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- PDB-3wu5: Reduced E.coli Lon Proteolytic domain -

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Basic information

Entry
Database: PDB / ID: 3wu5
TitleReduced E.coli Lon Proteolytic domain
ComponentsLon proteaseLon protease family
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: 2.07 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
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9930 Å2
ΔGint-115 kcal/mol
Surface area43350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.350, 86.350, 124.375
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 / Lon protease family


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
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.09 Å3/Da / Density % sol: 41.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.0M AMMONIUM SULFATE, 0.1M BIS-TRIS, 10MM DTT, 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: BL26B2 / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.069→50 Å / Num. obs: 63282 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rsym value: 0.08 / Net I/σ(I): 21.6
Reflection shellResolution: 2.07→2.14 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.996 / % 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: 2.07→40.79 Å / SU ML: 0.25 / σ(F): 1.98 / Phase error: 28.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.234 3209 5.08 %
Rwork0.183 --
obs0.185 63199 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.07→40.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8131 0 25 123 8279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088281
X-RAY DIFFRACTIONf_angle_d1.07211257
X-RAY DIFFRACTIONf_dihedral_angle_d15.1273102
X-RAY DIFFRACTIONf_chiral_restr0.0691365
X-RAY DIFFRACTIONf_plane_restr0.0051457
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0692-2.10.38631470.31882564100
2.1-2.13290.33351240.30132637100
2.1329-2.16780.33641680.28242584100
2.1678-2.20520.3331300.26772626100
2.2052-2.24530.29181470.23622564100
2.2453-2.28850.2891410.21622625100
2.2885-2.33520.31251280.21572641100
2.3352-2.3860.25881490.21242586100
2.386-2.44150.2881310.21072616100
2.4415-2.50250.2681380.21632615100
2.5025-2.57020.26781240.19742629100
2.5702-2.64580.23491450.18712590100
2.6458-2.73120.24541300.18182637100
2.7312-2.82870.26231460.19152578100
2.8287-2.9420.22791550.18432605100
2.942-3.07580.25531210.18852653100
3.0758-3.23790.27521280.19362615100
3.2379-3.44070.26691510.19542604100
3.4407-3.70620.26051560.18032590100
3.7062-4.07880.20211540.15842608100
4.0788-4.66830.16961390.14062590100
4.6683-5.87880.18731290.16932633100
5.8788-40.79530.20321280.1678260099
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)
10.1522-0.2882-0.64321.19571.79313.30950.1021-0.2309-0.29040.2368-0.0553-0.2413-0.12550.79540.0670.2576-0.02630.00490.4516-0.02210.291261.134327.05192.2782
20.7301-0.6392-0.80232.338-0.05791.53340.0489-0.2004-0.04670.2325-0.0493-0.406-0.04950.04650.05920.21170.0004-0.03760.37940.01750.056962.464634.93889.0139
31.96520.0659-0.50051.2858-0.04342.36380.139-0.5910.13080.4101-0.0048-0.0392-0.1086-0.0134-0.08160.35370.01420.04460.4847-0.02950.190560.422833.833713.6328
