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- PDB-5k4a: Structure of the amidase mutant E79A at 2.3 Angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 5k4a
TitleStructure of the amidase mutant E79A at 2.3 Angstrom resolution
ComponentsIntracellular protease/amidase
KeywordsLYASE / Heat Shock Protein
Function / homology
Function and homology information


D-lactate dehydratase / protein deglycase activity / DNA repair / cytoplasm
Similarity search - Function
Protein/nucleic acid deglycase HchA / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-lactate dehydratase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChowdhury, S.R. / Sen, U.
CitationJournal: To Be Published
Title: Structure of the amidase mutant E79A at 2.3 Angstrom resolution
Authors: Chowdhury, S.R. / Sen, U.
History
DepositionMay 20, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Intracellular protease/amidase
F: Intracellular protease/amidase
A: Intracellular protease/amidase
B: Intracellular protease/amidase
D: Intracellular protease/amidase
E: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)188,7216
Polymers188,7216
Non-polymers00
Water10,359575
1
C: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)31,4541
Polymers31,4541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)31,4541
Polymers31,4541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)31,4541
Polymers31,4541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)31,4541
Polymers31,4541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
D: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)31,4541
Polymers31,4541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
E: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)31,4541
Polymers31,4541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
C: Intracellular protease/amidase
D: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)62,9072
Polymers62,9072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-5 kcal/mol
Surface area21500 Å2
MethodPISA
8
F: Intracellular protease/amidase
E: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)62,9072
Polymers62,9072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-3 kcal/mol
Surface area21650 Å2
MethodPISA
9
A: Intracellular protease/amidase
B: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)62,9072
Polymers62,9072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-4 kcal/mol
Surface area21450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.395, 79.630, 106.412
Angle α, β, γ (deg.)90.00, 107.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Intracellular protease/amidase


Mass: 31453.518 Da / Num. of mol.: 6 / Mutation: E79A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) (bacteria)
Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: VC0395_0351, VC395_A0912 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3AFW5, D-lactate dehydratase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 575 / 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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 5% PEG 6000, 0.1M sodium citrate (pH 5.0), 8% MPD against a reservoir solution of 15% PEG 6000, 0.1M Tris-Hcl (pH 8.5), 5% MPD.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 68904 / % possible obs: 92.2 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 6.7
