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- PDB-6mjs: Azurin 122W/124W/126Re -

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Basic information

Entry
Database: PDB / ID: 6mjs
TitleAzurin 122W/124W/126Re
ComponentsAzurin
KeywordsELECTRON TRANSPORT / Electron Hopping
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 / Chem-REQ / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsTakematsu, K. / Zalis, S. / Gray, H.B. / Vlcek, A. / Winkler, J.R. / Williamson, H. / Kaiser, J.T. / Heyda, J. / Hollas, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01 DK019038 United States
CitationJournal: ACS Cent Sci / Year: 2019
Title: Two Tryptophans Are Better Than One in Accelerating Electron Flow through a Protein.
Authors: Takematsu, K. / Williamson, H.R. / Nikolovski, P. / Kaiser, J.T. / Sheng, Y. / Pospisil, P. / Towrie, M. / Heyda, J. / Hollas, D. / Zalis, S. / Gray, H.B. / Vlcek, A. / Winkler, J.R.
History
DepositionSep 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,40812
Polymers56,2404
Non-polymers2,1688
Water4,882271
1
A: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6023
Polymers14,0601
Non-polymers5422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6023
Polymers14,0601
Non-polymers5422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6023
Polymers14,0601
Non-polymers5422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6023
Polymers14,0601
Non-polymers5422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.072, 221.563, 89.996
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-347-

HOH

21B-363-

HOH

31B-364-

HOH

41C-371-

HOH

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Components

#1: Protein
Azurin /


Mass: 14059.922 Da / Num. of mol.: 4 / Mutation: W48F, Y72F, H83Q, Y108F, K122W, T124W, T126H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: azu, PA4922 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00282
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-REQ / (1,10 PHENANTHROLINE)-(TRI-CARBON MONOXIDE) RHENIUM (I)


Mass: 478.496 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H12N2O3Re / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7.2
Details: 100 mM imidiazole, 100 mM LiNO3, 6.25 mM CuCl2, 28% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 6, 2011 / Details: liquid nitrogen-cooled K-B focusing mirrors
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→34.926 Å / Num. all: 44003 / Num. obs: 44003 / % possible obs: 96.2 % / Redundancy: 3.3 % / Rpim(I) all: 0.048 / Rrim(I) all: 0.089 / Rsym value: 0.075 / Net I/av σ(I): 6.6 / Net I/σ(I): 8.3 / Num. measured all: 145966
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.85-1.953.40.8480.92181363690.5341.0060.8481.496.3
1.95-2.073.30.4961.52005060600.3210.5930.4962.596.9
2.07-2.213.40.2822.51910156130.1790.3350.2824.195.2
2.21-2.393.40.1983.51838353480.1260.2360.1985.698
2.39-2.623.30.1395.21582048310.090.1660.1397.495.7
2.62-2.933.30.0957.31510445250.0620.1140.09510.497.7
2.93-3.383.20.06510.21213538070.0430.0780.06514.393.6
3.38-4.143.30.0512.71101533780.0320.060.0519.497.2
4.14-5.853.10.04613.4805125860.030.0560.0462194.4
5.85-34.92630.04113.8449414860.0260.0490.0412093.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALA3.3.20data scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AZU

