[English] 日本語
Yorodumi
- PDB-4a22: Structure of Mycobacterium tuberculosis fructose 1,6-bisphosphate... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4a22
TitleStructure of Mycobacterium tuberculosis fructose 1,6-bisphosphate aldolase bound to N-(4-hydroxybutyl)- glycolohydroxamic acid bis- phosphate
ComponentsFRUCTOSE-BISPHOSPHATE ALDOLASE
KeywordsLYASE / LYASE-INHIBITOR COMPLEX
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / zymogen binding / cell wall / peptidoglycan-based cell wall / glycolytic process / zinc ion binding / extracellular region / plasma membrane / cytosol
Similarity search - Function
Fructose-bisphosphate aldolase, class II, yeast/E. coli subtype / Fructose-bisphosphate aldolase class-II signature 1. / Fructose-bisphosphate aldolase class-II signature 2. / Fructose-bisphosphate aldolase, class-II / Fructose-bisphosphate aldolase class-II / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-TD4 / Fructose-bisphosphate aldolase / Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.9 Å
AuthorsCoincon, M. / De la Paz Santangelo, M. / Gest, P.M. / Guerin, M.E. / Pham, H. / Ryan, G. / Puckett, S.E. / Spencer, J.S. / Gonzalez-Juarrero, M. / Daher, R. ...Coincon, M. / De la Paz Santangelo, M. / Gest, P.M. / Guerin, M.E. / Pham, H. / Ryan, G. / Puckett, S.E. / Spencer, J.S. / Gonzalez-Juarrero, M. / Daher, R. / Lenaerts, A.J. / Schnappinger, D. / Therisod, M. / Ehrt, S. / Jackson, M. / Sygusch, J.
CitationJournal: J. Biol. Chem. / Year: 2011
Title: Glycolytic and non-glycolytic functions of Mycobacterium tuberculosis fructose-1,6-bisphosphate aldolase, an essential enzyme produced by replicating and non-replicating bacilli.
Authors: de la Paz Santangelo, M. / Gest, P.M. / Guerin, M.E. / Coincon, M. / Pham, H. / Ryan, G. / Puckett, S.E. / Spencer, J.S. / Gonzalez-Juarrero, M. / Daher, R. / Lenaerts, A.J. / Schnappinger, ...Authors: de la Paz Santangelo, M. / Gest, P.M. / Guerin, M.E. / Coincon, M. / Pham, H. / Ryan, G. / Puckett, S.E. / Spencer, J.S. / Gonzalez-Juarrero, M. / Daher, R. / Lenaerts, A.J. / Schnappinger, D. / Therisod, M. / Ehrt, S. / Sygusch, J. / Jackson, M.
History
DepositionSep 21, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Atomic model
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Nov 30, 2011Group: Database references
Revision 2.0Nov 21, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / citation ...atom_site / citation / citation_author / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _atom_site.label_alt_id / _citation.journal_abbrev ..._atom_site.label_alt_id / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.label_alt_id_1
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FRUCTOSE-BISPHOSPHATE ALDOLASE
B: FRUCTOSE-BISPHOSPHATE ALDOLASE
C: FRUCTOSE-BISPHOSPHATE ALDOLASE
D: FRUCTOSE-BISPHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,02522
Polymers146,3424
Non-polymers1,68418