Reflection shellResolution: 2.3→2.42 Å

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N57
Resolution: 2.3→24.73 Å / SU ML: 0.33 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 28.68
RfactorNum. reflection% reflection
Rfree0.2462 3454 5.01 %
Rwork0.1797 --
obs0.1831 68904 92.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→24.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12996 0 0 575 13571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813370
X-RAY DIFFRACTIONf_angle_d1.16218166
X-RAY DIFFRACTIONf_dihedral_angle_d15.4864790
X-RAY DIFFRACTIONf_chiral_restr0.0791908
X-RAY DIFFRACTIONf_plane_restr0.0072395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2927-2.32410.35141260.2772510X-RAY DIFFRACTION88
2.3241-2.35720.35311340.26392598X-RAY DIFFRACTION93
2.3572-2.39240.35841210.25892647X-RAY DIFFRACTION93
2.3924-2.42970.30281360.23762678X-RAY DIFFRACTION93
2.4297-2.46950.31211550.24462599X-RAY DIFFRACTION94
2.4695-2.51210.38631290.24762658X-RAY DIFFRACTION94
2.5121-2.55770.31581390.23052688X-RAY DIFFRACTION95
2.5577-2.60690.31641470.22472663X-RAY DIFFRACTION95
2.6069-2.660.31831410.21952710X-RAY DIFFRACTION95
2.66-2.71780.27011470.21882654X-RAY DIFFRACTION95
2.7178-2.78090.37811210.21892699X-RAY DIFFRACTION95
2.7809-2.85040.28781390.22362699X-RAY DIFFRACTION95
2.8504-2.92730.27711380.21642691X-RAY DIFFRACTION95
2.9273-3.01330.30471440.21632671X-RAY DIFFRACTION95
3.0133-3.11040.26021540.20032690X-RAY DIFFRACTION94
3.1104-3.22130.27371270.19122675X-RAY DIFFRACTION94
3.2213-3.350.2461450.18112647X-RAY DIFFRACTION93
3.35-3.50210.23271550.17462608X-RAY DIFFRACTION93
3.5021-3.68620.23251370.16372656X-RAY DIFFRACTION92
3.6862-3.91630.21381570.15762569X-RAY DIFFRACTION92
3.9163-4.21730.23081430.14372570X-RAY DIFFRACTION90
4.2173-4.63910.18531140.13292581X-RAY DIFFRACTION90
4.6391-5.30470.18971480.14242515X-RAY DIFFRACTION88
5.3047-6.66160.2141350.15332437X-RAY DIFFRACTION85
6.6616-24.73150.16321220.1372337X-RAY DIFFRACTION80
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)
10.9772-0.7427-0.50881.88560.05422.8986-0.04650.02310.35260.15350.0507-0.4267-0.69450.46520.02340.3678-0.0518-0.07180.262-0.01630.3822-6.397227.325731.2791
20.42850.052-0.72242.1373-0.03141.21730.1925-0.3744-0.17220.02370.17750.07550.11140.93930.1010.4020.1023-0.34350.51060.14980.62817.20852.51945.8595
30.40580.125-0.26691.03350.16851.71450.0137-0.0752-0.00620.0384-0.0297-0.32630.06760.18730.03570.21740.0104-0.05170.22360.00140.2981-3.41938.222934.5057
41.9850.5441-0.54671.0870.04082.0692-0.07590.013-0.21430.1241-0.1185-0.36310.52870.05120.15830.46160.0268-0.03990.2453-0.0050.3456-7.6939-5.701630.535
50.42920.0846-0.22851.41310.00861.838-0.0199-0.02150.0140.0707-0.03050.07510.1906-0.25310.03070.3141-0.0254-0.02170.2264-0.01950.2514-15.95734.226642.5805
60.2870.4839-0.03691.1462-0.10171.15580.1148-0.10950.01060.4063-0.0941-0.1719-0.1351-0.1849-0.02260.39450.0038-0.04610.2845-0.01160.3047-15.732711.453647.5252
73.10730.2382-0.28712.75360.49982.9809-0.0227-0.5053-0.04890.1337-0.1381-0.32040.59210.34950.09040.5305-0.0021-0.11910.29420.03160.3243-0.8526-0.122950.1351
80.8445-0.3119-0.06830.21610.09460.03860.3441-0.21880.2767-0.02420.23450.3432-0.2011-0.1257-0.42670.62310.09760.18470.72740.02140.456-74.42512.096166.7866
