[English] 日本語
Yorodumi
- PDB-6kja: E. coli ATCase holoenzyme mutant - G128/130A (catalytic chain) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kja
TitleE. coli ATCase holoenzyme mutant - G128/130A (catalytic chain)
Components
  • Aspartate carbamoyltransferase catalytic subunit
  • Aspartate carbamoyltransferase regulatory chain
KeywordsTRANSFERASE / aspartate transcarbamoylase holoenzyme / de novo pyrimidine biosynthesis
Function / homology
Function and homology information


aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid binding / glutamine metabolic process / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding ...aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid binding / glutamine metabolic process / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Aspartate transcarbamylase regulatory subunit / Aspartate carbamoyltransferase regulatory subunit, C-terminal / Aspartate carbamoyltransferase regulatory subunit, N-terminal / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain superfamily / Aspartate carbamoyltransferase regulatory chain, allosteric domain / Aspartate carbamoyltransferase regulatory chain, metal binding domain / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain / Aspartate carbamoyltransferase ...Aspartate transcarbamylase regulatory subunit / Aspartate carbamoyltransferase regulatory subunit, C-terminal / Aspartate carbamoyltransferase regulatory subunit, N-terminal / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain superfamily / Aspartate carbamoyltransferase regulatory chain, allosteric domain / Aspartate carbamoyltransferase regulatory chain, metal binding domain / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain / Aspartate carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / SH3 type barrels. / Roll / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Aspartate carbamoyltransferase catalytic subunit / Aspartate carbamoyltransferase regulatory chain
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.064 Å
AuthorsLei, Z. / Zheng, J. / Jia, Z.C.
Funding support China, Canada, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21773014 China
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-04427 Canada
CitationJournal: Febs J. / Year: 2020
Title: New regulatory mechanism-based inhibitors of aspartate transcarbamoylase for potential anticancer drug development.
Authors: Lei, Z. / Wang, B. / Lu, Z. / Wang, N. / Tan, H. / Zheng, J. / Jia, Z.
History
DepositionJul 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Derived calculations / Category: citation / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aspartate carbamoyltransferase catalytic subunit
B: Aspartate carbamoyltransferase regulatory chain
C: Aspartate carbamoyltransferase catalytic subunit
D: Aspartate carbamoyltransferase regulatory chain
E: Aspartate carbamoyltransferase catalytic subunit
F: Aspartate carbamoyltransferase regulatory chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,7239
Polymers154,5266
Non-polymers1963
Water19811
1
A: Aspartate carbamoyltransferase catalytic subunit
B: Aspartate carbamoyltransferase regulatory chain
C: Aspartate carbamoyltransferase catalytic subunit
D: Aspartate carbamoyltransferase regulatory chain
E: Aspartate carbamoyltransferase catalytic subunit
F: Aspartate carbamoyltransferase regulatory chain
hetero molecules

