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- PDB-7qy6: Structure of E.coli Class 2 L-asparaginase EcAIII, wild type (WT ... -

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Basic information

Entry
Database: PDB / ID: 7qy6
TitleStructure of E.coli Class 2 L-asparaginase EcAIII, wild type (WT EcAIII)
Components
  • Beta-aspartyl-peptidase
  • Isoaspartyl peptidase
KeywordsHYDROLASE / L-asparaginase / mutation
Function / homology
Function and homology information


beta-aspartyl-peptidase / asparagine catabolic process via L-aspartate / asparaginase activity / beta-aspartyl-peptidase activity / protein autoprocessing / hydrolase activity / cytoplasm
Similarity search - Function
Peptidase T2, asparaginase 2 / Asparaginase / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
Beta-aspartyl-peptidase / Isoaspartyl peptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLoch, J.I. / Klonecka, A. / Kadziolka, K. / Bonarek, P. / Barciszewski, J. / Imiolczyk, B. / Brzezinski, K. / Jaskolski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2020/38/E/NZ1/00035 Poland
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Structural and biophysical studies of new L-asparaginase variants: lessons from random mutagenesis of the prototypic Escherichia coli Ntn-amidohydrolase.
Authors: Loch, J.I. / Klonecka, A. / Kadziolka, K. / Bonarek, P. / Barciszewski, J. / Imiolczyk, B. / Brzezinski, K. / Gilski, M. / Jaskolski, M.
History
DepositionJan 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Isoaspartyl peptidase
BBB: Beta-aspartyl-peptidase
CCC: Isoaspartyl peptidase
DDD: Beta-aspartyl-peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0018
Polymers66,8844
Non-polymers1174
Water7,386410
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14250 Å2
ΔGint-123 kcal/mol
Surface area20060 Å2
Unit cell
Length a, b, c (Å)50.478, 75.347, 147.991
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21CCC
32BBB
42DDD

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAALAALAAAAA4 - 1554 - 155
221ALAALAALAALACCCC4 - 1554 - 155
332THRTHRGLUGLUBBBB179 - 3131 - 135
442THRTHRGLUGLUDDDD179 - 3131 - 135

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4

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Components

#1: Protein Isoaspartyl peptidase / Beta-aspartyl-peptidase / EcAIII / Isoaspartyl dipeptidase


Mass: 19013.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: iaaA, spt, ybiK, b0828, JW0812 / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): BLg 21 Gold / References: UniProt: P37595, beta-aspartyl-peptidase
#2: Protein Beta-aspartyl-peptidase