90.6872-0.7171-0.47791.13910.45832.03360.1069-0.2380.4139-0.02620.00160.0928-0.8862-0.19170.03220.8743-0.0020.11470.4093-0.05860.4492-57.603314.705572.0814
100.1323-0.0564-0.04372.31481.20281.96370.1466-0.46380.2807-0.364-0.0816-0.3966-1.5234-0.4116-0.13421.29740.15020.13270.5153-0.01230.5329-60.077519.924970.9979
110.6280.3549-0.23751.30970.2431.2117-0.17740.1168-0.037-0.38060.3498-0.8403-1.04630.12750.07231.5244-0.55880.1270.6799-0.10880.6284-43.391819.661662.4905
121.5287-0.20620.63450.7495-0.02411.4037-0.02180.31330.06830.28770.3607-0.0855-1.38340.5158-0.15140.6715-0.17020.17320.3682-0.07330.4657-47.61569.169867.9888
133.07290.42610.86792.24420.63853.31980.1029-0.2025-0.06150.3980.396-0.1782-0.12670.6044-0.39420.4787-0.08850.06470.4954-0.13820.3891-47.92394.210775.8296
140.5095-0.0877-0.66131.9459-0.893.33750.0912-0.0780.1350.72790.424-0.03270.1018-0.0866-0.2920.506-0.01040.01830.349-0.02230.3041-52.63620.996578.4628
153.18171.62412.27661.09981.53972.576-0.1721-0.18610.52870.36750.4215-0.1107-0.81490.49160.00641.57970.01440.18850.4315-0.15780.4244-50.569919.017384.2975
161.21590.34230.31541.3856-0.6352.2406-0.03560.0803-0.1025-0.12140.06210.01790.0385-0.1279-0.01070.10160.01540.0070.1895-0.0440.2236-36.845949.469-4.9486
173.0524-1.3063-0.26931.97350.14453.67540.09830.32760.3366-0.6113-0.11810.1138-0.3907-0.0748-0.05070.3265-0.03730.06090.2583-0.05870.2196-30.967349.7718-19.1566
182.2764-0.3115-0.01981.82661.21070.8038-0.1071-0.3522-0.5248-0.04720.30130.17090.3808-0.2606-0.0720.1967-0.0042-0.01580.29390.06440.3934-33.97128.773617.621
190.07770.10680.14552.73630.68630.27220.0772-0.3586-0.05630.355-0.05120.5529-0.158-0.40760.0980.48860.14290.20090.55620.04870.3657-43.252549.917639.5862
200.44860.18060.33951.0068-0.50921.46610.0649-0.1068-0.0790.0986-0.01150.1177-0.2483-0.3519-0.01580.21040.05430.03820.277-0.01020.2458-35.251148.918523.2967
211.0169-0.19250.1821.75080.0671.69280.05060.0112-0.01370.3512-0.13210.1464-0.0426-0.8968-0.07750.19670.07980.04630.47910.04050.3651-45.390744.751926.4947
221.79240.46990.20782.63370.79532.9855-0.1915-0.00960.2688-0.06390.1084-0.1559-0.9742-0.33870.13670.52120.1127-0.04440.2846-0.00080.391-34.091865.836920.5494
231.02670.13560.28851.35950.29951.7933-0.0449-0.0677-0.09450.14990.0452-0.0777-0.23210.06460.01270.20340.0248-0.0080.21830.0070.1885-22.646249.666728.3487
242.2984-0.8149-0.35112.41670.12881.7025-0.137-0.2880.16791.03260.3432-0.2051-0.1454-0.4032-0.14370.45150.13120.03250.34650.0120.217-34.493153.776140.7226
251.14370.44210.92461.80440.4260.95280.41580.11250.56480.0443-0.138-0.1397-0.54920.5902-0.01250.2710.070.13360.32340.11650.53662.796519.078612.6222
262.02310.9749-0.70550.6494-0.23980.32250.03120.41650.4878-1.0008-0.36820.4057-0.2542-0.36640.2190.74070.4123-0.2170.8318-0.04190.6034-26.473822.05740.3051
270.5658-0.85120.12321.60890.01441.66740.29910.2003-0.0278-0.3401-0.27510.1676-0.0079-0.2295-0.04760.30540.0794-0.01750.2679-0.0210.2727-19.682413.139212.7676
281.86030.38290.30361.25140.30711.22770.52190.2613-0.2383-0.3944-0.4440.29430.4837-0.1199-0.08120.51890.1098-0.18250.3269-0.09010.3848-21.2783-0.15268.1831
291.0111-0.60270.51731.33360.37631.98070.87470.4371-0.2483-1.3262-0.5442-0.27010.2974-0.2227-0.08070.64810.41370.01670.4452-0.1210.2658-6.85421.70942.9109
300.7388-0.6201-0.0512.0495-0.05080.72320.74840.6862-0.264-0.9242-0.62390.228-0.0506-0.4044-0.1180.84640.3495-0.17470.6458-0.06610.3808-20.66348.4793-4.07
