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- PDB-1cc3: PURPLE CUA CENTER -

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Basic information

Entry
Database: PDB / ID: 1cc3
TitlePURPLE CUA CENTER
ComponentsPROTEIN (CUA AZURIN)
KeywordsELECTRON TRANSPORT / COPPER-A
Function / homology
Function and homology information


transition metal ion binding / periplasmic space / electron transfer activity / copper ion binding / zinc ion binding / identical protein binding
Similarity search - Function
Azurin / : / 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 / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsRobinson, H. / Ang, M.C. / Gao, Y.-G. / Hay, M.T. / Lu, Y. / Wang, A.H.-J.
CitationJournal: Biochemistry / Year: 1999
Title: Structural basis of electron transfer modulation in the purple CuA center.
Authors: Robinson, H. / Ang, M.C. / Gao, Y.G. / Hay, M.T. / Lu, Y. / Wang, A.H.
History
DepositionMar 3, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 23, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (CUA AZURIN)
B: PROTEIN (CUA AZURIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6326
Polymers28,3782
Non-polymers2544
Water9,116506
1
A: PROTEIN (CUA AZURIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3163
Polymers14,1891
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (CUA AZURIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3163
Polymers14,1891
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.630, 62.332, 51.230
Angle α, β, γ (deg.)90.00, 99.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (CUA AZURIN)


Mass: 14189.080 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: AZURINE WITH THE FOLLOWING MUTATIONS: THE LOOP 113-118 TFPGHS WAS REPLACED WITH 113-120 SELCGINH
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Description: LOOP DIRECTED MUTAGENESIS / Production host: Escherichia coli (E. coli) / References: UniProt: P00282
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / 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: 1.96 Å3/Da / Density % sol: 37 %
Crystal growpH: 5.1 / Details: pH 5.1
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 5 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
111.5 mg/mlprotein1drop
2125 mMammonium acetate1droppH5.1
30.05 Msodium acetate1droppH4.6
415 %PEG20001drop
50.2 Mammonium acetate1reservoir
60.1 Msodium acetate1reservoirpH4.6
720 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 11, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. obs: 26467 / % possible obs: 94.1 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 17
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 3.3 / % possible all: 96.4
Reflection
*PLUS
% possible obs: 97.8 %

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Processing

Software
NameClassification
d*TREKdata scaling
d*TREKdata reduction
X-PLORmodel building
SHELXL-97refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AZU

4azu


Resolution: 1.65→20 Å / Num. parameters: 9959 / Num. restraintsaints: 8058 / Cross valid method: THROUGHOUT UNTIL END / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: NO RESTRAINTS APPLIED TO COPPER ATOMS
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1317 5 %RANDOM
Rwork0.201 ---
all0.201 26123 --
obs0.201 26123 97.8 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2486
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1976 0 4 506 2486
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d2.476
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol0.048
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.053
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.007
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.189 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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