Water18,8441046
1
A: FRUCTOSE-BISPHOSPHATE ALDOLASE
B: FRUCTOSE-BISPHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,42414
Polymers73,1712
Non-polymers1,25312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-134.8 kcal/mol
Surface area23670 Å2
MethodPISA
2
C: FRUCTOSE-BISPHOSPHATE ALDOLASE
D: FRUCTOSE-BISPHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6018
Polymers73,1712
Non-polymers4306
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-131.1 kcal/mol
Surface area23570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)335.386, 42.977, 102.601
Angle α, β, γ (deg.)90.00, 99.39, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
FRUCTOSE-BISPHOSPHATE ALDOLASE / / FBP ALDOLASE / FBPA / FRUCTOSE-1 / 6-BISPHOSPHATE ALDOLASE


Mass: 36585.379 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P67475, UniProt: P9WQA3*PLUS, fructose-bisphosphate aldolase

-
Non-polymers , 5 types, 1064 molecules

#2: Chemical ChemComp-TD4 / 4-{hydroxy[(phosphonooxy)acetyl]amino}butyl dihydrogen phosphate


Mass: 323.132 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15NO10P2
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1046 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.65 % / Description: NONE
Crystal growDetails: 20% PEG 8000, 1.8 M LI2SO4, 50 MM TRIS/HOAC PH 7.5.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→47.9 Å / Num. obs: 114281 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 20.11 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10

-
Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.9→45.415 Å / SU ML: 0.46 / σ(F): 1.34 / Phase error: 21.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2206 8852 7.8 %
Rwork0.1793 --
obs0.1825 114263 99.27 %
Solvent computationShrinkage radii: 0.17 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.032 Å2 / ksol: 0.441 e/Å3
Displacement parametersBiso mean: 17.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.4473 Å20 Å20.7719 Å2
2--3.9552 Å20 Å2
3----4.4025 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9808 0 86 1046 10940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810072
X-RAY DIFFRACTIONf_angle_d1.18813646
X-RAY DIFFRACTIONf_dihedral_angle_d14.3193618
X-RAY DIFFRACTIONf_chiral_restr0.081524
X-RAY DIFFRACTIONf_plane_restr0.0071770
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.37133040.34993490X-RAY DIFFRACTION100
1.9216-1.94420.35112750.3073542X-RAY DIFFRACTION99
1.9442-1.96790.34833120.29963471X-RAY DIFFRACTION99
1.9679-1.99280.2983100.26513425X-RAY DIFFRACTION99
1.9928-2.0190.29333120.2323492X-RAY DIFFRACTION100
2.019-2.04670.26462870.21813530X-RAY DIFFRACTION100
2.0467-2.07590.26913060.2163442X-RAY DIFFRACTION100
2.0759-2.10690.25192870.19943513X-RAY DIFFRACTION100
2.1069-2.13990.23983140.19293553X-RAY DIFFRACTION100
2.1399-2.17490.23863150.18593431X-RAY DIFFRACTION100
2.1749-2.21240.2222810.18063476X-RAY DIFFRACTION100
2.2124-2.25270.24882940.17163569X-RAY DIFFRACTION100
