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- PDB-1pzb: THE CRYSTAL STRUCTURES OF REDUCED PSEUDOAZURIN FROM ALCALIGENES F... -

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Basic information

Entry
Database: PDB / ID: 1pzb
TitleTHE CRYSTAL STRUCTURES OF REDUCED PSEUDOAZURIN FROM ALCALIGENES FAECALIS S-6 AT TWO PH VALUES
ComponentsPSEUDOAZURIN
KeywordsELECTRON TRANSFER(CUPROPROTEIN)
Function / homology
Function and homology information


periplasmic space / electron transfer activity / copper ion binding
Similarity search - Function
Pseudoazurin / Amicyanin/Pseudoazurin / Blue (type 1) copper protein, plastocyanin-type / 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 ...Pseudoazurin / Amicyanin/Pseudoazurin / Blue (type 1) copper protein, plastocyanin-type / 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 / Pseudoazurin
Similarity search - Component
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsPetratos, K.
Citation
Journal: FEBS Lett. / Year: 1994
Title: The crystal structures of reduced pseudoazurin from Alcaligenes faecalis S-6 at two pH values.
Authors: Vakoufari, E. / Wilson, K.S. / Petratos, K.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1988
Title: Refinement of the Structure of Pseudoazurin from Alcaligenes Faecalis S-6 at 1.55 Angstroms Resolution
Authors: Petratos, K. / Dauter, Z. / Wilson, K.S.
History
DepositionAug 3, 1994Processing site: BNL
Revision 1.0Nov 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Remark 700SHEET THE NINE-STRANDED SHEET DESCRIBED BELOW IS ACTUALLY AN EIGHT-STRANDED BETA BARREL. THIS IS ...SHEET THE NINE-STRANDED SHEET DESCRIBED BELOW IS ACTUALLY AN EIGHT-STRANDED BETA BARREL. THIS IS DENOTED BY THE FIRST STRAND RECURRING AS THE LAST STRAND. STRAND 8 IS ADJACENT TO STRAND 9 (STRAND 1) BUT THERE ARE NO INTERSTRAND H-BONDS. THE SHEET PRESENTED AS *S1* ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED BETA-BARREL. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PSEUDOAZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4472
Polymers13,3841
Non-polymers641
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.950, 49.950, 98.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Atom site foot note1: CIS PROLINE - PRO 20
2: THE TERMINAL NZ ATOM OF LYS 38 WAS REFINED AT TWO POSITIONS (DENOTED AS A AND B) EACH OF WHICH WAS ASSIGNED OCCUPANCY COEFFICIENT = 0.50.
3: WATER MOLECULES WITH NUMBERS: 33, 67, 90, AND 93 WERE REFINED WITH OCCUPANCY COEFFICIENT SET TO 0.50.

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Components

#1: Protein PSEUDOAZURIN


Mass: 13383.511 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis (bacteria) / References: UniProt: P04377
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion / Details: Petratos, K., (1987) FEBS Lett., 218, 209.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.5 %protein 1drop
21.5 Mammonium sulfate1drop
350 mMpotassium phosphate1drop
43.0 Mammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 12660 / Num. measured all: 97396 / Rmerge(I) obs: 0.05

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Processing

Software
NameClassification
PROLSQrefinement
PROTINrefinement
RefinementResolution: 1.8→10 Å / σ(F): 1 /
RfactorNum. reflection
obs0.177 12654
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms917 0 1 92 1010
Software
*PLUS
Name: SFALL/PROTIN/PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_deg3.2
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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