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- PDB-3wu3: Reduced-form structure of E.coli Lon Proteolytic domain -

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Basic information

Entry
Database: PDB / ID: 3wu3
TitleReduced-form structure of E.coli Lon Proteolytic domain
ComponentsLon protease
KeywordsHYDROLASE / REDUCED FORM / LON PROTEASE / CATALYTIC DYAD SER-LYS / ATP BINDING
Function / homologyRibosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / 2-Layer Sandwich / Alpha Beta / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsNishii, W. / Kukimoto-Niino, M. / Terada, T. / Shirouzu, M. / Muramatsu, T. / Yokoyama, S.
CitationJournal: Nat. Chem. Biol. / Year: 2015
Title: A redox switch shapes the Lon protease exit pore to facultatively regulate proteolysis.
Authors: Nishii, W. / Kukimoto-Niino, M. / Terada, T. / Shirouzu, M. / Muramatsu, T. / Kojima, M. / Kihara, H. / Yokoyama, S.
History
DepositionApr 22, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Nov 8, 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 / pdbx_initial_refinement_model / 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 / _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: Lon protease
B: Lon protease
C: Lon protease
D: Lon protease
E: Lon protease
F: Lon protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,67911
Polymers128,1996
Non-polymers4805
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10780 Å2
ΔGint-114 kcal/mol
Surface area43660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.238, 86.238, 123.692
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Lon protease


Mass: 21366.500 Da / Num. of mol.: 6
Fragment: C-terminal proteolytic domain, UNP RESIDUES 585-784
Mutation: S679A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12, W3110 / Gene: lon, EcDH1_3170, ECDH1ME8569_0424 / Plasmid: PMAL-C2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C9QQ79, endopeptidase La
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.07 Å3/Da / Density % sol: 40.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.1M AMMONIUM SULFATE, 0.1M PIPES, PH 6.5., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Oct 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 90996 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rsym value: 0.09 / Net I/σ(I): 18.7
Reflection shellResolution: 1.82→1.89 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2 / Rsym value: 0.92 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(PHENIX.REFINE: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RR9
Resolution: 1.82→35.37 Å / σ(F): 1.96 / Phase error: 35.81 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.196 4556 5.01 %
Rwork0.16 --
obs0.163 90917 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.82→35.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8217 0 25 189 8431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078357
X-RAY DIFFRACTIONf_angle_d1.0511360
X-RAY DIFFRACTIONf_dihedral_angle_d13.4293125
X-RAY DIFFRACTIONf_chiral_restr0.0651373
X-RAY DIFFRACTIONf_plane_restr0.0051475
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8211-1.85250.37592200.3633437195
1.8525-1.88620.3472190.3194442695
1.8862-1.92250.36282280.3221438995
1.9225-1.96170.2742180.2982438595
1.9617-2.00430.25952200.2604438495
2.0043-2.05090.2892310.2519434895
2.0509-2.10220.24752390.2449440095
2.1022-2.1590.24752510.223434395
2.159-2.22250.23462330.2144436195