A: Aspartate carbamoyltransferase catalytic subunit
B: Aspartate carbamoyltransferase regulatory chain
C: Aspartate carbamoyltransferase catalytic subunit
D: Aspartate carbamoyltransferase regulatory chain
E: Aspartate carbamoyltransferase catalytic subunit
F: Aspartate carbamoyltransferase regulatory chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,44518
Polymers309,05312
Non-polymers3926
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area26510 Å2
ΔGint-83 kcal/mol
Surface area102290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.408, 127.408, 197.523
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 6 or (resid 7...
21(chain C and (resid 2 through 77 or resid 86...
31(chain E and (resid 2 through 6 or (resid 7...
12(chain B and (resid 16 through 45 or (resid 46...
22(chain D and (resid 16 through 18 or (resid 19...
32(chain F and (resid 16 through 18 or (resid 19...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNGLNGLN(chain A and (resid 2 through 6 or (resid 7...AA2 - 62 - 6
121LYSLYSLYSLYS(chain A and (resid 2 through 6 or (resid 7...AA77
131ASNASNVALVAL(chain A and (resid 2 through 6 or (resid 7...AA2 - 3092 - 309
141ASNASNVALVAL(chain A and (resid 2 through 6 or (resid 7...AA2 - 3092 - 309
151ASNASNVALVAL(chain A and (resid 2 through 6 or (resid 7...AA2 - 3092 - 309
161ASNASNVALVAL(chain A and (resid 2 through 6 or (resid 7...AA2 - 3092 - 309
211ASNASNALAALA(chain C and (resid 2 through 77 or resid 86...CC2 - 772 - 77
221GLUGLUTHRTHR(chain C and (resid 2 through 77 or resid 86...CC86 - 22886 - 228
231ARGARGARGARG(chain C and (resid 2 through 77 or resid 86...CC229229
241ALAALALEULEU(chain C and (resid 2 through 77 or resid 86...CC1 - 3101 - 310
251ALAALALEULEU(chain C and (resid 2 through 77 or resid 86...CC1 - 3101 - 310
261ALAALALEULEU(chain C and (resid 2 through 77 or resid 86...CC1 - 3101 - 310
271ALAALALEULEU(chain C and (resid 2 through 77 or resid 86...CC1 - 3101 - 310
311ASNASNGLNGLN(chain E and (resid 2 through 6 or (resid 7...EE2 - 62 - 6
321LYSLYSLYSLYS(chain E and (resid 2 through 6 or (resid 7...EE77
331ALAALALEULEU(chain E and (resid 2 through 6 or (resid 7...EE1 - 3101 - 310
341ALAALALEULEU(chain E and (resid 2 through 6 or (resid 7...EE1 - 3101 - 310
351ALAALALEULEU(chain E and (resid 2 through 6 or (resid 7...EE1 - 3101 - 310
361ALAALALEULEU(chain E and (resid 2 through 6 or (resid 7...EE1 - 3101 - 310
112THRTHRGLYGLY(chain B and (resid 16 through 45 or (resid 46...BB16 - 4516 - 45
122LEULEULEULEU(chain B and (resid 16 through 45 or (resid 46...BB4646
132THRTHRASNASN(chain B and (resid 16 through 45 or (resid 46...BB16 - 15316 - 153
142THRTHRASNASN(chain B and (resid 16 through 45 or (resid 46...BB16 - 15316 - 153
152THRTHRASNASN(chain B and (resid 16 through 45 or (resid 46...BB16 - 15316 - 153
162THRTHRASNASN(chain B and (resid 16 through 45 or (resid 46...BB16 - 15316 - 153
212THRTHRILEILE(chain D and (resid 16 through 18 or (resid 19...DD16 - 1816 - 18
222ASPASPHISHIS(chain D and (resid 16 through 18 or (resid 19...DD19 - 2019 - 20
232THRTHRASNASN(chain D and (resid 16 through 18 or (resid 19...DD16 - 15316 - 153
242THRTHRASNASN(chain D and (resid 16 through 18 or (resid 19...DD16 - 15316 - 153
252THRTHRASNASN(chain D and (resid 16 through 18 or (resid 19...DD16 - 15316 - 153
262THRTHRASNASN(chain D and (resid 16 through 18 or (resid 19...DD16 - 15316 - 153
312THRTHRILEILE(chain F and (resid 16 through 18 or (resid 19...FF16 - 1816 - 18
322ASPASPHISHIS(chain F and (resid 16 through 18 or (resid 19...FF19 - 2019 - 20
332THRTHRASNASN(chain F and (resid 16 through 18 or (resid 19...FF16 - 15316 - 153
342THRTHRASNASN(chain F and (resid 16 through 18 or (resid 19...FF16 - 15316 - 153
352THRTHRASNASN(chain F and (resid 16 through 18 or (resid 19...FF16 - 15316 - 153
362THRTHRASNASN(chain F and (resid 16 through 18 or (resid 19...FF16 - 15316 - 153

NCS ensembles :
ID
1
2

-
Components

#1: Protein Aspartate carbamoyltransferase catalytic subunit / Aspartate transcarbamylase / ATCase


Mass: 34365.156 Da / Num. of mol.: 3 / Mutation: G128A, G130A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: pyrB, b4245, JW4204 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A786, aspartate carbamoyltransferase
#2: Protein Aspartate carbamoyltransferase regulatory chain


Mass: 17143.625 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: pyrI / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7F3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.0, 30% Jeffamine M-600 pH 7.0, and 10% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS IV / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.04→50 Å / Num. obs: 36586 / % possible obs: 99.8 % / Redundancy: 4.8 % / CC1/2: 0.999 / Net I/σ(I): 16
Reflection shellResolution: 3.04→3.09 Å / Num. unique obs: 1813 / CC1/2: 0.88

