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- PDB-3n2j: Azurin H117G, oxidized form -

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Basic information

Entry
Database: PDB / ID: 3n2j
TitleAzurin H117G, oxidized form
ComponentsAzurin
KeywordsELECTRON TRANSPORT / copper proteins / electron transfer / pseudo-translation
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsHoffmann, M. / Alagaratnam, S. / Canters, G.W. / Einsle, O.
CitationJournal: Febs J. / Year: 2011
Title: Probing the reactivity of different forms of azurin by flavin photoreduction.
Authors: Alagaratnam, S. / Meeuwenoord, N.J. / Navarro, J.A. / Hervas, M. / De la Rosa, M.A. / Hoffmann, M. / Einsle, O. / Ubbink, M. / Canters, G.W.
History
DepositionMay 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 14, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 6, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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_ref_seq_dif.details / _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
C: Azurin
D: Azurin
E: Azurin
F: Azurin
G: Azurin
H: Azurin
I: Azurin
J: Azurin
K: Azurin
L: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,09436
Polymers166,56812
Non-polymers1,52524
Water28,3201572
1
A: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0083
Polymers13,8811
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0083
Polymers13,8811
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0083
Polymers13,8811
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0083
Polymers13,8811
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0083
Polymers13,8811
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0083
Polymers13,8811
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0083
Polymers13,8811
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0083
Polymers13,8811
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0083
Polymers13,8811
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0083
Polymers13,8811
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0083
Polymers13,8811
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0083
Polymers13,8811
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.545, 170.008, 85.737
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Azurin


Mass: 13880.704 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: azu, PA4922 / Production host: Escherichia coli (E. coli) / References: UniProt: P00282
#2: Chemical...
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1572 / 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: 2.08 Å3/Da / Density % sol: 40.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.7
Details: 31 % PEG 2000 MME 0.1 M Tris/HCl pH 8.7 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→100 Å / Num. obs: 273202 / % possible obs: 91.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.79 % / Biso Wilson estimate: 20.89 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 7.6
Reflection shellResolution: 1.35→1.45 Å / Redundancy: 2.26 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.6 / Num. unique all: 26249 / % possible all: 88.8

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
BUSTER2.9.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AZU

4azu


Resolution: 1.35→47.28 Å / Cor.coef. Fo:Fc: 0.9673 / Cor.coef. Fo:Fc free: 0.9604 / SU R Cruickshank DPI: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2018 13389 5.03 %RANDOM
Rwork0.1724 ---
obs0.1739 266404 89.77 %-
Displacement parametersBiso mean: 24.12 Å2
Baniso -1Baniso -2Baniso -3
1--1.686 Å20 Å20.7042 Å2
2--2.3173 Å20 Å2
3----0.6313 Å2
Refine analyzeLuzzati coordinate error obs: 0.166 Å
Refinement stepCycle: LAST / Resolution: 1.35→47.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11616 0 24 1572 13212
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01118202
X-RAY DIFFRACTIONt_angle_deg1.34159482
X-RAY DIFFRACTIONt_dihedral_angle_d41402
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes3482
X-RAY DIFFRACTIONt_gen_planes16805
X-RAY DIFFRACTIONt_it1182020
X-RAY DIFFRACTIONt_nbd45
X-RAY DIFFRACTIONt_omega_torsion4.21
X-RAY DIFFRACTIONt_other_torsion17.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion15605
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact154424
LS refinement shellResolution: 1.35→1.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.1544 949 5.09 %
Rwork0.1341 17695 -
all0.1352 18644 -
obs--89.77 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.40170.095-0.10140.2443-0.05970.3222-0.0067-0.0278-0.0120.0140.00090.0024-0.00910.01160.0057-0.01250.00080.0065-0.0097-0.0055-0.009524.99583.095532.5906
20.54410.0478-0.15630.2240.02590.3561-0.0238-0.027-0.0064-0.00690.0043-0.01290.0091-0.00080.0195-0.0107-0.00070.0055-0.01320.0129-0.012824.6128-52.748131.391
30.7064-0.0886-0.32470.30920.11150.4313-0.00940.0267-0.01350.0043-0.004-0.0028-0.0127-0.02340.0134-0.02440.0070.0075-0.00950.017-0.011522.9079-25.032552.753
40.4033-0.07530.07380.2089-0.08040.2863-0.01780.01790.0147-0.012-0.00170.00990.015700.0195-0.0190.00170.0035-0.0123-0.0078-0.00821.22091.165810.4331
51.641-0.35350.33910.2861-0.07810.6526-0.02840.0904-0.0882-0.02220.0007-0.02280.03870.07920.0277-0.03080.00320.0104-0.017-0.0011-0.013126.4412-24.32599.6934
60.46920.0175-0.28940.19230.03840.8020.02420.02880.0002-0.0074-0.01840.0282-0.0599-0.0907-0.0058-0.01560.01370.012-0.01470.0067-0.0071-2.41520.06953.4265
70.8681-0.0619-0.19210.3217-0.00370.6069-0.006-0.03160.0020.0107-0.0159-0.0451-0.01780.06210.0219-0.0218-0.00580.0055-0.01910.00680.00622.5927-27.883831.41
80.54420.1350.22280.16630.08840.359-0.0056-0.03950.01080.0133-0.0013-0.00180.005-0.020.0068-0.0181-0.00370.0049-0.00580.0038-0.0079-0.792629.319-9.7426
90.70330.14760.21880.46180.26130.8219-0.0008-0.05860.0210.0056-0.00130.01990.0246-0.04880.0022-0.033-0.00260.0159-0.01680.0071-0.01-1.0807-27.7218-10.9051
100.75920.07790.14380.16540.01730.4921-0.00320.0284-0.0186-0.011-0.0032-0.0262-0.00110.04360.0064-0.02550.00230.0022-0.0188-0.0008-0.003126.509532.149311.5471
110.42-0.05810.17490.28890.04850.66940.0188-0.02380.01110.0041-0.02850.01970.061-0.07640.0098-0.0145-0.0130.0045-0.01240.0026-0.002921.41384.1412-10.45
121.61660.2528-0.41120.2587-0.02940.6805-0.0577-0.08290.0710.02910.0097-0.0118-0.01690.08540.0481-0.0237-0.00090.0017-0.0047-0.0001-0.01012.805528.601633.3173
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 131
2X-RAY DIFFRACTION2{ B|* }B1 - 131
3X-RAY DIFFRACTION3{ C|* }C1 - 131
4X-RAY DIFFRACTION4{ D|* }D1 - 131
5X-RAY DIFFRACTION5{ E|* }E1 - 131
6X-RAY DIFFRACTION6{ F|* }F1 - 131
7X-RAY DIFFRACTION7{ G|* }G1 - 131
8X-RAY DIFFRACTION8{ H|* }H1 - 131
9X-RAY DIFFRACTION9{ I|* }I1 - 131
10X-RAY DIFFRACTION10{ J|* }J1 - 131
11X-RAY DIFFRACTION11{ K|* }K1 - 131
12X-RAY DIFFRACTION12{ L|* }L1 - 131

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