2.2225-2.29430.23942240.208434395
2.2943-2.37620.22062310.2023436895
2.3762-2.47130.19752260.2005444195
2.4713-2.58370.24242200.1958432095
2.5837-2.71980.1862300.1733440495
2.7198-2.89010.20772480.1722436095
2.8901-3.11290.17862140.1547436295
3.1129-3.42570.17272420.1329437095
3.4257-3.92030.16662500.1096430894
3.9203-4.93490.14992240.0921406188
4.9349-28.23140.19731680.1183363379
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.11040.71131.07592.76652.80566.0842-0.21290.2618-0.289-0.11480.0222-0.35750.27920.18050.29810.3169-0.03190.07680.23050.02420.292133.36247.1197-9.863
22.6684-1.5965-0.00554.8243-2.18613.7152-0.0320.1297-0.0855-0.154-0.03760.09420.0471-0.19580.07720.2138-0.02340.00230.2274-0.02940.164321.771614.7482-10.9375
33.0241-0.0477-0.00593.9767-0.90190.8175-0.01750.4926-0.0235-0.4695-0.1256-0.23070.062-0.07050.10680.3098-0.00510.02750.3367-0.00460.150828.305214.7444-14.826
42.822-0.96470.50134.32382.06886.5493-0.05050.00960.2343-0.06730.1323-0.4856-0.07220.1914-0.10350.2535-0.10160.00510.22910.02630.217434.805221.7165-6.8193
54.10582.0331-1.01764.48691.60124.33280.1313-0.7313-1.13730.341-0.3147-1.0310.19580.10010.01250.38660.0091-0.04110.40760.04440.326542.131714.67285.1452
69.3632-3.59994.54592.6754-3.38669.0971-0.2074-0.3152-0.10290.40140.1722-0.323-0.25990.2556-0.03340.3442-0.0953-0.07090.3080.0270.342942.383324.91093.0943
75.7443-2.18342.55494.4143.40747.31850.49791.13720.4068-0.99350.0683-1.1088-0.49580.2448-0.5160.4445-0.03090.07730.4650.03580.289340.793322.8533-14.6411
83.04660.32312.35442.62260.26973.96650.1525-0.052-0.58010.0277-0.0787-0.28450.3387-0.22790.07390.2775-0.03010.06870.27880.0210.432919.5807-14.0712-8.24
93.11352.1512-0.92432.4149-0.84643.8001-0.05030.04350.1333-0.09890.09070.0563-0.1331-0.08440.04380.2402-0.00120.00350.1592-0.00710.274818.574-2.1149-12.7183
108.43750.2874-1.56723.04070.13255.0771-0.06631.0296-0.0179-0.6290.1266-0.0652-0.3266-0.1944-0.00060.4652-0.01560.07840.3098-0.08420.302421.0903-4.5491-23.2157
113.5761-0.5248-2.25420.63970.4264.4376-0.22190.2566-0.1991-0.25160.0197-0.21290.1907-0.14960.24230.3339-0.05560.05040.218-0.0030.326121.7034-10.1082-10.4529
122.6388-0.2081.64272.3179-1.24685.67680.00020.2686-0.225-0.145-0.1163-0.49390.23950.06080.02560.1933-0.00150.0980.267-0.0580.404731.2181-10.1581-9.8349
137.02421.04743.12374.27444.06344.567-0.4227-0.3849-1.16770.4556-0.21130.83850.7843-0.46010.72120.45050.00470.13240.31220.07130.848428.7532-21.29820.8483
144.3994-1.08330.10556.9259-1.19975.8933-0.2017-0.5609-0.88210.52730.2114-0.0660.5170.4076-0.10340.33730.09150.08390.41940.09170.936737.8095-16.3988-0.5913
155.77911.82362.25862.62023.89945.90990.06980.2744-0.9593-0.54760.474-1.0908-0.00440.421-0.39310.39750.01310.16310.383-0.04430.567734.6315-13.8275-18.485
162.5265-0.23280.87753.7937-4.33695.32960.3054-0.1385-0.0892-0.02440.29030.46250.1185-0.1384-0.77660.3201-0.0130.03370.2515-0.02010.4028-7.2707-15.1798-10.4893
175.9151-0.549-0.96193.346-1.03315.6162-0.21160.40020.295-0.2446-0.00830.0234-0.11290.07020.2050.2604-0.0649-0.01020.2243-0.00520.22352.4372-7.7155-14.4273
183.7274-1.3169-0.76144.91120.87395.49710.12590.846-0.4045-1.0994-0.3665-0.1346-0.26930.3550.05180.45320.0076-0.00190.3997-0.02370.38171.4205-10.48-25.2588
192.3117-1.51-0.55423.42991.50742.9899-0.01180.2478-0.1635-0.2703-0.11260.1709-0.0339-0.09110.25340.2702-0.03540.04120.2435-0.02090.2439-3.1122-14.7821-12.8592