4azu


Resolution: 1.85→34.926 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.37
RfactorNum. reflection% reflection
Rfree0.1978 2203 5.01 %
Rwork0.1687 --
obs0.1702 43951 95.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.92 Å2 / Biso mean: 33.13 Å2 / Biso min: 14.83 Å2
Refinement stepCycle: final / Resolution: 1.85→34.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3805 0 96 271 4172
Biso mean--28.94 42.13 -
Num. residues----505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123991
X-RAY DIFFRACTIONf_angle_d1.4165428
X-RAY DIFFRACTIONf_chiral_restr0.078588
X-RAY DIFFRACTIONf_plane_restr0.006691
X-RAY DIFFRACTIONf_dihedral_angle_d12.5421376
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.89020.35151340.31922578271295
1.8902-1.93420.34131450.30122588273397
1.9342-1.98260.2931330.26142591272497
1.9826-2.03620.29511560.24462565272196
2.0362-2.09610.25581380.21872551268995
2.0961-2.16370.22681410.19652558269996
2.1637-2.2410.21521180.18082654277297
2.241-2.33070.25151190.17772635275497
2.3307-2.43680.22441250.18032668279397
2.4368-2.56520.23181490.18012493264293
2.5652-2.72590.19991380.16592668280698
2.7259-2.93630.19221440.1742639278397
2.9363-3.23160.191280.15682621274996
3.2316-3.69870.16151510.14612546269793
3.6987-4.65830.16271230.13562703282696
4.6583-34.93190.16931610.15612690285193
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)
14.5556-4.5441-0.01264.70311.06537.63920.64171.02650.3683-0.9426-0.9929-1.0109-0.26471.07880.13370.296-0.0036-0.02960.57030.13710.512535.0471-34.36364.5466
25.8439-1.8589-3.172.23411.16464.74290.1450.31520.527-0.5244-0.2114-0.5496-0.52660.1633-0.03410.36150.0056-0.01280.26080.05160.343922.5842-27.33824.3826
38.328-2.46341.18340.91360.67835.7025-0.15290.10130.1622-0.0506-0.152-2.09630.7661.26690.10890.33190.1540.00140.37280.07670.658435.8905-43.3319-0.9898
42.7498-0.4947-0.90931.71270.87823.1539-0.1107-0.21680.18090.47890.1627-0.63940.12360.65650.00350.2218-0.0086-0.13560.34190.06550.262229.329-31.222311.0652
52.0949-0.8643-0.39037.04443.87144.30760.0207-0.2547-0.18470.476-0.1151-0.10310.56240.01370.07880.22490.024-0.03830.20220.06530.185920.0786-36.907110.1969
64.5608-2.1601-1.22083.85610.77344.32760.0124-0.2665-0.54240.5523-0.07870.16830.4587-0.04490.09440.3694-0.0718-0.05740.23060.08240.32217.1497-42.524414.1931
74.7256-3.4961-3.40384.56663.74824.8406-0.5005-0.5528-0.20741.41220.4157-0.47760.90420.61090.02590.32780.031-0.12190.27750.04330.334830.1869-38.381512.3281
88.7221-4.8677-3.90275.93121.31132.3026-0.5195-0.6720.25570.35961.0865-1.33551.8071.4883-0.45110.63080.1463-0.04250.5295-0.19530.466227.5394-49.985-3.6658
97.7552-5.726-4.25777.53123.95495.90310.08760.352-0.42310.0051-0.25340.17830.2077-0.15850.12320.15380.0001-0.04520.13330.01760.170820.6797-37.6633.0273
102.3666-2.60890.28538.2499-1.96182.56460.0625-0.0943-0.3344-0.15870.00310.89850.3228-0.3467-0.08010.2407-0.07420.00670.2517-0.04230.3675-5.206-18.58143.5063
113.6203-0.72250.17876.00010.0512.3693-0.1054-0.1077-0.05590.39170.0512-0.12350.23270.05490.07030.21150.04130.0520.1682-0.01750.1356.659-20.182210.5226
123.9983-2.3451.22075.9832-1.18382.0622-0.1912-0.42830.22220.55090.18230.2257-0.212-0.21330.0360.28370.00570.05190.2431-0.03710.24541.8134-12.817111.7299
137.1795-5.51112.9844.3071-2.72013.0523-0.02470.11660.1903-0.0009-0.1956-0.18260.12560.0060.1610.1782-0.02680.02890.1738-0.02370.195.1544-17.71932.7851
145.1805-0.67283.02442.782-1.01286.73170.1349-0.0664-1.4232-0.32880.13690.14980.5751-0.6705-0.24450.2826-0.05170.01370.31760.01720.529211.5944-23.0536-18.9238
154.36780.0678-0.10872.11930.44151.9056-0.06120.1875-0.5201-0.10630.0402-0.0716-0.03710.119-0.03120.1214-0.01220.04320.2610.0030.286417.1523-18.1943-18.4055
