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- PDB-1a3z: REDUCED RUSTICYANIN AT 1.9 ANGSTROMS -

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Basic information

Entry
Database: PDB / ID: 1a3z
TitleREDUCED RUSTICYANIN AT 1.9 ANGSTROMS
ComponentsRUSTICYANIN
KeywordsELECTRON TRANSPORT / CUPREDOXIN / METALLOPROTEIN / REDOX POTENTIAL / ACIDOPHILIC
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 (I) ION / Rusticyanin / Rusticyanin
Similarity search - Component
Biological speciesAcidithiobacillus ferrooxidans (bacteria)
MethodX-RAY DIFFRACTION / PHASES TAKEN FROM THE OXIDIZED FORM, PDB ENTRY 1RCY / Resolution: 1.9 Å
AuthorsZhao, D. / Shoham, M.
Citation
Journal: Biophys.J. / Year: 1998
Title: Rusticyanin: Extremes in acid stability and redox potential explained by the crystal structure.
Authors: Zhao, D. / Shoham, M.
#1: 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 II, R.C. / Proctor, P. / Shoham, M.
#2: Journal: J.Mol.Biol. / Year: 1996
Title: NMR Solution Structure of Cu(I) Rusticyanin from Thiobacillus Ferrooxidans: Structural Basis for the Extreme Acid Stability and Redox Potential
Authors: Botuyan, M.V. / Toy-Palmer, A. / Chung, J. / Blake II, R.C. / Beroza, P. / Case, D.A. / Dyson, H.J.
#3: 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.
History
DepositionJan 27, 1998Processing site: BNL
Revision 1.0Jul 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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 / _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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RUSTICYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6332
Polymers16,5701
Non-polymers641
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.450, 60.590, 38.080
Angle α, β, γ (deg.)90.00, 108.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RUSTICYANIN


Mass: 16569.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: REDUCED FORM / Source: (natural) Acidithiobacillus ferrooxidans (bacteria) / Cellular location: PERIPLASM / References: UniProt: P24930, UniProt: P0C918*PLUS
#2: Chemical ChemComp-CU1 / COPPER (I) ION


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


Mass: 18.015 Da / Num. of mol.: 85 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.6
Details: VAPOR DIFFUSION IN HANGING DROPS AGAINST 100 MM-SODIUM CITRATE, PH 4.6, 200 MM LITHIUM CHLORIDE AND 25%(W/V) PEG 8000 AT 277K. CRYSTALS SOAKED IN 10MM DITHIONITE FOR 3 DAYS PRIOR TO DATA ...Details: VAPOR DIFFUSION IN HANGING DROPS AGAINST 100 MM-SODIUM CITRATE, PH 4.6, 200 MM LITHIUM CHLORIDE AND 25%(W/V) PEG 8000 AT 277K. CRYSTALS SOAKED IN 10MM DITHIONITE FOR 3 DAYS PRIOR TO DATA COLLECTION., vapor diffusion - hanging drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: ADSC / Detector: AREA DETECTOR / Date: Jun 1, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. obs: 9718 / % possible obs: 87.4 % / Observed criterion σ(I): 0 / Redundancy: 1.97 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 13.3
Reflection shellResolution: 1.9→1.969 Å / Redundancy: 1.42 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 3.02 / Rsym value: 0.199 / % possible all: 78

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
ADSCdata collection
X-PLOR3.8phasing
RefinementMethod to determine structure: PHASES TAKEN FROM THE OXIDIZED FORM, PDB ENTRY 1RCY
Starting model: PDB ENTRY 1RCY

1rcy


Resolution: 1.9→100 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.272 518 5 %RANDOM
Rwork0.213 ---
obs0.213 9664 87.4 %-
Displacement parametersBiso mean: 19 Å2
Refinement stepCycle: LAST / Resolution: 1.9→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1135 0 0 85 1220
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.7
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.042
X-RAY DIFFRACTIONx_mcangle_it3.984
X-RAY DIFFRACTIONx_scbond_it4.24
X-RAY DIFFRACTIONx_scangle_it5.579
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.368 52 5 %
Rwork0.312 990 -
obs--77.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPH19.PEP
X-RAY DIFFRACTION2TOPH19.SOL
X-RAY DIFFRACTION3TOPHCSDX.PRO

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