311.00780.26860.24171.44650.9062.847-0.225-0.07650.06660.60520.32380.2893-0.3881-0.9942-0.03740.62640.24050.07140.79660.03830.4087-75.877813.522746.8826
321.8584-0.6509-0.64121.4834-0.85281.6934-0.4872-0.3617-0.22210.64370.46540.12220.447-0.1227-0.00270.59530.20620.04940.46850.04560.2882-59.2033.952641.7458
331.3476-0.9081-0.97911.99540.74281.068-0.2799-0.1688-0.11160.52350.33420.45621.1923-0.4771-0.00750.6772-0.0040.12460.6570.10660.4862-68.1251-1.629344.3015
340.7741-0.29360.02391.4790.19241.0682-0.4129-0.39610.08480.59350.4763-0.23960.31160.2789-0.02610.49380.3135-0.10.541-0.06960.3081-48.56698.423839.9856
351.20940.1195-0.01350.9427-0.09592.1918-0.3604-0.17320.2050.31280.2703-0.0353-0.4219-0.10530.09570.34950.1582-0.06240.4033-0.01810.2893-59.12820.051733.7186
362.77410.590.3462.91770.07683.50790.010.6141-0.3167-0.52770.00560.07470.6166-0.2225-0.02350.43020.0078-0.00910.3714-0.06830.2249-58.69061.341927.1813
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 5 through 30 )
2X-RAY DIFFRACTION2chain 'C' and (resid 31 through 50 )
3X-RAY DIFFRACTION3chain 'C' and (resid 51 through 124 )
4X-RAY DIFFRACTION4chain 'C' and (resid 125 through 148 )
5X-RAY DIFFRACTION5chain 'C' and (resid 149 through 222 )
6X-RAY DIFFRACTION6chain 'C' and (resid 223 through 264 )
7X-RAY DIFFRACTION7chain 'C' and (resid 265 through 285 )
8X-RAY DIFFRACTION8chain 'F' and (resid 5 through 30 )
9X-RAY DIFFRACTION9chain 'F' and (resid 31 through 76 )
10X-RAY DIFFRACTION10chain 'F' and (resid 77 through 129 )
11X-RAY DIFFRACTION11chain 'F' and (resid 130 through 148 )
12X-RAY DIFFRACTION12chain 'F' and (resid 149 through 175 )
13X-RAY DIFFRACTION13chain 'F' and (resid 176 through 222 )
14X-RAY DIFFRACTION14chain 'F' and (resid 223 through 264 )
15X-RAY DIFFRACTION15chain 'F' and (resid 265 through 285 )
16X-RAY DIFFRACTION16chain 'A' and (resid 5 through 264 )
17X-RAY DIFFRACTION17chain 'A' and (resid 265 through 285 )
18X-RAY DIFFRACTION18chain 'B' and (resid 5 through 30 )
19X-RAY DIFFRACTION19chain 'B' and (resid 31 through 50 )
20X-RAY DIFFRACTION20chain 'B' and (resid 51 through 107 )
21X-RAY DIFFRACTION21chain 'B' and (resid 108 through 130 )
22X-RAY DIFFRACTION22chain 'B' and (resid 131 through 148 )
23X-RAY DIFFRACTION23chain 'B' and (resid 149 through 264 )
24X-RAY DIFFRACTION24chain 'B' and (resid 265 through 285 )
25X-RAY DIFFRACTION25chain 'D' and (resid 5 through 30 )
26X-RAY DIFFRACTION26chain 'D' and (resid 31 through 50 )
27X-RAY DIFFRACTION27chain 'D' and (resid 51 through 161 )
28X-RAY DIFFRACTION28chain 'D' and (resid 162 through 197 )
29X-RAY DIFFRACTION29chain 'D' and (resid 198 through 240 )
30X-RAY DIFFRACTION30chain 'D' and (resid 241 through 285 )
31X-RAY DIFFRACTION31chain 'E' and (resid 5 through 40 )
32X-RAY DIFFRACTION32chain 'E' and (resid 41 through 107 )
33X-RAY DIFFRACTION33chain 'E' and (resid 108 through 130 )
34X-RAY DIFFRACTION34chain 'E' and (resid 131 through 197 )
35X-RAY DIFFRACTION35chain 'E' and (resid 198 through 264 )
36X-RAY DIFFRACTION36chain 'E' and (resid 265 through 285 )

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Yorodumi

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  • 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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