168.1417-2.71153.60457.6326-2.34815.75-0.4537-0.31270.61150.09460.06640.2562-0.0921-0.69620.46730.30430.05440.06570.244-0.01030.391810.0671-4.2284-13.5178
176.33483.8495.00845.20435.03798.5347-0.03920.67890.0774-0.63890.2769-0.7229-0.76680.6289-0.19310.2708-0.02220.02340.39540.11440.446613.9028-3.6455-23.8397
186.87110.16060.94722.41590.57795.57210.0560.55540.3044-0.19350.1053-0.2927-0.6330.5292-0.13660.17540.00650.04170.23680.04490.305217.7224-9.729-20.3269
191.9713-0.91741.07152.6641-0.51185.8357-0.06190.22580.08140.14580.0701-0.4659-0.78830.7607-0.10420.1859-0.02830.03010.32060.00580.376425.6337-15.2815-15.8203
203.0002-0.42450.61342.736-1.63357.14870.037-0.1843-0.01660.28710.040.2676-0.40620.28670.0190.1107-0.00570.06230.28-0.01120.262314.2701-13.2418-10.1124
210.4606-0.22550.66950.97420.09431.21570.19350.11690.04360.1906-0.08150.4499-0.0939-0.6501-0.03070.0730.01050.01660.35270.05240.225710.569-17.1262-10.4218
225.3175-0.0278-2.56482.63320.74184.66750.44260.19671.6756-0.15020.02-0.4561-0.6950.1792-0.34830.2321-0.00450.03450.31140.06930.517214.2112-33.5575-18.2463
236.36372.69474.8793.17772.03633.7380.0159-0.65851.84260.1792-0.15290.6803-0.4524-1.34040.30580.27780.0827-0.00150.563-0.03150.449-0.4429-34.3242-7.194
246.68530.1186-2.3291.91420.40114.1901-0.05650.44320.11230.06540.0138-0.22410.2933-0.23380.04650.1726-0.0171-0.0230.2013-0.04240.255213.7737-43.3845-18.16
255.04910.552-1.9842.24561.18161.8939-0.27860.7909-0.6478-0.0008-0.014-0.0590.9089-0.68110.13710.3494-0.11160.020.3233-0.07610.355211.5143-49.9607-20.4288
264.6131-0.1502-0.49910.62530.25394.9183-0.0213-0.0539-0.13730.13390.00950.15310.4777-1.13150.11560.2899-0.06440.00660.3505-0.01520.37271.9897-41.6499-10.0801
275.234-0.9521-2.40092.65121.67445.0943-0.1296-0.1762-0.09460.08020.0149-0.2070.23850.33140.0640.1833-0.0008-0.02290.20930.03040.254315.1288-40.7687-11.2341
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 8 )A1 - 8
2X-RAY DIFFRACTION2chain 'A' and (resid 9 through 18 )A9 - 18
3X-RAY DIFFRACTION3chain 'A' and (resid 19 through 27 )A19 - 27
4X-RAY DIFFRACTION4chain 'A' and (resid 28 through 40 )A28 - 40
5X-RAY DIFFRACTION5chain 'A' and (resid 41 through 55 )A41 - 55
6X-RAY DIFFRACTION6chain 'A' and (resid 56 through 85 )A56 - 85
7X-RAY DIFFRACTION7chain 'A' and (resid 86 through 101 )A86 - 101
8X-RAY DIFFRACTION8chain 'A' and (resid 102 through 107 )A102 - 107
9X-RAY DIFFRACTION9chain 'A' and (resid 108 through 128 )A108 - 128
10X-RAY DIFFRACTION10chain 'B' and (resid 3 through 34 )B3 - 34
11X-RAY DIFFRACTION11chain 'B' and (resid 35 through 64 )B35 - 64
12X-RAY DIFFRACTION12chain 'B' and (resid 65 through 107 )B65 - 107
13X-RAY DIFFRACTION13chain 'B' and (resid 108 through 128 )B108 - 128
14X-RAY DIFFRACTION14chain 'C' and (resid 3 through 18 )C3 - 18
15X-RAY DIFFRACTION15chain 'C' and (resid 19 through 52 )C19 - 52
16X-RAY DIFFRACTION16chain 'C' and (resid 53 through 66 )C53 - 66
17X-RAY DIFFRACTION17chain 'C' and (resid 67 through 75 )C67 - 75
18X-RAY DIFFRACTION18chain 'C' and (resid 76 through 91 )C76 - 91
19X-RAY DIFFRACTION19chain 'C' and (resid 92 through 101 )C92 - 101
20X-RAY DIFFRACTION20chain 'C' and (resid 102 through 116 )C102 - 116
21X-RAY DIFFRACTION21chain 'C' and (resid 117 through 127 )C117 - 127
22X-RAY DIFFRACTION22chain 'D' and (resid 3 through 18 )D3 - 18
23X-RAY DIFFRACTION23chain 'D' and (resid 19 through 27 )D19 - 27
24X-RAY DIFFRACTION24chain 'D' and (resid 28 through 64 )D28 - 64
25X-RAY DIFFRACTION25chain 'D' and (resid 65 through 91 )D65 - 91
26X-RAY DIFFRACTION26chain 'D' and (resid 92 through 107 )D92 - 107
27X-RAY DIFFRACTION27chain 'D' and (resid 108 through 128 )D108 - 128

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