2.2527-2.2960.24413160.17963435X-RAY DIFFRACTION100
2.296-2.34290.22312680.16763536X-RAY DIFFRACTION100
2.3429-2.39380.22722760.16893600X-RAY DIFFRACTION100
2.3938-2.44950.21172660.16683455X-RAY DIFFRACTION100
2.4495-2.51070.24193390.17483537X-RAY DIFFRACTION100
2.5107-2.57860.22862960.16443497X-RAY DIFFRACTION100
2.5786-2.65450.21293010.16373528X-RAY DIFFRACTION100
2.6545-2.74010.22562790.1823498X-RAY DIFFRACTION99
2.7401-2.83810.24193010.17793528X-RAY DIFFRACTION100
2.8381-2.95170.2252650.17573521X-RAY DIFFRACTION99
2.9517-3.0860.2143150.17313541X-RAY DIFFRACTION99
3.086-3.24860.20942740.17763487X-RAY DIFFRACTION98
3.2486-3.45210.19592670.16513515X-RAY DIFFRACTION98
3.4521-3.71850.16992830.15133494X-RAY DIFFRACTION98
3.7185-4.09250.17692570.14063552X-RAY DIFFRACTION98
4.0925-4.68420.16112990.13923508X-RAY DIFFRACTION97
4.6842-5.89960.19343120.16333552X-RAY DIFFRACTION98
5.8996-45.42840.21783410.20593693X-RAY DIFFRACTION98
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)
10.0484-0.0399-0.02460.03390.01430.02780.08510.0150.0288-0.0385-0.0262-0.1264-0.01350.01440.00840.07-0.002-0.01870.0772-0.01260.19364.547-58.4901-43.1506
20.02990.014-0.0262-0.009-0.00230.0614-0.06340.01280.03710.01750.0465-0.0181-0.0925-0.0798-0.01160.07650.0115-0.00640.061-0.0150.1231-9.3491-53.9571-40.7255
30.0093-0.0078-0.00050.01-0.00020.0021-0.00990.0011-0.0597-0.0122-0.07460.06490.0495-0.0634-0.00010.10270.00090.02950.14920.00840.1937-24.2173-67.4725-43.4513
40.0189-0.00170.02650.0097-0.00210.0229-0.02560.0018-0.07070.0147-0.0424-0.01660.10280.043400.0983-0.00250.01420.0996-0.00160.1568-14.1002-60.5997-50.7496
50.0499-0.00910.04380.0152-0.00250.03240.01850.0613-0.09930.11790.00310.06950.0225-0.028600.1427-0.01310.01210.0992-0.01470.1799-10.2432-66.9658-41.4238
60.02070.0212-0.01750.0222-0.01760.03830.05590.0096-0.0558-0.05040.00220.0070.00550.06210.00740.12930.0044-0.0060.1216-0.05290.1899-7.0915-73.6553-51.316
70.03730.00790.02070.0345-0.04240.11150.00550.0472-0.1310.0380.0449-0.0189-0.0306-0.03870.03410.06690.00280.02350.0634-0.0160.12-6.0677-71.0739-42.0076
80.0563-0.01770.02460.0082-0.00740.01370.0956-0.0047-0.07430.1435-0.0116-0.1830.0553-0.00690.05890.1641-0.0249-0.0543-0.0503-0.01540.3281-1.0496-79.5123-37.716
90.2202-0.08770.05450.06250.01250.0789-0.0151-0.1041-0.04750.07250.14150.0114-0.0139-0.05730.10190.09730.03150.0050.0186-0.01110.1802-4.4517-69.9199-33.7234
100.05870.052-0.02170.0934-0.01590.01120.1017-0.0421-0.01310.1959-0.0519-0.06640.01520.02690.0060.237-0.0085-0.11860.03250.09270.28594.1668-75.3937-24.5923
110.1225-0.0490.06560.0209-0.02840.04640.06820.04260.010.03330.0185-0.0799-0.02750.0989-0.00450.10010.0004-0.01550.0595-0.02480.22736.1802-71.7172-37.1899
120.0002-0.0013-0.00250.0242-0.04460.09810.0455-0.10040.04740.1160.00340.1396-0.155-0.08350.04060.3291-0.04460.04410.1872-0.10570.2045-9.6558-60.9548-19.9444