41.0091-0.40340.91130.82320.12513.75920.0647-0.7643-0.73990.24080.12620.21660.64490.0650.8310.25650.03260.1890.55280.03-0.635854.00726.034311.3426
53.0876-1.8897-0.97822.0801-0.1031.5878-0.0639-0.1816-0.9705-0.2614-0.0180.7054-0.103-0.03180.01530.1813-0.0150.0590.423-0.21830.006649.159229.1256-1.8747
60.9533-2.5309-0.52247.46721.75212.81050.38251.2061-1.0947-1.586-0.32810.60210.2447-0.370.20840.4862-0.0748-0.02970.632-0.15270.527643.154523.124-10.7852
73.4172-1.9999-0.54972.51120.72044.5349-0.0678-0.8032-0.74070.4773-0.12950.74210.4351-0.56520.27230.3165-0.1290.10330.6573-0.04390.232144.459526.29988.8022
82.82350.1873-0.66442.6726-0.27166.430.17520.0042-0.9883-0.09870.0964-0.5015-0.11810.332-0.1670.2255-0.00420.04030.3040.03820.667788.005324.49122.5454
92.23430.0778-0.38872.0648-0.29090.50490.1214-0.3770.21990.09680.0983-0.30970.00050.0018-0.18690.2190.0174-0.03030.34830.04990.338381.239630.858412.0022
101.88940.6840.93872.2278-0.80431.11670.1463-0.5594-0.14010.3875-0.05140.2152-0.1948-0.0248-0.08890.25620.00680.0570.4440.09510.254581.881428.004615.9993
110.5382-0.2675-0.4141.76740.42893.5955-0.1386-0.4816-0.75180.0922-0.0462-0.22350.46380.4966-0.07110.23650.0347-0.06460.40770.14580.489179.420317.86158.4433
125.49941.26690.16261.8636-0.94010.6122-0.4722-0.5747-0.5103-0.06390.2486-0.22050.54780.4338-0.24930.29780.24050.25740.4029-0.04580.632389.166515.19-4.3719
131.28770.7196-0.79932.5438-0.47763.84250.638-0.2377-0.402-0.0632-0.02820.42260.5010.2045-0.19130.3650.0172-0.04380.24730.11491.05782.890711.75143.0245
144.57760.01141.84740.0657-0.0560.98940.31081.0684-0.6563-0.9385-0.07090.04680.79030.4473-0.2760.93810.152-0.00350.4391-0.04931.117984.15626.9304-6.3976
151.6397-0.55731.15780.71420.37071.87640.3479-0.543-1.20870.3608-0.2622-0.03580.2757-0.0933-0.26550.36910.01630.00270.24840.17430.841579.928411.214410.8054
161.72220.8101-2.33312.4696-1.06035.33560.0281-0.07740.69970.2559-0.2101-0.0843-0.949-0.70930.01740.33450.12920.05010.4760.07770.2807104.001947.65665.5746
175.4909-3.2179-4.65493.33183.52124.55370.29290.51690.1895-0.0625-0.0094-0.3987-0.26330.0481-0.08860.29180.03610.00950.49940.09190.4304101.719449.833712.632
182.22110.6652-0.04192.0152-0.4540.15950.1192-0.2530.63930.32010.00140.8736-0.0891-0.5941-0.17920.2345-0.00760.09610.3079-0.05050.228492.119343.223713.7714
191.8484-0.12830.38871.6004-0.03190.45860.0065-0.18430.0620.45480.0315-0.0598-0.0567-0.1268-0.05090.38770.0499-0.00630.37040.05210.165697.552544.587618.0748
202.0279-0.1148-0.68922.55070.35854.8024-0.0862-0.195-0.17060.70090.2949-0.10160.14710.2836-0.16730.29110.116-0.01970.3438-0.00880.2048105.351636.988211.8129
212.59840.2697-0.1174.52480.17994.57970.04090.41480.0552-0.10840.17760.08970.0960.5641-0.20370.14850.0444-0.01360.4331-0.04910.3225113.284737.30211.5116
222.96360.6688-1.90941.21450.25193.0562-0.1034-0.0357-0.54250.3814-0.0052-0.5787-0.04620.1463-0.01450.35510.0988-0.11780.44440.05580.3896113.96335.754611.5677
230.5392-0.3220.3052.4556-2.97136.450.3190.2060.4441-0.81490.0964-0.1510.4128-1.425-0.44130.3433-0.0123-0.22210.5016-0.02560.73692.64772.91235.5905
