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- PDB-1rkr: CRYSTAL STRUCTURE OF AZURIN-I FROM ALCALIGENES XYLOSOXIDANS NCIMB... -

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Basic information

Entry
Database: PDB / ID: 1rkr
TitleCRYSTAL STRUCTURE OF AZURIN-I FROM ALCALIGENES XYLOSOXIDANS NCIMB 11015
ComponentsAZURIN-I
KeywordsELECTRON TRANSPORT
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-1
Similarity search - Component
Biological speciesAchromobacter xylosoxidans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsLi, C. / Inoue, T. / Gotowda, M. / Suzuki, S. / Yamaguchi, K. / Kataoka, K. / Kai, Y.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure of azurin I from the denitrifying bacterium Alcaligenes xylosoxidans NCIMB 11015 at 2.45 A resolution.
Authors: Li, C. / Inoue, T. / Gotowda, M. / Suzuki, S. / Yamaguchi, K. / Kunishige, K. / Kai, Y.
#1: Journal: Chem.Lett. / Year: 1995
Title: Isolation and Characterization of Two Distinct Azurins from Alcaligenes Xylosoxidans Subsp. Xylosoxidans Ncib11015 or Gifu1051
Authors: Yamaguchi, K. / Deligeer / Nakamura, N. / Shidara, S. / Iwasaki, H. / Suzuki, S.
#2: Journal: J.Biochem.(Tokyo) / Year: 1994
Title: Structure of Azurin from Achromobacter Xylosoxidans Ncib11015 at 2.5 A Resolution
Authors: Inoue, T. / Shibata, N. / Nakanishi, H. / Koyama, S. / Ishii, H. / Kai, Y. / Harada, S. / Kasai, N. / Ohshiro, Y. / Suzuki, S. / Kohzuma, T. / Yamaguchi, K. / Shidara, S. / Iwasaki, H.
History
DepositionMay 17, 1997Processing site: BNL
Revision 1.0May 20, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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_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_asym_id / _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_asym_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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AZURIN-I
B: AZURIN-I
C: AZURIN-I
D: AZURIN-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8748
Polymers55,6194
Non-polymers2544
Water1,45981
1
A: AZURIN-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9682
Polymers13,9051
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AZURIN-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9682
Polymers13,9051
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: AZURIN-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9682
Polymers13,9051
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: AZURIN-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9682
Polymers13,9051
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
A: AZURIN-I
hetero molecules

A: AZURIN-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9374
Polymers27,8102
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area890 Å2
ΔGint-14 kcal/mol
Surface area11560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.670, 54.260, 74.550
Angle α, β, γ (deg.)90.00, 95.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
AZURIN-I


Mass: 13904.841 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Achromobacter xylosoxidans (bacteria) / Strain: NCIMB 11015 / References: UniProt: P56547
#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.: 81 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 48 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: HANGING-DROP VAPOR DIFFUSION METHOD, pH 8.0, vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.1 MTris-HCl1drop
316 %(w/v)PEG1drop
40.1 MTris-HCl1reservoir
528 %(w/v)PEG1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 20, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 11462 / % possible obs: 90.5 % / Observed criterion σ(I): 1 / Redundancy: 1.7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 11.7
Reflection shellResolution: 2.45→2.5 Å / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 3.47 / % possible all: 82.3
Reflection
*PLUS
Num. measured all: 19618
Reflection shell
*PLUS
% possible obs: 82.3 % / Num. unique obs: 904 / Num. measured obs: 1087

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Processing

Software
NameVersionClassification
PROCESSdata reduction
AMoREphasing
X-PLOR3refinement
PROCESSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AZURIN-II FROM THE SAME BACTERIUM

Resolution: 2.45→8 Å / Data cutoff low absF: 0 / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.236 568 5 %
Rwork0.173 --
obs0.173 10895 58.6 %
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.45→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3888 0 4 81 3973
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.024
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg5.488
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.32
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.473
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.32
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.473

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