Mass: 14428.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: iaaA, HLZ50_00315 / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: A0A246NXR9, beta-aspartyl-peptidase
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 20% PEG 6000, 0.2 M MgCl2 in 0.1M Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.55→75.35 Å / Num. obs: 83105 / % possible obs: 99.5 % / Redundancy: 12.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.167 / Rrim(I) all: 0.158 / Net I/σ(I): 9.36
Reflection shellResolution: 1.55→1.64 Å / Rmerge(I) obs: 1.39 / Mean I/σ(I) obs: 1.62 / Num. unique obs: 13084 / CC1/2: 0.904 / Rrim(I) all: 1.237 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZAL
Resolution: 1.65→67.236 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.235 / WRfactor Rwork: 0.193 / SU B: 5.112 / SU ML: 0.085 / Average fsc free: 0.8974 / Average fsc work: 0.9105 / Cross valid method: FREE R-VALUE / ESU R: 0.098 / ESU R Free: 0.102
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2348 814 1.188 %
Rwork0.1926 67730 -
all0.193 --
obs-68544 99.587 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.294 Å2
Baniso -1Baniso -2Baniso -3
1-4.036 Å20 Å20 Å2
2---0.969 Å20 Å2
3----3.067 Å2
Refinement stepCycle: LAST / Resolution: 1.65→67.236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4209 0 4 410 4623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134298
X-RAY DIFFRACTIONr_bond_other_d0.0030.0154113
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.635831
X-RAY DIFFRACTIONr_angle_other_deg1.5641.579441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8485585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.41822.178202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85715686
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9171529
X-RAY DIFFRACTIONr_chiral_restr0.0860.2574
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025001
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02937
X-RAY DIFFRACTIONr_nbd_refined0.210.2938
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.24171
X-RAY DIFFRACTIONr_nbtor_refined0.1660.22150
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.22110
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2325
X-RAY DIFFRACTIONr_metal_ion_refined0.1120.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1740.213
X-RAY DIFFRACTIONr_nbd_other0.2110.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1590.224
X-RAY DIFFRACTIONr_mcbond_it1.3482.0532322
X-RAY DIFFRACTIONr_mcbond_other1.3462.0522321
X-RAY DIFFRACTIONr_mcangle_it2.0393.0692898
X-RAY DIFFRACTIONr_mcangle_other2.0393.0712899
X-RAY DIFFRACTIONr_scbond_it1.6052.3371976
X-RAY DIFFRACTIONr_scbond_other1.6022.3331974
X-RAY DIFFRACTIONr_scangle_it2.5383.4162928
X-RAY DIFFRACTIONr_scangle_other2.5383.4162928
X-RAY DIFFRACTIONr_lrange_it5.27426.8564898
X-RAY DIFFRACTIONr_lrange_other5.19126.3384824
X-RAY DIFFRACTIONr_ncsr_local_group_10.0810.054515
X-RAY DIFFRACTIONr_ncsr_local_group_20.0670.053793
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.08130.05008
12CCCX-RAY DIFFRACTIONLocal ncs0.08130.05008
23BBBX-RAY DIFFRACTIONLocal ncs0.066530.0501
24DDDX-RAY DIFFRACTIONLocal ncs0.066530.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.6930.206470.2444981X-RAY DIFFRACTION99.9404
1.693-1.7390.277590.2494862X-RAY DIFFRACTION99.9797
1.739-1.790.271440.2394688X-RAY DIFFRACTION99.9789
1.79-1.8450.221510.2234567X-RAY DIFFRACTION99.9351
1.845-1.9050.314650.2324425X-RAY DIFFRACTION99.8888
1.905-1.9720.272600.2344270X-RAY DIFFRACTION99.2664
1.972-2.0460.282430.2134120X-RAY DIFFRACTION99.7843
2.046-2.130.22490.2153981X-RAY DIFFRACTION99.3345
2.13-2.2240.283410.213821X-RAY DIFFRACTION99.1782
2.224-2.3330.258400.1983658X-RAY DIFFRACTION99.1421
2.333-2.4590.258470.1933475X-RAY DIFFRACTION99.2952
2.459-2.6080.186500.1833301X-RAY DIFFRACTION99.2301
2.608-2.7880.229380.1943098X-RAY DIFFRACTION98.8962
2.788-3.0110.227360.1812906X-RAY DIFFRACTION99.3919
3.011-3.2980.219330.1792694X-RAY DIFFRACTION99.7075
3.298-3.6860.206300.1742464X-RAY DIFFRACTION99.9199
3.686-4.2540.209300.1572178X-RAY DIFFRACTION99.4147
4.254-5.2060.297160.1621862X-RAY DIFFRACTION99.5758
5.206-7.3440.322180.1961489X-RAY DIFFRACTION100
7.344-67.2360.185170.211879X-RAY DIFFRACTION99.5556
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)
10.1626-0.3725-0.0371.21550.21730.07160.03240.05640.0107-0.2240.0076-0.0828-0.02040.0422-0.040.1582-0.02930.02360.0802-0.00680.085816.65474.939824.4714