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZA1
Resolution: 3.064→42.287 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2834 1966 5.62 %
Rwork0.2488 33032 -
obs0.2507 34998 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.93 Å2 / Biso mean: 68.8878 Å2 / Biso min: 23.92 Å2
Refinement stepCycle: final / Resolution: 3.064→42.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10005 0 3 11 10019
Biso mean--57.83 56.69 -
Num. residues----1311
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2712X-RAY DIFFRACTION4.25TORSIONAL
12C2712X-RAY DIFFRACTION4.25TORSIONAL
13E2712X-RAY DIFFRACTION4.25TORSIONAL
21B1182X-RAY DIFFRACTION4.25TORSIONAL
22D1182X-RAY DIFFRACTION4.25TORSIONAL
23F1182X-RAY DIFFRACTION4.25TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0644-3.1410.39671380.33742360100
3.141-3.22590.39591390.32862338100
3.2259-3.32080.33931340.3163231699
3.3208-3.42790.38331440.30632390100
3.4279-3.55040.36311460.30042355100
3.5504-3.69250.3281410.2884232799
3.6925-3.86040.28921380.2681234899
3.8604-4.06380.32121410.2658231697
4.0638-4.31810.29661380.2355232198
4.3181-4.65120.2521370.2138232897
4.6512-5.11850.19431410.2005236498
5.1185-5.85750.24111410.2224237098
5.8575-7.37350.31021470.2565243799
7.3735-42.2870.20941410.1999246296
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)
10.02250.0103-0.0055-0.02220.022-0.02460.43080.2288-0.5216-0.02510.30260.26360.2709-0.04-0-1.49520.79650.6440.6229-0.6809-0.0326-16.870220.4201-64.8139
20.0182-0.0005-0.0085-0.002-0.0169-0.00020.10670.2941-0.3630.32390.1104-0.0470.0368-0.06-0-0.93810.1437-0.08390.6765-0.22310.3297-26.72820.6722-53.5694
30.0147-0.0153-0.0352-0.0254-0.002-0.03010.27930.0185-0.43940.72040.0185-0.2113-0.2960.09750-1.70621.73020.5107-0.6119-0.87860.5322-0.31849.585-49.7173
40.02540.021-0.06630.05450.02090.0502-0.0230.20630.0183-0.01760.0508-0.387-0.0187-0.1134-0-0.34040.0948-0.47941.0217-0.52980.46010.139321.2332-58.3121
5-0.00090.00030.0038-0.00050.0004-0.0013-0.0044-0.0016-0.01040.02660.0186-0.00070.0036-0.0108-00.94210.0465-0.05010.8414-0.16680.9331-40.338-15.6297-35.2173
60.0034-0.0021-0.00290.0035-0.00140.00050.0340.0112-0.0076-0.04970.04370.035-0.0196-0.0596-00.624-0.1928-0.07480.6308-0.20370.8458-46.1989-5.6083-38.4311
7-0.00530.00110.00250.01020.00280.0006-0.01240.0812-0.03830.0461-0.04740.00620.04310.030900.9862-0.2964-0.20840.8934-0.3511.2238-43.7598-14.4909-39.2863
80.0036-0.00690.00340.00670.0025-0.0045-0.02550.01130.0234-0.008-0.0021-0.05510.0474-0.0311-00.9338-0.0166-0.12060.8456-0.17141.2917-40.1121-17.704-42.4114
90.0027-0.0075-0.00070.00460.0036-0.0039-0.0150.0210.0468-0.02-0.0452-0.06450.0329-0.0203-00.9943-0.08170.07180.8672-0.21851.1771-39.2084-20.6584-47.0346
100.0042-0.0019-0.01280.0016-0.0031-0.00010.01160.0251-0.08280.02960.00710.0181-0.0119-0.0213-00.31450.01750.0070.5109-0.10750.6661-30.22785.4825-43.8592
110.00080.00450.00430.00170.0011-0.0024-0.0527-0.0244-0.11990.0052-0.0246-0.0370.0401-0.0118-00.37710.1233-0.24970.5266-0.20080.9329-22.3583-1.5766-44.986
120.00150.00060.00160.0022-0.00090.0017-0.00450.00260.0324-0.0001-0.017-0.01690.02840.020900.85330.19450.07960.8248-0.08920.8937-24.2269-1.5586-36.3818
