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- PDB-2cak: 1.27Angstrom Structure of Rusticyanin from Thiobacillus ferrooxidans -

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Basic information

Entry
Database: PDB / ID: 2cak
Title1.27Angstrom Structure of Rusticyanin from Thiobacillus ferrooxidans
ComponentsRUSTICYANIN
KeywordsELECTRON TRANSPORT / RUSTICYANIN / IRON RESPIRATORY ELECTRON TRANSPORT CHAIN / BLUE COPPER PROTEIN / COPPER / METAL-BINDING / PERIPLASMIC / TRANSPORT
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 speciesTHIOBACILLUS FERROOXIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsBarrett, M.L. / Harvey, I. / Sundararajan, M. / Surendran, R. / Hall, J.F. / Ellis, M.J. / Hough, M.A. / Strange, R.W. / Hillier, I.H. / Hasnain, S.S.
CitationJournal: Biochemistry / Year: 2006
Title: Atomic Resolution Crystal Structures, Exafs, and Quantum Chemical Studies of Rusticyanin and its Two Mutants Provide Insight Into its Unusual Properties.
Authors: Barrett, M.L. / Harvey, I. / Sundararajan, M. / Surendran, R. / Hall, J.F. / Ellis, M.J. / Hough, M.A. / Strange, R.W. / Hillier, I.H. / Hasnain, S.S.
History
DepositionDec 21, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.4Dec 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 / struct_conn / struct_site
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 / _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

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Assembly

Deposited unit
A: RUSTICYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5132
Polymers16,4501
Non-polymers641
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)32.473, 60.823, 38.121
Angle α, β, γ (deg.)90.00, 108.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RUSTICYANIN


Mass: 16449.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) THIOBACILLUS FERROOXIDANS (bacteria) / 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.: 86 / Source method: isolated from a natural source / Formula: H2O
Compound detailsELECTRON CARRIER FROM CYTOCHROME C552 TO THE A-TYPE OXIDASE

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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: 2.18 Å3/Da / Density % sol: 50.1 %
Crystal growpH: 3.8 / Details: pH 3.80

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: SINGLE CRYSTAL SI MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.27→12 Å / Num. obs: 37281 / % possible obs: 99.7 % / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.7
Reflection shellResolution: 1.27→1.3 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A8Z

1a8z


Resolution: 1.27→12 Å / Num. parameters: 11830 / Num. restraintsaints: 15010 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 5 PERCENT
RfactorNum. reflection% reflectionSelection details
Rfree0.1378 5514 7.7 %RANDOM
all0.1202 71842 --
obs0.1207 -100 %-
Refine analyzeNum. disordered residues: 12 / Occupancy sum hydrogen: 1092 / Occupancy sum non hydrogen: 1272
Refinement stepCycle: LAST / Resolution: 1.27→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1158 0 1 86 1245
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0309
X-RAY DIFFRACTIONs_zero_chiral_vol0.1
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.103
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.031
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.046
X-RAY DIFFRACTIONs_approx_iso_adps0.108

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