204.0096-0.02571.71924.369-1.55158.31910.25490.3737-0.1658-0.5871-0.0714-0.38530.3799-0.3014-0.21350.35620.01450.05060.2375-0.01950.17331.6368-22.9869-13.1173
214.43091.79533.58152.82710.34773.5027-0.05420.2904-0.65180.2470.16890.72710.1637-0.0987-0.01180.3957-0.038-0.02060.3247-0.01870.3923-8.8999-27.506-2.3347
228.75531.6073-3.52064.1902-0.91985.91850.1752-0.0515-0.2395-0.0939-0.0999-0.30140.0960.2623-0.1160.3101-0.0084-0.02930.173-0.03890.39420.0235-32.952-4.6935
232.1414-1.42224.0027.6865-3.21147.60130.44680.8452-0.5797-0.134-0.1605-0.11820.58960.2893-0.47450.40320.00910.02340.3734-0.10660.3393-0.2817-27.3785-21.9767
243.09171.2643-0.12462.9129-0.46453.30880.008-0.17020.355-0.15770.0061.0194-0.3734-0.33190.12740.3589-0.0291-0.06510.3016-0.10170.6548-21.77287.7567-10.0979
252.53160.4357-0.41363.10841.23615.5252-0.01550.0883-0.0456-0.2816-0.05510.251-0.10.20640.18810.2219-0.0073-0.03350.21940.0350.3841-10.47383.6839-14.7301
262.18710.8853-0.64962.21180.17844.5745-0.14610.27320.0308-0.3536-0.05930.2515-0.0159-0.02720.18290.3219-0.0003-0.07220.27-0.02620.4575-15.97894.6788-19.6092
274.97830.6116-2.64981.1604-1.4264.608-0.0096-0.1027-0.0204-0.04540.07860.6084-0.0327-0.3756-0.04230.2853-0.0934-0.03720.3254-0.05630.6937-27.3941-1.5549-10.1415
285.1178-2.24-3.23974.53721.77377.6055-0.2984-0.4281-0.30050.0493-0.01530.51640.2939-0.0590.32850.284-0.10350.00740.3639-0.00640.8173-33.2227-8.2085-6.8388
296.4861-3.6154-1.82586.08960.21237.2703-0.17410.9782-0.5253-0.1982-0.00090.36260.0442-0.65740.0030.3541-0.0541-0.08590.4406-0.03670.7418-28.1406-2.7956-23.4346
301.8749-0.0881-1.36852.5050.46852.85510.15680.03430.7380.04820.10610.2457-0.1771-0.0416-0.00660.2796-0.0242-0.08780.2906-0.00740.6265-9.067931.8129-6.6762
311.15761.09370.02293.3682-0.74931.9744-0.18190.0799-0.0509-0.48350.04290.0953-0.21730.08940.14980.3357-0.0193-0.03870.3058-0.01560.3881-1.366522.508-12.9803
322.65330.628-0.66064.5556-0.61194.5715-0.2450.28250.0024-0.6817-0.05240.35630.1809-0.27890.10540.3095-0.0535-0.06640.2140.01250.4148-12.980120.5969-16.6035
334.9113-0.34772.97862.7061-1.77244.9714-0.10090.87390.337-1.054-0.24020.7024-0.01590.50030.16350.470.0144-0.21270.34910.0470.4314-4.670625.8541-22.5299
342.9279-0.70741.52652.2483-1.04783.4407-0.14830.04050.3084-0.1586-0.02750.5496-0.198-0.11460.1190.25760.0008-0.05250.2054-0.0230.4803-10.651128.2503-9.9863
352.7514-0.8771-2.95891.65170.08837.04910.2030.10350.3301-0.02360.1131.1873-0.1728-0.155-0.18870.2608-0.0124-0.08540.28880.0090.8366-20.109428.3587-11.2823
367.14270.6677-3.28249.27260.03859.41130.0801-0.71331.02920.7034-0.00520.5863-0.8620.0021-0.51550.4363-0.02160.13380.3707-0.11470.9067-20.167337.45011.5208
371.96960.92880.62721.3605-1.5183.93690.2437-0.16310.3420.53480.19151.1875-0.561-1.027-0.11610.11490.09980.15750.4689-0.0112.0141-28.865633.2308-2.9764
384.2748-1.8614.66860.7757-1.97454.9387-0.2466-0.04550.67480.1395-0.0448-0.8168-0.2770.03190.10440.33920.0213-0.08820.33310.020.7445-24.983834.4774-25.0272
394.93460.2-1.4813.86541.44537.2016-0.0263-0.63210.01520.1896-0.2298-0.0255-0.23950.70750.260.2392-0.005-0.01850.3623-0.00550.354716.931533.27690.4671
404.41560.0979-0.83331.8724-0.54741.8515-0.1530.15880.167-0.19090.04540.26080.1269-0.03690.16510.2716-0.0213-0.04110.2166-0.02070.227111.556927.1748-11.0046
416.6104-2.6010.39152.0139-0.50696.1320.02241.25141.3971-1.87940.02870.3484-0.5401-0.19550.11570.5484-0.0683-0.06830.49950.2280.71717.699136.6321-25.2975
