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- PDB-1nwp: CRYSTALLOGRAPHIC STUDY OF AZURIN FROM PSEUDOMONAS PUTIDA -

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Basic information

Entry
Database: PDB / ID: 1nwp
TitleCRYSTALLOGRAPHIC STUDY OF AZURIN FROM PSEUDOMONAS PUTIDA
ComponentsAZURIN
KeywordsELECTRON TRANSPORT / CUPREDOXIN / ELECTRON TRANSFER
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 speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMathews, F.S. / Chen, Z.-W.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallographic study of azurin from Pseudomonas putida.
Authors: Chen, Z.W. / Barber, M.J. / McIntire, W.S. / Mathews, F.S.
#1: Journal: Arch.Biochem.Biophys. / Year: 1993
Title: The Amino Acid Sequence of Pseudomonas Putida Azurin
Authors: Barber, M.J. / Trimboli, A.J. / Mcintire, W.S.
History
DepositionSep 6, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)27,8648
Polymers27,4752
Non-polymers3896
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: AZURIN
hetero molecules

B: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8648
Polymers27,4752
Non-polymers3896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_654x+1,y,z-11
Buried area640 Å2
ΔGint-76 kcal/mol
Surface area12400 Å2
MethodPISA
3
B: AZURIN
hetero molecules

A: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8648
Polymers27,4752
Non-polymers3896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area730 Å2
ΔGint-66 kcal/mol
Surface area12320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.760, 51.220, 54.960
Angle α, β, γ (deg.)90.00, 103.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein AZURIN


Mass: 13737.709 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria) / Strain: NCIB 9869 / References: UniProt: P34097
#2: Chemical ChemComp-CU / COPPER (II) ION


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


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: HANGING DROP METHOD AT 4 C BY MIXING 5 MICROLITER PROTEIN AT 10- 15MG PER ML WITH PEG8000 SOLUTION CONTAINING 5MM TRIS-HCL BUFFER, PH 5 MICROLITER 30-36% 6.5-7.5 ,100MM NACL AND 180MM ZINC ...Details: HANGING DROP METHOD AT 4 C BY MIXING 5 MICROLITER PROTEIN AT 10- 15MG PER ML WITH PEG8000 SOLUTION CONTAINING 5MM TRIS-HCL BUFFER, PH 5 MICROLITER 30-36% 6.5-7.5 ,100MM NACL AND 180MM ZINC ACETATE., pH 7.0, vapor diffusion - hanging drop, temperature 277K
PH range: 6.5-7.5
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop / PH range low: 7.5 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-7.5 mg/mlprotein1drop
215-18 %PEG80001drop
32.5 mMTris-HCl1drop
450 mM1dropNaCl
530-36 %PEG80001reservoir
65 mMTris-HCl1reservoir
7100 mM1reservoirNaCl
8180 mMzinc acetate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Apr 1, 1992 / Details: CU KA RADIATION
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 27846 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.7
Reflection shellResolution: 1.6→1.72 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 1.9 / % possible all: 78
Reflection
*PLUS
Num. measured all: 241088

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Processing

Software
NameVersionClassification
SOFTWAREFROM HAMLIN MULTIWIRE AREA DETECTORdata collection
SOFTWAREFROM HAMLIN MULTIWIRE AREA DETECTORdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
HAMLINdata reduction
HAMLINdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AZURIN FROM ALCALIGENES DENITRIFICANS (ENTRY NO. 2AZA)

2aza


Resolution: 1.6→10 Å / σ(F): 1.5
RfactorNum. reflection% reflection
Rfree0.248 -9.3 %
Rwork0.181 --
obs0.181 26978 93.5 %
Displacement parametersBiso mean: 18 Å2
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1916 0 6 222 2144
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg0.975
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.57
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.03
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it2.18
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.6→1.67 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.336 -5.8 %
Rwork0.272 1768 -
obs--57.76 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.57

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