130.05820.033-0.00370.02930.0669-0.0440.69090.540.27330.8520.13750.27460.0971-0.1138-0-1.42530.09780.04230.97140.09720.3741-38.246443.1189-59.8305
140.06420.0164-0.01810.05190.00860.0350.13150.07450.04110.49670.31550.18480.0315-0.0067-00.2197-0.0097-0.030.69970.15610.3415-57.528731.963-46.674
150.0295-0.02530.03340.035-0.00790.0016-0.0020.2902-0.36730.12340.05920.15610.18210.10690-0.24150.0147-0.24250.79940.140.1921-46.725325.829-57.3378
160.0011-0.0018-0.0037-0.0004-0.00440.0001-0.0212-0.01860.0104-0.0234-0.0090.0209-0.0211-0.001500.9980.25380.0961.09650.10061.3139-58.218579.7221-36.2614
17-0.00080.0007-0.00150.0007-0.0013-0.0016-0.01220.0205-0.032-0.0144-0.00270.0407-0.01490.029500.75560.1534-0.03590.57930.10981.1933-46.201679.5149-39.6034
180.0016-0.0024-0.00180.0037-0.0006-0.0017-0.0121-0.01070.0202-0.0114-0.0303-0.03220.0101-0.0226-01.19710.19330.03141.1248-0.0291.4795-57.040384.9927-32.1185
190.0005-0.00260.00010.0004-0.0009-0.0011-0.0231-0.0052-0.02880.02310.01760.0244-0.0004-0.004701.09150.13270.02841.02720.20571.2646-52.410184.9946-45.4837
200.00250.0004-0.0007-0.0003-0.0014-0.0005-0.0148-0.0222-0.0169-0.04390.0180.0205-0.0105-0.0034-00.69640.17820.11190.97010.07991.3055-57.691772.8594-44.5836
210.0007-0.0015-0.00230.00020.00060.0013-0.0051-0.01030.00630.0117-0.00390.01040.00520.001301.3936-0.00640.07141.35250.17891.4025-59.093688.434-47.9723
220.0053-0.0011-0.0030.0245-0.0043-0.0014-0.01940.0057-0.0336-0.012-0.0056-0.0007-0.05150.0068-01.11110.07260.01130.99930.07041.3775-63.000980.9662-47.7227
230.004-0.00470.00140.01-0.00740.00710.0616-0.01240.07930.04870.0356-0.0320.00880.023500.30260.02330.15090.68040.20180.9723-47.77559.7268-44.2431
240.00190.00080.0020.0063-0.00580.00230.0084-0.02630.03270.0197-0.07170.02180.0461-0.040400.28530.05080.33140.62660.30310.8251-53.636255.5487-44.4454
250.00180.0016-0.00380.00090.00060.00070.00350.00020.02590.02480.0122-0.0042-0.0093-0.0192-00.6859-0.01920.18960.8515-0.00830.9143-53.804658.6856-36.5973
260.0151-0.03410.00830.0630.06230.01380.10820.29140.01430.42490.4244-0.01730.10170.1681-0-0.0647-0.04360.20591.00780.14140.1753-10.801847.8339-63.3916
270.01680.0165-0.02990.0147-0.0214-0.02990.28240.47380.0290.32690.2558-0.17950.12110.0033-00.07630.07850.02310.77620.09590.2498-5.753547.5867-57.0922
280.0529-0.00650.00540.0247-0.00350.00860.18080.11940.35120.56210.26550.28410.28410.1701-00.3332-0.03340.21810.60250.3930.6046-10.384171.2743-49.1874
290.02790.01410.04370.0110.01240.00090.24130.28280.19120.03550.27910.3759-0.01490.1482-0-0.3021-0.14690.33710.97520.43590.3117-18.771659.6248-60.4576
300.0008-0.00030.001-0.00010.0043-0.0010.0320.0135-0.00010.04190.0074-0.03920.00590.0203-00.5514-0.1013-0.14620.6796-0.07370.713734.171147.8434-38.4557
310.0006-0.0096-0.00050.002-0.01220.0051-0.02740.0301-0.04480.0385-0.0878-0.11590.03840.054200.36570.0983-0.02910.8506-0.05030.627632.617740.2101-40.4145
320.0027-0.00080.00020.00110.0018-0.00130.01370.0089-0.0029-0.0123-0.0110.0312-0.0114-0.002900.5706-0.111-0.28350.8359-0.08870.671727.34250.5744-46.078
