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- PDB-2cal: Crystal structure of His143Met rusticyanin -

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Basic information

Entry
Database: PDB / ID: 2cal
TitleCrystal structure of His143Met rusticyanin
ComponentsRUSTICYANIN
KeywordsELECTRON TRANSPORT / RUSTICYANIN / IRON RESPIRATORY ELECTRON TRANSPORT CHAIN / BLUE COPPER PROTEIN / 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: 1.1 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 1.0Jan 5, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Version format compliance
Revision 2.0Dec 13, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_alt_id / _atom_site.label_atom_id / _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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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)16,5392
Polymers16,4761
Non-polymers641
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)32.297, 60.133, 37.236
Angle α, β, γ (deg.)90.00, 107.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RUSTICYANIN


Mass: 16475.891 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THIOBACILLUS FERROOXIDANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / 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.: 274 / Source method: isolated from a natural source / Formula: H2O
Compound detailsELECTRON CARRIER FROM CYTOCHROME C552 TO THE A-TYPE OXIDASE ENGINEERED RESIDUE IN CHAIN A, HIS 175 TO MET
Sequence detailsH143M MUTANT

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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: 2.09 Å3/Da / Density % sol: 41.25 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.85
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 1.1→35.6 Å / Num. obs: 48379 / % possible obs: 89.4 % / Redundancy: 17 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 2.9 / % possible all: 72.6

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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: 1.1→35.6 Å / Cross valid method: THROUGHOUT / σ(F): 0
Rfactor% reflectionSelection details
Rfree0.17 -RANDOM
obs0.14 89.4 %-
Refinement stepCycle: LAST / Resolution: 1.1→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1151 0 1 274 1426
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d1.621
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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