426.4956-0.78333.3496.7389-0.96437.43110.0970.6230.213-0.6664-0.350.23090.17720.13630.03960.27790.02820.00260.26350.00060.262414.726225.8966-17.8334
432.3878-0.33630.99943.7048-1.09283.3564-0.11610.25830.1623-0.2545-0.10120.1495-0.13050.12540.21190.2702-0.0275-0.05280.2584-0.02910.26413.954832.4893-7.4235
444.56351.09360.6184.32661.8185.9519-0.1792-0.02690.929-0.25290.03810.2475-0.28350.04530.18610.280.0223-0.07150.1749-0.00230.27799.745840.7262-7.2053
453.78252.8001-4.10959.20650.78587.74580.0189-0.80970.55250.54580.0945-0.845-0.30920.7842-0.03460.3688-0.0186-0.04980.4919-0.16990.455317.998443.12415.7046
466.0340.91.64664.7272-0.10698.2157-0.0619-0.35730.76640.2572-0.12230.3771-0.7484-0.08580.10350.42030.0188-0.04440.2595-0.14080.639810.018149.23442.5865
475.24161.4090.89424.08560.92998.3808-0.19850.91761.0401-0.78190.1316-0.0135-0.31640.6980.16080.4818-0.045-0.05170.34590.11560.618312.92846.0403-13.7928
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 586:619 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 620:647 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 648:693 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 694:718 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 719:732 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 733:762 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 763:775 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 595:619 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 620:647 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 648:669 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 670:693 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 694:718 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 719:732 )
14X-RAY DIFFRACTION14CHAIN B AND (RESID 733:762 )
15X-RAY DIFFRACTION15CHAIN B AND (RESID 763:775 )
16X-RAY DIFFRACTION16CHAIN C AND (RESID 595:619 )
17X-RAY DIFFRACTION17CHAIN C AND (RESID 620:647 )
18X-RAY DIFFRACTION18CHAIN C AND (RESID 648:669 )
19X-RAY DIFFRACTION19CHAIN C AND (RESID 670:693 )
20X-RAY DIFFRACTION20CHAIN C AND (RESID 694:718 )
21X-RAY DIFFRACTION21CHAIN C AND (RESID 719:732 )
22X-RAY DIFFRACTION22CHAIN C AND (RESID 733:762 )
23X-RAY DIFFRACTION23CHAIN C AND (RESID 763:775 )
24X-RAY DIFFRACTION24CHAIN D AND (RESID 595:619 )
25X-RAY DIFFRACTION25CHAIN D AND (RESID 620:647 )
26X-RAY DIFFRACTION26CHAIN D AND (RESID 648:693 )
27X-RAY DIFFRACTION27CHAIN D AND (RESID 694:732 )
28X-RAY DIFFRACTION28CHAIN D AND (RESID 733:762 )
29X-RAY DIFFRACTION29CHAIN D AND (RESID 763:775 )
30X-RAY DIFFRACTION30CHAIN E AND (RESID 595:619 )
31X-RAY DIFFRACTION31CHAIN E AND (RESID 620:631 )
32X-RAY DIFFRACTION32CHAIN E AND (RESID 632:652 )
33X-RAY DIFFRACTION33CHAIN E AND (RESID 653:669 )
34X-RAY DIFFRACTION34CHAIN E AND (RESID 670:693 )
35X-RAY DIFFRACTION35CHAIN E AND (RESID 694:718 )
36X-RAY DIFFRACTION36CHAIN E AND (RESID 719:732 )
37X-RAY DIFFRACTION37CHAIN E AND (RESID 733:762 )
38X-RAY DIFFRACTION38CHAIN E AND (RESID 763:784 )
39X-RAY DIFFRACTION39CHAIN F AND (RESID 595:609 )
40X-RAY DIFFRACTION40CHAIN F AND (RESID 610:647 )
41X-RAY DIFFRACTION41CHAIN F AND (RESID 648:657 )
42X-RAY DIFFRACTION42CHAIN F AND (RESID 658:669 )
43X-RAY DIFFRACTION43CHAIN F AND (RESID 670:693 )
44X-RAY DIFFRACTION44CHAIN F AND (RESID 694:718 )
45X-RAY DIFFRACTION45CHAIN F AND (RESID 719:732 )
46X-RAY DIFFRACTION46CHAIN F AND (RESID 733:762 )
47X-RAY DIFFRACTION47CHAIN F AND (RESID 763:773 )

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