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- PDB-1azc: STRUCTURE OF APO-AZURIN FROM ALCALIGENES DENITRIFICANS AT 1.8 ANG... -

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Basic information

Entry
Database: PDB / ID: 1azc
TitleSTRUCTURE OF APO-AZURIN FROM ALCALIGENES DENITRIFICANS AT 1.8 ANGSTROMS RESOLUTION
ComponentsAZURIN
KeywordsELECTRON TRANSPORT(COPPER)
Function / homology
Function and homology information


periplasmic space / electron transfer activity / copper ion 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 speciesAchromobacter xylosoxidans (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsBaker, E.N. / Shepard, W.E.B. / Kingston, R.L.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Structure of apo-azurin from Alcaligenes denitrificans at 1.8 A resolution.
Authors: Shepard, W.E. / Kingston, R.L. / Anderson, B.F. / Baker, E.N.
#1: Journal: J.Am.Chem.Soc. / Year: 1990
Title: Copper Coordination Geometry in Azurin Undergoes Minimal Change on Reduction of Copper(II) to Copper (I)
Authors: Shepard, W.E.B. / Anderson, B.F. / Lewandoski, D.A. / Norris, G.E. / Baker, E.N.
#2: Journal: J.Mol.Biol. / Year: 1988
Title: Structure of Azurin from Alcaligenes Denitrificans Refinement at 1.8 Angstroms Resolution and Comparison of the Two Crystallographically Independent Molecules
Authors: Baker, E.N.
#3: Journal: J.Mol.Biol. / Year: 1983
Title: Structure of Azurin from Alcaligenes Denitrificans at 2.5 Angstroms Resolution
Authors: Norris, G.E. / Anderson, B.F. / Baker, E.N.
#4: Journal: J.Mol.Biol. / Year: 1979
Title: Purification and Preliminary Crystallographic Studies on Azurin and Cytochrome C' from Alcaligenes Denitrificans and Alcaligenes Sp. Ncib 11015
Authors: Norris, G.E. / Anderson, B.F. / Baker, E.N. / Rumball, S.V.
History
DepositionDec 16, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _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

Downloads & links

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Assembly

Deposited unit
A: AZURIN
B: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5278
Polymers28,0162
Non-polymers5116
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-52 kcal/mol
Surface area11750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.100, 74.100, 99.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.098, 0.995, 0.018), (0.995, 0.098, 0.031), (0.029, 0.021, -0.999)
Vector: 0.738, -1.069, 24.5)
DetailsTHE ASYMMETRIC UNIT CONTAINS TWO CRYSTALLOGRAPHICALLY INDEPENDENT MOLECULES, A AND B, RELATED BY AN APPROXIMATE TWO-FOLD AXIS. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR MOLECULE A WHEN APPLIED TO MOLECULE B.

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Components

#1: Protein AZURIN


Mass: 14008.003 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter xylosoxidans (bacteria) / References: UniProt: P00280
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAMINO ACID SEQUENCE IS AS IN C.W.G. HOITINK, L.P. WOUDT, J.C.M. TURENHOUT, M. VAN DE KAMP, G.W. ...AMINO ACID SEQUENCE IS AS IN C.W.G. HOITINK, L.P. WOUDT, J.C.M. TURENHOUT, M. VAN DE KAMP, G.W. CARTERS (1990) GENE 90, 15-20.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal grow
*PLUS
pH: 6 / Method: interface diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Mphosphate11
240 %satammonium sulphate11
314 mg/mlprotein11
480 %satammonium sulfate12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 24722 / % possible obs: 89 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.055

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→10 Å / σ(F): 0 /
RfactorNum. reflection
obs0.16 22667
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1954 0 22 246 2222
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Num. reflection all: 22667 / σ(F): 0 / Rfactor all: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 0.045

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