 %-
Refinement stepCycle: LAST / Resolution: 1.82→53.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 8 136 2484
Refinement
*PLUS
Rfactor obs: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.8

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