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- PDB-6mjr: Azurin 122W/124F/126Re -

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Basic information

Entry
Database: PDB / ID: 6mjr
TitleAzurin 122W/124F/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 / plasma membrane
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.012 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 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)58,25212
Polymers56,0844
Non-polymers2,1688
Water10,359575
1
A: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5633
Polymers14,0211
Non-polymers5422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5633
Polymers14,0211
Non-polymers5422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5633
Polymers14,0211
Non-polymers5422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5633
Polymers14,0211
Non-polymers5422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.250, 63.260, 133.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Azurin


Mass: 14020.887 Da / Num. of mol.: 4 / Mutation: W48F, Y72F, H83Q, Y108F, K122W, T124F, 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


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


Mass: 18.015 Da / Num. of mol.: 575 / 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: 47.59 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 4.5
Details: 0.1 M NaOAc, 120 mM/150 mM Li2SO4, and 48.6% PEG 400/27.7% PEG 8000 at pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.01→45.95 Å / Num. obs: 34806 / % possible obs: 97.6 % / Redundancy: 2.8 % / Biso Wilson estimate: 21.54 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.05 / Rrim(I) all: 0.089 / Net I/σ(I): 10.5 / Num. measured all: 98612 / Scaling rejects: 31
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.01-2.062.60.217659224930.8210.1560.2695.196.2
9-45.952.70.05910533880.9860.0410.07316.985.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.03 Å45.56 Å
Translation3.03 Å45.56 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA0.1.26data scaling
PHASER2.5.2phasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.012→22.973 Å / FOM work R set: 0.8862 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1893 1748 5.04 %
Rwork0.1452 32915 -
obs0.1474 34663 96.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.22 Å2 / Biso mean: 26.97 Å2 / Biso min: 8.71 Å2
Refinement stepCycle: final / Resolution: 2.012→22.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3877 0 96 575 4548
Biso mean--19.67 33.88 -
Num. residues----512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084061
X-RAY DIFFRACTIONf_angle_d1.2325507
X-RAY DIFFRACTIONf_chiral_restr0.074596
X-RAY DIFFRACTIONf_plane_restr0.004706
X-RAY DIFFRACTIONf_dihedral_angle_d13.1461424
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.012-2.07120.20771320.16462656278895
2.0712-2.1380.21311470.14912687283497
2.138-2.21440.20451420.15432705284797
2.2144-2.30290.21791460.15782705285197
2.3029-2.40760.18871700.15212720289098
2.4076-2.53440.20871500.1522758290898
2.5344-2.6930.21231650.14962750291598
2.693-2.90060.22241420.15492776291898
2.9006-3.19180.1971330.15672792292598
3.1918-3.6520.19121460.13792778292497
3.652-4.59510.15471380.13222788292696
4.5951-22.97480.15531370.13332800293792
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)
15.3807-2.87173.64492.6305-3.59575.68480.52290.47130.2429-0.7814-0.4346-0.93270.1911.1048-0.02670.1773-0.04860.00450.42240.02660.4283-1.9038-1.654423.9772
25.4024-5.7571-2.52757.56751.89734.89930.0730.27260.137-0.5790.0488-0.1968-0.18780.1808-0.11180.2213-0.0612-0.01090.21290.01250.2631-15.53962.033221.076
32.0750.4786-0.38352.1179-0.12790.08310.2670.631-0.4124-0.1656-0.238-0.82480.48491.1910.10610.16280.0853-0.0210.4047-0.03870.37640.4137-12.178124.2617