242.399-1.09791.60232.6760.60452.0134-0.2409-0.18360.33140.15180.0468-0.1074-0.0026-0.26080.18520.20410.0357-0.01160.3273-0.05720.421188.398764.28413.1837
256.6752-0.3067-2.4220.54820.06840.86750.3743-1.187-0.41370.8226-0.4598-0.34480.57210.3004-0.13970.78760.1828-0.1580.8313-0.11160.447992.046461.259328.7395
262.64130.39060.95912.14722.09522.7922-0.6772-0.06940.94580.22180.01420.2553-0.5853-0.00210.36610.32470.1114-0.10140.2836-0.09570.416189.45668.534513.0678
271.53430.9487-0.99432.1501-0.79293.9424-0.2488-0.24120.9650.08620.2034-0.1249-0.20760.50940.05590.2334-0.001-0.11420.3982-0.04230.736101.260368.888813.1449
280.11380.08540.0533.6869-1.172.09840.02410.12010.123-0.4007-0.2803-0.694-0.16180.43430.24510.366-0.0536-0.0920.35450.03620.8985107.576476.09764.4154
297.4141-2.2225-1.2936.8996-2.64783.0147-0.5051-1.25360.94740.43340.1062-0.753-0.3366-0.21660.19670.49380.047-0.32790.4771-0.24380.8432103.110472.921422.2047
303.42821.16811.23933.5143-2.30225.13050.0757-0.34771.13280.12180.19850.69950.32910.2631-0.06750.34450.0644-0.05130.39280.04181.060863.548675.95843.6742
314.47352.52-0.64536.2956-3.18992.5442-0.55830.5171.4015-0.34460.15680.5015-0.4488-0.68870.2350.38070.133-0.12910.375-0.15930.90662.203972.12198.7042
321.57360.29210.52580.4915-0.28460.79980.0116-0.37120.30220.13990.0706-0.190.03570.3056-0.05260.26910.0757-0.05140.3223-0.13430.536972.024166.490611.8739
331.74921.89171.17752.13371.02420.85670.0073-1.09840.33481.0510.43420.02380.4380.0259-0.17690.57240.0811-0.13760.681-0.43020.723468.75369.232623.7311
340.6819-0.9022-0.77982.27041.36991.0459-0.2529-0.34090.94290.23140.0990.43180.15780.1498-0.06590.38110.0745-0.08260.3557-0.20650.785766.669272.92748.4994
352.9518-1.6342-3.80011.64741.28025.88980.30460.46720.76450.36890.49011.3227-1.1046-2.1029-0.23340.53950.2073-0.03370.6602-0.03961.470561.37183.469113.4682
362.1539-1.2283-0.96640.95261.10771.91970.33070.57580.7172-0.3613-0.0144-0.3111-0.41790.2386-0.13810.3391-0.0459-0.09260.37050.03941.383971.403383.06992.5997
370.82890.34281.18891.40092.55465.4503-0.44590.25640.4409-0.5380.5187-0.9385-0.95890.3596-0.50890.6215-0.0086-0.03950.4378-0.07121.586875.225690.32321.41
383.2662-1.5160.89372.3163-3.50336.13950.33860.51521.0648-0.03990.76510.6896-0.6214-0.7718-0.39570.73850.0778-0.16040.47760.14241.853668.816692.79022.9081
390.1131-0.6133-0.58162.74522.6472.4532-0.1916-0.0074-1.54450.6592-0.09830.65180.8702-0.198-0.00150.55530.0456-0.07280.3699-0.25291.137568.805688.750123.8358
402.8201-0.4247-0.5721.9496-0.89596.938-0.52430.51050.1338-0.1787-0.09210.19620.4692-0.4680.32440.38-0.0203-0.16820.3998-0.05780.336248.923452.0196-1.7437
412.65410.4187-0.49981.9203-0.50681.4040.0993-0.45530.82260.2593-0.06790.0905-0.01310.0775-0.09530.25560.0186-0.00610.389-0.16470.284455.718254.943811.3891
420.72790.23720.87781.25621.35941.9096-0.038-0.82470.80660.6866-0.1340.1240.1322-0.023-0.26490.57820.08980.01070.5401-0.6557-0.261855.250452.052319.0665
431.1131-0.04810.59292.63860.26912.0318-0.0513-0.36550.60720.4842-0.03880.70890.0168-0.52220.2060.29220.03660.05030.5006-0.09180.348347.197454.26327.1105