130.08060.0343-0.11810.0787-0.12870.30230.1116-0.0241-0.03580.13570.094-0.0612-0.03480.09140.06110.1408-0.0284-0.07640.1296-0.01920.203110.6722-67.2122-25.4036
140.05240.0414-0.01120.0306-0.00080.0538-0.1281-0.0332-0.02980.12070.0853-0.0277-0.0162-0.06090.01930.10860.0219-0.01880.079-0.02410.112-11.1362-53.5538-29.1861
150.1156-0.0451-0.10620.19620.05340.29930.1360.14810.0327-0.0307-0.092-0.0457-0.0338-0.10020.01880.11810.02860.00130.0959-0.01040.11-22.5287-45.0475-39.4857
160.0598-0.02440.00760.2158-0.09980.0492-0.0850.10560.0039-0.1765-0.034-0.03910.0927-0.0016-0.0380.1674-0.0303-0.04120.194-0.06780.1297-34.9011-64.3386-69.8622
170.04390.00130.00360.0155-0.0090.00870.0251-0.0579-0.0976-0.0290.0246-0.0004-0.0462-0.03690.00140.0818-0.004-0.00430.1447-0.0190.0995-33.5115-59.2224-56.0557
180.00530.003-0.00350.0134-0.0040.00210.0744-0.03150.0752-0.08570.06530.024-0.12790.01460.00050.13640.0070.01140.1297-0.01690.0839-19.1282-45.3139-52.6909
190.0408-0.02930.01730.02140.00760.03060.02440.0881-0.0301-0.0271-0.0707-0.0515-0.025-0.0322-0.00010.1171-0.0107-0.00520.1189-0.02940.112-23.8388-60.1857-58.0292
200.0065-0.00180.00760.0099-0.00070.00650.0077-0.0296-0.04250.04410.03940.0594-0.0101-0.068100.2998-0.0411-0.00570.2595-0.010.1084-24.177-41.9607-65.46
210.01550.0005-0.00110.10320.0190.00380.08620.0120.07180.0317-0.04860.0417-0.01140.0769-0.00150.17890.04060.01330.2771-0.01740.1013-16.7952-53.8721-70.1742
220.04310.01650.02450.0159-0.00530.05550.01980.0268-0.0126-0.06320.0637-0.0441-0.18760.09920.00460.18110.03690.00290.1521-0.03790.1141-25.7941-50.4963-69.0726
230.0022-0.00320.00420.0027-0.00790.01-0.01310.12870.0284-0.02860.11120.0176-0.11690.0873-00.1753-0.00450.00490.16780.00660.0909-27.2197-44.9426-78.1053
240.00110.0024-0.00170.0043-0.00420.0068-0.0043-0.0288-0.00910.1092-0.0519-0.04-0.1713-0.09480.00010.230.03640.00160.2273-0.02690.1198-33.5519-47.0988-69.6637
250.09630.05920.01720.0749-0.01220.0353-0.0021-0.10570.18440.07410.07570.19780.00780.0213-0.0010.20010.02770.02950.2342-0.01460.243-41.9702-44.5654-71.0314
260.17850.14820.04770.4451-0.02650.04540.15480.02480.04810.11390.02590.1681-0.0013-0.15470.10770.10380.0219-0.0130.3202-0.0540.1451-46.3958-51.7374-70.7665
270.11770.0175-0.02920.1245-0.06710.1553-0.02540.0021-0.00840.04750.02690.03830.06930.00530.08070.06710.0225-0.01070.0765-0.01850.0815-34.307-56.072-40.1145
280.0128-0.002-0.01080.00240.00440.00930.0130.02660.02040.02680.04530.1398-0.0309-0.03380.04890.17420.1413-0.02960.39620.00460.2639-74.8055-23.5595-17.1628
290.1092-0.00780.04270.1464-0.02040.1276-0.02520.0633-0.00860.0364-0.05430.073-0.03-0.1529-0.080.09980.05880.01640.1982-0.01260.1207-60.1922-31.4528-13.2215
300.0041-0.00320.00290.00670.00080.00230.02710.0228-0.0630.01470.0206-0.00740.0285-0.0156-00.2729-0.06860.10380.50240.02570.3641-69.2893-45.9908-7.1239
310.0045-0.00210.0010.00120.00170.00240.0388-0.047-0.0280.02860.0423-0.0162-0.0184-0.0242-00.180.00170.05030.4508-0.01740.1929-71.0352-33.52080.7734