44.4482-1.5974-0.54253.18661.17712.4041-0.0109-0.05840.48270.02390.0648-0.3753-0.38030.3152-0.01050.1984-0.0525-0.0330.16630.01180.2358-11.96194.089629.231
57.8812-1.8681-4.56373.90892.01516.86440.04810.0804-0.05050.2228-0.05370.02570.0591-0.11210.02180.164-0.004-0.02510.09530.01050.1397-19.3732-9.93134.0895
67.8395-7.124-0.15016.95380.97083.3182-0.4795-0.25980.28470.32070.3868-0.3161-0.3660.22430.11440.1743-0.0199-0.03970.1749-0.02330.1444-18.8963-0.455640.8336
72.5115-0.2508-0.30633.7696-1.24323.382-0.0012-0.25580.29180.8568-0.0938-0.4769-0.29720.25730.10860.20020.0001-0.03040.1816-0.04680.1912-12.1349-2.210736.2602
84.0926-2.7334-0.59646.61920.20142.70720.0858-0.4006-0.06060.6060.1626-0.22340.03870.6022-0.17520.18060.0039-0.11830.2893-0.08060.3524-2.8544-6.182333.7426
93.4577-3.14944.42864.1008-4.76976.11771.21980.477-1.2396-0.4414-0.4249-0.7632.330.7905-0.49250.52420.0564-0.14140.2876-0.0850.5869-6.9164-20.275727.4917
104.2841-1.9601-0.79613.19061.51523.42930.008-0.0162-0.11280.05360.08480.0144-0.07030.1388-0.10520.1046-0.01700.10460.00640.1363-15.468-7.313726.0251
114.90144.9784.04785.11084.36565.23660.768-0.0898-1.29360.26390.1541-1.39390.29110.7774-1.10060.2880.0085-0.0360.27530.00270.3972-13.2196-31.128346.1605
129.69122.07096.31123.57622.53264.58780.2187-0.1796-0.11380.05260.01020.08020.4605-0.1321-0.2380.19740.00770.0120.14690.01140.2075-27.5995-34.626343.0204
135.0811.043.42671.2726-0.04986.4792-0.04010.1956-0.1624-0.02690.0065-0.2329-0.12560.6473-0.01670.17180.02330.01460.1240.00160.1756-16.3877-28.080845.7216
143.06670.07991.02013.40431.78544.3917-0.0380.01960.18560.18160.0260.115-0.0511-0.08920.03970.2083-0.01850.0040.11910.02680.1885-30.304-20.760544.7689
158.09143.45522.01884.13624.39095.4906-0.03610.36430.3606-0.34590.0102-0.1313-0.5456-0.04130.01630.19120.0028-0.00910.1280.0510.189-29.8736-15.009638.1258
162.76860.68650.67241.2662-0.98841.4574-0.19240.16390.2375-0.03570.01850.1339-0.31380.20410.13450.16-0.0096-0.01790.13050.03940.1614-23.6776-19.040541.4777
172.19681.27482.20592.83982.29785.05340.06860.2355-0.0582-0.10470.3483-0.4263-0.91650.9425-0.29170.2255-0.0814-0.02690.25060.01730.2386-14.2395-20.362946.2042
184.19841.90272.21622.23750.7764.26490.0446-0.34350.08540.2044-0.10980.0068-0.2666-0.00690.10570.1824-0.00330.00250.1194-0.01280.0918-25.6684-25.197352.0144
193.98384.6764-3.9915.5573-4.41445.93940.62471.81311.46490.0164-0.04260.3177-0.7196-1.0706-0.96330.24730.0067-0.00190.43250.19360.2814-32.8376-16.08488.0433
209.2304-4.2934-4.94688.16494.63893.78730.53490.51090.5425-0.5237-0.2596-0.6866-0.75460.2272-0.39210.218-0.00910.02730.24940.08510.2497-17.801-16.77645.782
218.56270.2739-4.40826.9372.37736.98980.14870.13711.00240.1379-0.05250.77810.1043-0.2843-0.07920.2185-0.00550.0060.15480.02140.2163-36.3636-13.67417.836
224.2635-3.1307-4.81563.49953.60197.90350.0030.3997-0.1571-0.1419-0.0049-0.02740.0732-0.178-0.0230.1571-0.0170.00290.1415-0.00550.1244-22.9837-24.44795.16
232.42310.32962.77618.36150.63724.6967-0.2067-0.03150.02180.4010.2473-0.6317-0.06350.3962-0.02950.25010.03320.02180.17470.00150.2385-17.9886-25.794821.3767
249.80731.9346-2.36512.4342-2.35872.3163-0.53260.3285-1.4942-0.71140.1287-0.33730.95860.27730.06680.530.09960.05340.1598-0.01680.338-17.1467-37.189312.5154
255.3348-2.7049-3.18673.14832.10262.6392-0.27430.1718-0.60710.3822-0.0792-0.01150.7116-0.39930.37080.4697-0.00990.08690.2095-0.01280.2752-21.9753-32.819719.581
264.087-0.8578-2.41881.25870.68353.1706-0.23570.4845-0.3918-0.0869-0.02710.10840.4321-0.26660.20050.2022-0.0315-0.01570.1681-0.03110.1729-29.4098-26.363411.1739
275.54864.0697-2.02563.1407-1.14731.47650.20870.38540.73620.78540.22110.4214-0.8745-0.3961-0.36940.34380.08020.04510.27880.0250.3593-30.9643-15.02926.7671
288.9013-5.0324-7.76175.06215.26878.5278-0.0458-0.01010.0362-0.05790.02760.04820.14160.1402-0.01740.13710.0032-0.02450.10560.01350.0929-20.0011-19.209915.8481
