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- PDB-1rcy: RUSTICYANIN (RC) FROM THIOBACILLUS FERROOXIDANS -

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Basic information

Entry
Database: PDB / ID: 1rcy
TitleRUSTICYANIN (RC) FROM THIOBACILLUS FERROOXIDANS
ComponentsRUSTICYANIN
KeywordsMETALLOPROTEIN / COPPER CONTAINING PROTEIN / OXIDATION POTENTIAL / PH STABILITY / REDOX PROTEIN
Function / homology
Function and homology information


electron transfer activity / periplasmic space / 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 speciesAcidithiobacillus ferrooxidans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MULTIWAVELENGTH ANOMALOUS DISPERSION / Resolution: 1.9 Å
AuthorsWalter, R.L. / Friedman, A.M. / Ealick, S.E. / Blake II, R.C. / Proctor, P. / Shoham, M.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Multiple wavelength anomalous diffraction (MAD) crystal structure of rusticyanin: a highly oxidizing cupredoxin with extreme acid stability.
Authors: Walter, R.L. / Ealick, S.E. / Friedman, A.M. / Blake 2nd., R.C. / Proctor, P. / Shoham, M.
#1: Journal: To be Published
Title: Madprb: A New Suite of Programs for MAD Data Analysis Incorporating Robust Estimation, Maximum Likelihood and Bayesian Inference
Authors: Friedman, A.M. / Fischmann, T.O. / Shamoo, Y. / Ealick, S.E.
#2: Journal: FEBS Lett. / Year: 1995
Title: Complete 13C Assignments for Recombinant Cu(I) Rusticyanin. Prediction of Secondary Structure from Patterns of Chemical Shifts
Authors: Toy-Palmer, A. / Prytulla, S. / Dyson, H.J.
#3: Journal: Biochemistry / Year: 1995
Title: X-Ray Absorption Studies and Homology Modeling Define the Structural Features that Specify the Nature of the Copper Site in Rusticyanin
Authors: Grossmann, J.G. / Ingledew, W.J. / Harvey, I. / Strange, R.W. / Hasnain, S.S.
#4: Journal: J.Mol.Biol. / Year: 1994
Title: Nuclear Magnetic Resonance 15N and 1H Resonance Assignments and Global Fold of Rusticyanin. Insights Into the Ligation and Acid Stability of the Blue Copper Site
Authors: Hunt, A.H. / Toy-Palmer, A. / Assa-Munt, N. / Cavanagh, J. / Blake II, R.C. / Dyson, H.J.
#5: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization and Preliminary X-Ray Crystallographic Studies of Rusticyanin from Thiobacillus Ferrooxidans
Authors: Djebli, A. / Proctor, P. / Blake II, R.C. / Shoham, M.
#6: Journal: Geomicrobiol.J. / Year: 1992
Title: Respiratory Components in Acidophilic Bacteria that Respire on Iron
Authors: Blake II, R.C. / Shute, E.A. / Waskovsky, J. / Harrison Junior, A.P.
#7: Journal: Biochemistry / Year: 1991
Title: Amino Acid Sequence of the Blue Copper Protein Rusticyanin from Thiobacillus Ferrooxidans
Authors: Ronk, M. / Shively, J.E. / Shute, E.A. / Blake II, R.C.
#8: Journal: Adv.Protein Chem. / Year: 1991
Title: Copper Protein Structures
Authors: Adman, E.T.
#9: Journal: J.Biol.Chem. / Year: 1987
Title: Respiratory Enzymes of Thiobacillus Ferrooxidans. A Kinetic Study of Electron Transfer between Iron and Rusticyanin in Sulfate Media
Authors: Blake II, R.C. / Shute, E.A.
#10: Journal: Biochem.J. / Year: 1978
Title: The Purification and Some Properties of Rusticyanin, a Blue Copper Protein Involved in Iron(II) Oxidation from Thiobacillus Ferro-Oxidans
Authors: Cox, J.C. / Boxer, D.H.
#11: Journal: FEBS Lett. / Year: 1975
Title: The Respiratory Chain of Thiobacillus Ferrooxidans: The Reduction of Cytochromes by Fe2+ and the Preliminary Characterization of Rusticyanin, a Novel 'Blue' Copper Protein
Authors: Cobley, J.G. / Haddock, B.A.
History
DepositionApr 10, 1996Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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_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

Downloads & links

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Assembly

Deposited unit
A: RUSTICYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2612
Polymers16,1981
Non-polymers641
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.510, 60.670, 38.140
Angle α, β, γ (deg.)90.00, 108.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RUSTICYANIN /


Mass: 16197.503 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: OXIDIZED FORM (CU(II))
Source: (gene. exp.) Acidithiobacillus ferrooxidans (bacteria)
Cellular location: PERIPLASM / References: UniProt: P24930, UniProt: P0C918*PLUS
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43 %
Crystal growpH: 4.6 / Details: pH 4.6
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Djebli, A., (1992) J.Mol.Biol., 227, 581.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14.5 mg/mlprotein1drop
250 mMsodium citrate1drop
3100 mMlithium chloride1drop
412.5 %(w/v)PEG80001drop
5100 mMsodium citrate1reservoir
6200 mMlithium chloride1reservoir
725 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Oct 20, 1993 / Details: COLLIMATOR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. obs: 9167 / % possible obs: 82 % / Observed criterion σ(I): 2 / Redundancy: 1.5 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 23.5
Reflection shellResolution: 1.9→2.05 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.0383 / Mean I/σ(I) obs: 10.1 / % possible all: 63
Reflection
*PLUS
Num. measured all: 14468

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
SDMSdata reduction
SDMSdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MULTIWAVELENGTH ANOMALOUS DISPERSION
Resolution: 1.9→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.252 954 10 %
Rwork0.175 --
obs0.175 9098 82 %
Displacement parametersBiso mean: 14.3 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1141 0 1 128 1270
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.405
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.55
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.255
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.99 Å / % reflection obs: 50 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.559
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.255

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