320.0290.0143-0.00130.0124-0.01530.0254-0.0461-0.0193-0.01880.07180.06890.0715-0.0596-0.1359-0.00150.14250.03460.02180.3114-0.03260.1906-72.7413-37.1523-7.9499
330.00030.0039-0.0010.00150.0008-0.00030.0111-0.0482-0.012-0.00360.10480.01450.077-0.148400.1823-0.07290.02960.5678-0.03680.3424-82.0095-41.9067-6.7955
340.00230.0008-0.0010.0145-0.02680.0377-0.0456-0.0453-0.01230.05230.0743-0.048-0.069-0.0667-0.01410.13920.05960.03760.423-0.06750.2362-75.0796-40.721-15.1637
350.06510.0182-0.0460.0066-0.01390.12960.0834-0.0463-0.0157-0.01420.08240.06410.0279-0.08410.12340.0441-0.0494-0.01320.44580.00220.307-86.4199-40.4988-17.163
360.0022-0.0020.00050.00330.00440.01-0.040.0195-0.0024-0.0836-0.018-0.0753-0.02660.073-0.00010.53490.129-0.04460.4139-0.09370.281-69.4632-46.6695-30.418
370.1003-0.0173-0.0420.05440.08540.13290.05890.0251-0.0459-0.04930.18630.01940.0529-0.05130.1382-0.1477-0.1175-0.12850.75260.03950.2191-88.2955-35.9675-25.7837
380.0210.0738-0.00970.2779-0.03340.0067-0.00750.10510.0117-0.1471-0.05850.03870.13130.01870.0120.15040.0708-0.00380.4892-0.0530.1508-72.0728-36.6923-28.9905
390.06910.0232-0.09550.0547-0.0450.1680.11060.0510.1474-0.0131-0.0046-0.05990.0102-0.06130.1130.07410.0366-0.01420.102-0.04690.0964-37.8179-37.6636-23.1011
400.0222-0.02460.00480.1802-0.01980.02270.02730.01820.0394-0.04020.0423-0.0579-0.0407-0.07450.07180.08170.0997-0.01040.17090.01710.0586-56.5478-27.8923-24.7498
410.04350.013-0.03860.0223-0.03370.06040.0244-0.02340.03590.17480.0113-0.01070.0513-0.06710.01230.2134-0.0006-0.02920.0916-0.00370.1153-39.4459-31.021314.4153
420.22650.0044-0.15360.0576-0.00480.10340.01220.102-0.09680.08270.0463-0.0516-0.01990.00220.06990.14830.0173-0.00780.0469-0.02630.0935-40.6867-35.49830.3992
430.0025-0.00020.00220.0020.00050.00210.04640.0263-0.0353-0.0354-0.06430.0051-0.0917-0.01900.22220.02670.0180.1909-0.02710.1506-46.6211-21.7786-13.3865
440.0210.01690.04610.01280.02520.07250.01270.0506-0.00230.0422-0.02190.0137-0.1565-0.0555-0.00010.19690.020.00290.1011-0.00610.0984-45.6368-25.0703-0.9562
450.00030.0016-0.01620.0004-0.00410.0623-0.0521-0.0190.0152-0.0317-0.10890.11480.0271-0.0542-0.08430.03670.32320.1504-0.2078-0.2925-0.0831-49.8377-15.56284.9019
460.0498-0.02840.02650.0493-0.02340.2891-0.07140.0493-0.0362-0.09350.0227-0.0789-0.0997-0.128-0.05790.1890.00930.02990.0425-0.01520.1176-38.0046-14.43665.7629
470.0370.01730.02620.03910.00960.0199-0.01610.03580.0079-0.10420.01050.00210.01080.0325-0.00790.17530.03540.02610.0781-0.01710.1124-32.2924-19.61943.486
480.0414-0.02250.02210.0496-0.0240.0152-0.0310.0062-0.0208-0.0228-0.0465-0.21730.04820.0498-0.00160.15950.01020.03260.0948-0.00960.1892-25.3727-18.25798.2112
490.0026-0.0024-0.00060.0038-0.00220.00190.01390.00170.00370.00950.00470.0181-0.00110.0078-00.3870.10990.05140.33640.04570.3846-16.8754-31.2226-6.4708