292.1012.3083.36712.71383.70515.35611.33250.4068-2.09461.0945-0.247-1.71011.08540.8989-0.9340.29870.0163-0.13620.3641-0.02570.5998-16.577-6.19832.0981
308.49253.64155.24878.13194.22173.91950.4603-0.0888-1.12420.7353-0.0688-0.06811.0282-0.2687-0.35420.3181-0.0693-0.04440.28690.04130.3682-31.4077-9.73050.6813
314.09310.2001-5.00945.2572-0.34116.162-0.043-0.3043-0.93190.16590.0376-0.7738-0.15531.2324-0.05320.2833-0.0518-0.00830.4733-0.02950.2418-14.45322.00047.9486
320.21420.09930.73431.15060.9462.8272-0.11811.2179-0.7848-0.25080.4464-0.47940.20170.6886-0.27440.2298-0.03790.01740.3617-0.20110.3584-26.7255-6.9892-6.7584
335.657-0.77491.99042.1702-0.2892.418-0.22730.42080.4367-0.09440.09580.1208-0.18820.18820.17720.256-0.0755-0.02870.19070.03450.1632-33.00598.0072-3.0374
341.4037-1.46630.17433.40891.48871.5395-0.31220.96690.5133-1.2477-0.1665-0.2323-0.53990.4257-0.73940.569-0.40330.02170.58520.2734-0.084-31.63364.5273-13.9073
352.07920.85571.83763.45791.84192.0894-0.41741.2983-0.0746-0.87950.2375-0.0841-0.35060.9325-0.34960.2813-0.20370.12010.4643-0.12770.2072-25.81062.3031-8.6196
365.907-0.23690.38317.08853.35117.72160.26090.6815-0.2043-0.1605-0.1588-0.4085-0.32860.4178-0.09470.2164-0.130.03530.5045-0.08020.3037-16.75012.9233-3.5784
374.79991.05011.22751.75510.19023.1542-0.11950.06280.0841-0.00520.136-0.1105-0.2570.2337-0.03390.1889-0.0345-0.00240.1211-0.01240.1438-28.49513.08723.3294
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 48 )A28 - 48
5X-RAY DIFFRACTION5chain 'A' and (resid 49 through 66 )A49 - 66
6X-RAY DIFFRACTION6chain 'A' and (resid 67 through 75 )A67 - 75
7X-RAY DIFFRACTION7chain 'A' and (resid 76 through 91 )A76 - 91
8X-RAY DIFFRACTION8chain 'A' and (resid 92 through 101 )A92 - 101
9X-RAY DIFFRACTION9chain 'A' and (resid 102 through 107 )A102 - 107
10X-RAY DIFFRACTION10chain 'A' and (resid 108 through 128 )A108 - 128
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 8 )B1 - 8
12X-RAY DIFFRACTION12chain 'B' and (resid 9 through 18 )B9 - 18
13X-RAY DIFFRACTION13chain 'B' and (resid 19 through 40 )B19 - 40
14X-RAY DIFFRACTION14chain 'B' and (resid 41 through 66 )B41 - 66
15X-RAY DIFFRACTION15chain 'B' and (resid 67 through 75 )B67 - 75
16X-RAY DIFFRACTION16chain 'B' and (resid 76 through 91 )B76 - 91
17X-RAY DIFFRACTION17chain 'B' and (resid 92 through 101 )B92 - 101
18X-RAY DIFFRACTION18chain 'B' and (resid 102 through 128 )B102 - 128
19X-RAY DIFFRACTION19chain 'C' and (resid 1 through 8 )C1 - 8
20X-RAY DIFFRACTION20chain 'C' and (resid 9 through 18 )C9 - 18
21X-RAY DIFFRACTION21chain 'C' and (resid 19 through 27 )C19 - 27
22X-RAY DIFFRACTION22chain 'C' and (resid 28 through 48 )C28 - 48
23X-RAY DIFFRACTION23chain 'C' and (resid 49 through 64 )C49 - 64
24X-RAY DIFFRACTION24chain 'C' and (resid 65 through 70 )C65 - 70
25X-RAY DIFFRACTION25chain 'C' and (resid 71 through 80 )C71 - 80
26X-RAY DIFFRACTION26chain 'C' and (resid 81 through 101 )C81 - 101
27X-RAY DIFFRACTION27chain 'C' and (resid 102 through 107 )C102 - 107
28X-RAY DIFFRACTION28chain 'C' and (resid 108 through 128 )C108 - 128
29X-RAY DIFFRACTION29chain 'D' and (resid 1 through 8 )D1 - 8
30X-RAY DIFFRACTION30chain 'D' and (resid 9 through 18 )D9 - 18
31X-RAY DIFFRACTION31chain 'D' and (resid 19 through 27 )D19 - 27
32X-RAY DIFFRACTION32chain 'D' and (resid 28 through 48 )D28 - 48
33X-RAY DIFFRACTION33chain 'D' and (resid 49 through 66 )D49 - 66
34X-RAY DIFFRACTION34chain 'D' and (resid 67 through 75 )D67 - 75
35X-RAY DIFFRACTION35chain 'D' and (resid 76 through 91 )D76 - 91
36X-RAY DIFFRACTION36chain 'D' and (resid 92 through 101 )D92 - 101
37X-RAY DIFFRACTION37chain 'D' and (resid 102 through 128 )D102 - 128

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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