443.25290.6221-0.73990.3882-0.05751.5847-0.13010.17160.2405-0.23520.2410.1412-0.5612-0.4146-0.0630.39640.0776-0.1890.3677-0.01610.76245.484461.6158-1.6457
452.406-0.721-0.70190.97292.06174.96210.08750.08920.8769-0.2181-0.041-0.292-0.738-0.3820.09640.48990.2075-0.21540.54630.03141.134241.183568.4499-4.4033
462.17931.19431.64150.72280.61123.00530.33080.29080.583-0.3319-0.17450.9672-0.0268-0.93170.36780.26890.1392-0.34650.7542-0.22551.205536.007463.9535-3.3417
472.79070.2102-0.80170.0665-0.22530.7074-0.2511-0.3107-0.10970.0815-0.04590.22360.04720.0421-0.3374-0.23370.60370.24290.5803-0.5490.920240.084962.698812.042
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 594:606 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 607:647 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 648:680 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 681:703 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 704:740 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 741:754 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 755:775 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 595:608 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 609:648 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 649:693 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 694:718 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 719:728 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 729:740 )
14X-RAY DIFFRACTION14CHAIN B AND (RESID 741:754 )
15X-RAY DIFFRACTION15CHAIN B AND (RESID 755:772 )
16X-RAY DIFFRACTION16CHAIN C AND (RESID 595:606 )
17X-RAY DIFFRACTION17CHAIN C AND (RESID 607:619 )
18X-RAY DIFFRACTION18CHAIN C AND (RESID 620:648 )
19X-RAY DIFFRACTION19CHAIN C AND (RESID 649:693 )
20X-RAY DIFFRACTION20CHAIN C AND (RESID 694:718 )
21X-RAY DIFFRACTION21CHAIN C AND (RESID 719:746 )
22X-RAY DIFFRACTION22CHAIN C AND (RESID 747:775 )
23X-RAY DIFFRACTION23CHAIN D AND (RESID 595:606 )
24X-RAY DIFFRACTION24CHAIN D AND (RESID 607:647 )
25X-RAY DIFFRACTION25CHAIN D AND (RESID 648:661 )
26X-RAY DIFFRACTION26CHAIN D AND (RESID 662:693 )
27X-RAY DIFFRACTION27CHAIN D AND (RESID 694:718 )
28X-RAY DIFFRACTION28CHAIN D AND (RESID 719:762 )
29X-RAY DIFFRACTION29CHAIN D AND (RESID 763:775 )
30X-RAY DIFFRACTION30CHAIN E AND (RESID 594:606 )
31X-RAY DIFFRACTION31CHAIN E AND (RESID 607:619 )
32X-RAY DIFFRACTION32CHAIN E AND (RESID 620:647 )
33X-RAY DIFFRACTION33CHAIN E AND (RESID 648:667 )
34X-RAY DIFFRACTION34CHAIN E AND (RESID 668:693 )
35X-RAY DIFFRACTION35CHAIN E AND (RESID 694:703 )
36X-RAY DIFFRACTION36CHAIN E AND (RESID 704:732 )
37X-RAY DIFFRACTION37CHAIN E AND (RESID 733:746 )
38X-RAY DIFFRACTION38CHAIN E AND (RESID 747:762 )
39X-RAY DIFFRACTION39CHAIN E AND (RESID 763:784 )
40X-RAY DIFFRACTION40CHAIN F AND (RESID 595:609 )
41X-RAY DIFFRACTION41CHAIN F AND (RESID 610:652 )
42X-RAY DIFFRACTION42CHAIN F AND (RESID 653:669 )
43X-RAY DIFFRACTION43CHAIN F AND (RESID 670:703 )
44X-RAY DIFFRACTION44CHAIN F AND (RESID 704:732 )
45X-RAY DIFFRACTION45CHAIN F AND (RESID 733:746 )
46X-RAY DIFFRACTION46CHAIN F AND (RESID 747:762 )
47X-RAY DIFFRACTION47CHAIN F AND (RESID 763:772 )

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