22.1966-1.15313.49011.9213-0.70876.52120.188-0.2885-0.03290.1482-0.0921-0.02350.5324-0.6803-0.09590.1538-0.10180.02950.09880.00910.04158.7635-8.34111.1388
30.47810.3230.04320.46360.22840.4170.03310.04150.0485-0.0396-0.0544-0.02410.0241-0.08880.02140.0633-0.00040.00990.05830.01290.09437.72567.502422.4458
40.67130.1675-0.06030.1682-0.28390.6585-0.06560.02210.0363-0.00350.0692-0.0156-0.0028-0.0875-0.00360.03440.0227-0.0040.0672-0.00750.12621.91749.656638.7215
50.22410.4646-0.50514.73992.52834.5448-0.00890.11160.02710.03710.01960.06690.0608-0.4317-0.01070.0073-0.001-0.02110.11870.02920.0957-8.0718.048730.5301
60.5752-1.05230.42645.49961.48971.75970.24210.0521-0.0234-0.556-0.37040.26640.1249-0.14610.12840.2027-0.04160.01420.0797-0.04210.0331-4.9514-9.555822.2295
73.28352.690.59952.33970.76490.73870.0639-0.0469-0.02840.1052-0.0457-0.04490.10510.0453-0.01820.0514-0.0041-0.00210.05810.02050.112414.46658.549430.8303
80.3820.243-0.18550.1593-0.15770.5741-0.05420.00920.0779-0.0490.00390.03130.20930.07210.05040.0790.02490.01020.03720.0040.119614.5385-1.456238.4839
91.21120.6024-0.16510.3985-0.26120.3472-0.03950.08690.0294-0.1263-0.034-0.02720.19520.13780.07350.11180.08390.04180.07820.02150.087823.4966-5.120933.4114
102.38783.60370.66256.27621.5620.6538-0.0181-0.01570.0051-0.04340.011-0.02860.05760.11670.00710.07850.06540.03590.11120.02040.082722.5341-0.30826.7824
110.46740.1752-0.72922.80210.20911.2450.06010.0291-0.0468-0.0255-0.0877-0.2048-0.0842-0.02170.02760.06620.03260.02420.09880.00030.091319.59695.651218.7056
123.392-3.85042.09115.9566-5.26056.559-0.2988-0.20920.08960.15880.1027-0.16150.17410.11940.19610.12220.04450.03820.0313-0.01020.069818.3843-7.287317.0472
130.0174-0.0642-0.15020.27560.63761.4765-0.0219-0.02620.01520.06020.0745-0.01850.13980.1882-0.05260.07810.0544-0.00040.09440.0060.098916.0168-5.837966.0043
143.70751.225-3.93312.32680.98466.89690.33190.2365-0.0534-0.1395-0.3548-0.058-0.6885-0.76250.02290.18040.0961-0.05690.12020.00530.04138.08748.915578.7628
150.08740.06850.11510.0715-0.04591.2842-0.0051-0.11340.0017-0.0084-0.0853-0.00310.1012-0.19270.09030.0630.01120.00710.1518-0.00430.05745.6795-6.535466.9994
160.9012-0.26390.00420.11080.09420.7918-0.079-0.06550.02090.00870.0402-0.01330.1277-0.06560.03880.0878-0.03460.02110.0447-0.00310.09880.7606-9.403950.3788
170.77561.61361.99514.85943.20465.7935-0.0932-0.21290.0272-0.00160.04780.1007-0.2955-0.83450.04540.05910.10270.00120.2398-0.00560.0433-8.5805-1.097662.3093
181.1083-0.0326-2.71292.67321.89067.9090.24390.06370.15980.0771-0.12250.3381-0.4593-0.2556-0.12140.24810.0936-0.01490.1032-0.10440.1743-6.126313.698664.8502
191.911-1.4490.07721.59680.450.5358-0.042-0.02910.0626-0.01790.0001-0.0325-0.02290.00170.0420.0740.06050.0290.05030.02340.102812.5672-7.613659.2345
200.1311-0.11570.07490.1048-0.09110.4538-0.0428-0.00190.0010.0366-0.00380.0074-0.02470.07230.04670.04880.0374-0.00070.05210.01070.119715.29171.248851.4596
213.013-2.61260.82965.0379-0.02480.4072-0.14140.01020.15390.22560.1131-0.1757-0.01470.05780.02830.033-0.0165-0.01090.13540.01810.064326.40524.462657.7305
220.4852-0.69780.16281.2387-0.3470.1596-0.0189-0.08040.0001-0.02650.00850.0327-0.0010.09710.01040.05860.0107-0.01990.16880.01860.070920.78642.006959.5207
230.6687-0.5303-0.13463.59820.4590.22890.0534-0.02980.08430.323-0.1044-0.03580.00130.16160.05090.1016-0.0143-0.02410.20510.04620.046116.9116-2.772369.5967
240.01-0.17530.09575.4729-0.95581.13250.00070.01370.00290.1357-0.0395-0.05730.01220.20090.03870.07360.0236-0.02980.09920.01170.059317.7243-0.24373.8943
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA3 - 14
2X-RAY DIFFRACTION2ALLAAA15 - 24
3X-RAY DIFFRACTION3ALLAAA25 - 77
4X-RAY DIFFRACTION4ALLAAA78 - 133
5X-RAY DIFFRACTION5ALLAAA134 - 147
6X-RAY DIFFRACTION6ALLAAA148 - 156
7X-RAY DIFFRACTION7ALLBBB179 - 200
8X-RAY DIFFRACTION8ALLBBB201 - 253
9X-RAY DIFFRACTION9ALLBBB254 - 281
10X-RAY DIFFRACTION10ALLBBB282 - 294
11X-RAY DIFFRACTION11ALLBBB295 - 309
12X-RAY DIFFRACTION12ALLBBB310 - 313
13X-RAY DIFFRACTION13ALLCCC3 - 14
14X-RAY DIFFRACTION14ALLCCC15 - 24
15X-RAY DIFFRACTION15ALLCCC25 - 78
16X-RAY DIFFRACTION16ALLCCC79 - 136
17X-RAY DIFFRACTION17ALLCCC137 - 149
18X-RAY DIFFRACTION18ALLCCC150 - 157
19X-RAY DIFFRACTION19ALLDDD179 - 201
20X-RAY DIFFRACTION20ALLDDD202 - 255
21X-RAY DIFFRACTION21ALLDDD256 - 266
22X-RAY DIFFRACTION22ALLDDD267 - 292
23X-RAY DIFFRACTION23ALLDDD293 - 303
24X-RAY DIFFRACTION24ALLDDD304 - 313

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