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- PDB-1e30: Crystal structure of the Met148Gln mutant of rusticyanin at 1.5 A... -

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Basic information

Entry
Database: PDB / ID: 1.0E+30
TitleCrystal structure of the Met148Gln mutant of rusticyanin at 1.5 Angstrom resolution
ComponentsRUSTICYANIN
KeywordsRUSTICYANIN / MUTANT / AXIAL LIGAND / CUPREDOXIN
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 (II) ION / Rusticyanin / Rusticyanin
Similarity search - Component
Biological speciesTHIOBACILLUS FERROOXIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHough, M.A. / Strange, R.W. / Hasnain, S.S.
CitationJournal: Biochemistry / Year: 1999
Title: Role of the Axial Ligand in Type 1 Cu Centers Studied by Point Mutations of met148 in Rusticyanin
Authors: Hall, J.F. / Kanbi, L.D. / Strange, R.W. / Hasnain, S.S.
History
DepositionJun 2, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _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
B: RUSTICYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2594
Polymers33,1322
Non-polymers1272
Water3,225179
1
A: RUSTICYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6292
Polymers16,5661
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RUSTICYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6292
Polymers16,5661
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.861, 61.380, 53.330
Angle α, β, γ (deg.)90.00, 96.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RUSTICYANIN


Mass: 16565.869 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THIOBACILLUS FERROOXIDANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P74919, UniProt: P0C918*PLUS
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B ENGINEERED MUTATION MET148GLN

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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: 41.3 %
Crystal growMethod: vapor diffusion / pH: 4
Details: 30% PEG-8000, 100MM MES, 50MM CITRIC ACID, PH 4.0 VAPOUR DIFFUSION. PROTEIN CONCENTRATION 7 MG./ML
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop
Details: drop was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
210 mM1dropH2SO4
330 %PEG80001reservoir
4100 mMMES1reservoir
550 mMcitric acid1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Apr 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→52.7 Å / Num. obs: 33706 / % possible obs: 76.5 % / Redundancy: 2.1 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 12
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.203 / % possible all: 70.7
Reflection
*PLUS
Num. measured all: 62663
Reflection shell
*PLUS
% possible obs: 70.7 % / Mean I/σ(I) obs: 3

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→52.7 Å / SU B: 1.60728 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.1
Details: THE TWO N-TERMINAL RESIDUES ARE NOT SEEN IN ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1665 5 %RANDOM
Rwork0.182 ---
obs0.182 32036 76 %-
Displacement parametersBiso mean: 11 Å2
Refinement stepCycle: LAST / Resolution: 1.5→52.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2322 0 2 179 2503
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.0270.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0310.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.1232
X-RAY DIFFRACTIONp_mcangle_it1.643
X-RAY DIFFRACTIONp_scbond_it1.8252
X-RAY DIFFRACTIONp_scangle_it2.6993
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd00.3
X-RAY DIFFRACTIONp_multtor_nbd0.2490.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1290.3
X-RAY DIFFRACTIONp_planar_tor4.17
X-RAY DIFFRACTIONp_staggered_tor14.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor30.620
X-RAY DIFFRACTIONp_special_tor015

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