330.0068-0.0049-0.00390.0090.00390.0017-0.0003-00.01420.0032-0.00430.0131-0.0077-0.0057-00.89360.02790.21951.019-0.17471.024141.450344.1102-48.9124
340.00230.0010.0090.0026-0.00790.0102-0.01180.0072-0.0276-0.0405-0.0748-0.0048-0.0055-0.0085-00.3026-0.04330.04110.9066-0.0520.629825.682249.7288-48.6412
350.00190.00110.0091-0.0007-0.01290.0197-0.01690.0248-0.01950.064-0.00580.0209-0.13470.038-00.4009-0.0105-0.00190.7313-0.04710.45649.37551.4331-45.7124
360.00090.0007-0.00140.00090.00120.0013-0.00440.0083-0.01390.0123-0.00010.025500.0035-00.4632-0.1083-0.07560.6591-0.12850.51213.265954.7192-38.4349
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 66 )A2 - 66
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 134 )A67 - 134
3X-RAY DIFFRACTION3chain 'A' and (resid 135 through 247 )A135 - 247
4X-RAY DIFFRACTION4chain 'A' and (resid 248 through 309 )A248 - 309
5X-RAY DIFFRACTION5chain 'B' and (resid 16 through 25 )B16 - 25
6X-RAY DIFFRACTION6chain 'B' and (resid 26 through 41 )B26 - 41
7X-RAY DIFFRACTION7chain 'B' and (resid 42 through 74 )B42 - 74
8X-RAY DIFFRACTION8chain 'B' and (resid 75 through 89 )B75 - 89
9X-RAY DIFFRACTION9chain 'B' and (resid 90 through 99 )B90 - 99
10X-RAY DIFFRACTION10chain 'B' and (resid 100 through 123 )B100 - 123
11X-RAY DIFFRACTION11chain 'B' and (resid 124 through 143 )B124 - 143
12X-RAY DIFFRACTION12chain 'B' and (resid 144 through 153 )B144 - 153
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 149 )C1 - 149
14X-RAY DIFFRACTION14chain 'C' and (resid 150 through 247 )C150 - 247
15X-RAY DIFFRACTION15chain 'C' and (resid 248 through 310 )C248 - 310
16X-RAY DIFFRACTION16chain 'D' and (resid 16 through 25 )D16 - 25
17X-RAY DIFFRACTION17chain 'D' and (resid 26 through 41 )D26 - 41
18X-RAY DIFFRACTION18chain 'D' and (resid 42 through 57 )D42 - 57
19X-RAY DIFFRACTION19chain 'D' and (resid 58 through 67 )D58 - 67
20X-RAY DIFFRACTION20chain 'D' and (resid 68 through 81 )D68 - 81
21X-RAY DIFFRACTION21chain 'D' and (resid 82 through 89 )D82 - 89
22X-RAY DIFFRACTION22chain 'D' and (resid 90 through 99 )D90 - 99
23X-RAY DIFFRACTION23chain 'D' and (resid 100 through 130 )D100 - 130
24X-RAY DIFFRACTION24chain 'D' and (resid 131 through 143 )D131 - 143
25X-RAY DIFFRACTION25chain 'D' and (resid 144 through 153 )D144 - 153
26X-RAY DIFFRACTION26chain 'E' and (resid 1 through 87 )E1 - 87
27X-RAY DIFFRACTION27chain 'E' and (resid 88 through 149 )E88 - 149
28X-RAY DIFFRACTION28chain 'E' and (resid 150 through 265 )E150 - 265
29X-RAY DIFFRACTION29chain 'E' and (resid 266 through 310 )E266 - 310
30X-RAY DIFFRACTION30chain 'F' and (resid 16 through 25 )F16 - 25
31X-RAY DIFFRACTION31chain 'F' and (resid 26 through 67 )F26 - 67
32X-RAY DIFFRACTION32chain 'F' and (resid 68 through 81 )F68 - 81
33X-RAY DIFFRACTION33chain 'F' and (resid 82 through 89 )F82 - 89
34X-RAY DIFFRACTION34chain 'F' and (resid 90 through 109 )F90 - 109
35X-RAY DIFFRACTION35chain 'F' and (resid 110 through 143 )F110 - 143
36X-RAY DIFFRACTION36chain 'F' and (resid 144 through 153 )F144 - 153

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

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

-
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

Read more