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- PDB-1a8z: STRUCTURE DETERMINATION OF A 16.8KDA COPPER PROTEIN RUSTICYANIN A... -

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Basic information

Entry
Database: PDB / ID: 1a8z
TitleSTRUCTURE DETERMINATION OF A 16.8KDA COPPER PROTEIN RUSTICYANIN AT 2.1A RESOLUTION USING ANOMALOUS SCATTERING DATA WITH DIRECT METHODS
ComponentsRUSTICYANIN
KeywordsELECTRON TRANSPORT / DIRECT METHODS / SAS / MEDIUM RESOLUTION / METALLOPROTEIN / COPPER PROTEIN
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 / SYNCHROTRON / ANOMALOUS SCATTERING, DIRECT METHODS / Resolution: 2.1 Å
AuthorsHarvey, I. / Hao, Q. / Duke, E.M.H. / Ingledew, W.J. / Hasnain, S.S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure determination of a 16.8 kDa copper protein at 2.1 A resolution using anomalous scattering data with direct methods.
Authors: Harvey, I. / Hao, Q. / Duke, E.M. / Ingledew, W.J. / Hasnain, S.S.
#1: Journal: To be Published
Title: Oasis-A Computer Program for Breaking the Phase Ambiguity in Oas or Sir Protein Data
Authors: Hao, Q. / Gu, Y.X. / Zheng, C.D. / Fan, H.F.
#2: 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.
#3: 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.
#4: 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.
#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: 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.
#7: Journal: Adv.Protein Chem. / Year: 1991
Title: Copper Protein Structures
Authors: Adman, E.T.
#8: 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.
#9: 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
DepositionMar 30, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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

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Assembly

Deposited unit
A: RUSTICYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4722
Polymers16,4091
Non-polymers641
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.430, 60.680, 38.010
Angle α, β, γ (deg.)90.00, 107.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RUSTICYANIN


Mass: 16408.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: REDUCED FORM (CU(I)) / 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.: 57 / 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: 2.1 Å3/Da / Density % sol: 38 %
Crystal growpH: 3.8
Details: SIMILAR TO THOSE DESCRIBED IN DJEBLI ET AL., J. MOL. BIOL. 229, 581 (1992)., pH 3.8
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 4.6 / Method: vapor diffusion, hanging drop
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: SRS / Beamline: PX9.5 / Wavelength: 1.376
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 4, 1996 / Details: COLLIMATOR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.376 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 7898 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.029 / Net I/σ(I): 7.9
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.106 / Mean I/σ(I) obs: 6.1 / Rsym value: 0.066 / % possible all: 91.9
Reflection
*PLUS
Num. measured all: 80752
Reflection shell
*PLUS
% possible obs: 91.9 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
CCP4(SCALA)data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: ANOMALOUS SCATTERING, DIRECT METHODS
Resolution: 2.1→8 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.219 612 8 %RANDOM
Rwork0.187 ---
obs0.187 7656 95.5 %-
Displacement parametersBiso mean: 14.9 Å2
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1160 0 1 57 1218
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: 2.1→2.19 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.278 71 8 %
Rwork0.251 893 -
obs--91.9 %
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
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.55
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.255
LS refinement shell
*PLUS
Rfactor obs: 0.251

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