500.21880.1868-0.16970.2797-0.18520.3049-0.151-0.01440.0201-0.1739-0.0509-0.3180.0919-0.0267-0.130.14170.0975-0.04180.0908-0.01420.2003-23.3929-28.18599.6628
510.5668-0.0043-0.31010.2470.02910.27520.03390.1909-0.01940.11780.0022-0.01210.1186-0.130.01570.12110.01170.00960.041-0.02780.0849-41.5995-43.6476-13.6347
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:19)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 20:53)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 54:67)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 68:85)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 86:105)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 106:118)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 119:136)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 137:154)
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 155:167)
10X-RAY DIFFRACTION10CHAIN A AND (RESSEQ 181:194)
11X-RAY DIFFRACTION11CHAIN A AND (RESSEQ 195:204)
12X-RAY DIFFRACTION12CHAIN A AND (RESSEQ 205:223)
13X-RAY DIFFRACTION13CHAIN A AND (RESSEQ 224:248)
14X-RAY DIFFRACTION14CHAIN A AND (RESSEQ 249:293)
15X-RAY DIFFRACTION15CHAIN A AND (RESSEQ 294:343)
16X-RAY DIFFRACTION16CHAIN B AND (RESSEQ 2:19)
17X-RAY DIFFRACTION17CHAIN B AND (RESSEQ 20:53)
18X-RAY DIFFRACTION18CHAIN B AND (RESSEQ 54:67)
19X-RAY DIFFRACTION19CHAIN B AND (RESSEQ 68:94)
20X-RAY DIFFRACTION20CHAIN B AND (RESSEQ 95:105)
21X-RAY DIFFRACTION21CHAIN B AND (RESSEQ 106:118)
22X-RAY DIFFRACTION22CHAIN B AND (RESSEQ 119:136)
23X-RAY DIFFRACTION23CHAIN B AND (RESSEQ 137:154)
24X-RAY DIFFRACTION24CHAIN B AND (RESSEQ 155:167)
25X-RAY DIFFRACTION25CHAIN B AND (RESSEQ 181:223)
26X-RAY DIFFRACTION26CHAIN B AND (RESSEQ 224:276)
27X-RAY DIFFRACTION27CHAIN B AND (RESSEQ 277:343)
28X-RAY DIFFRACTION28CHAIN C AND (RESSEQ 2:19)
29X-RAY DIFFRACTION29CHAIN C AND (RESSEQ 20:94)
30X-RAY DIFFRACTION30CHAIN C AND (RESSEQ 95:105)
31X-RAY DIFFRACTION31CHAIN C AND (RESSEQ 106:118)
32X-RAY DIFFRACTION32CHAIN C AND (RESSEQ 119:136)
33X-RAY DIFFRACTION33CHAIN C AND (RESSEQ 137:154)
34X-RAY DIFFRACTION34CHAIN C AND (RESSEQ 155:167)
35X-RAY DIFFRACTION35CHAIN C AND (RESSEQ 181:204)
36X-RAY DIFFRACTION36CHAIN C AND (RESSEQ 205:223)
37X-RAY DIFFRACTION37CHAIN C AND (RESSEQ 224:248)
38X-RAY DIFFRACTION38CHAIN C AND (RESSEQ 249:276)
39X-RAY DIFFRACTION39CHAIN C AND (RESSEQ 277:312)
40X-RAY DIFFRACTION40CHAIN C AND (RESSEQ 313:343)
41X-RAY DIFFRACTION41CHAIN D AND (RESSEQ 2:19)
42X-RAY DIFFRACTION42CHAIN D AND (RESSEQ 20:53)
43X-RAY DIFFRACTION43CHAIN D AND (RESSEQ 54:67)
44X-RAY DIFFRACTION44CHAIN D AND (RESSEQ 68:105)
45X-RAY DIFFRACTION45CHAIN D AND (RESSEQ 106:118)
46X-RAY DIFFRACTION46CHAIN D AND (RESSEQ 119:154)
47X-RAY DIFFRACTION47CHAIN D AND (RESSEQ 155:167)
48X-RAY DIFFRACTION48CHAIN D AND (RESSEQ 181:214)
49X-RAY DIFFRACTION49CHAIN D AND (RESSEQ 215:223)
50X-RAY DIFFRACTION50CHAIN D AND (RESSEQ 224:276)
51X-RAY DIFFRACTION51CHAIN D AND (RESSEQ 277:343)

+
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