[English] 日本語
Yorodumi
- PDB-6dwe: Crystal structure of tryptophan synthase from M. tuberculosis - a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dwe
TitleCrystal structure of tryptophan synthase from M. tuberculosis - aminoacrylate- and BRD0059-bound form
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/LYASE INHIBITOR / PLP / heterotetramer / amino acid biosynthesis / substrate channeling / allostery / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tryptophan synthase, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain / Tryptophan synthase beta chain/beta chain-like / Tryptophan synthase beta chain pyridoxal-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme ...Tryptophan synthase, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain / Tryptophan synthase beta chain/beta chain-like / Tryptophan synthase beta chain pyridoxal-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / FORMIC ACID / Chem-HDJ / MALONIC ACID / MALONATE ION / Chem-P1T / TRIETHYLENE GLYCOL / Tryptophan synthase beta chain / Tryptophan synthase alpha chain
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.691 Å
AuthorsChang, C. / Michalska, K. / Maltseva, N.I. / Jedrzejczak, R. / McCarren, P. / Nag, P.P. / Joachimiak, A. / Satchell, K. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of tryptophan synthase from M. tuberculosis - closed form with BRD6309 bound
Authors: Chang, C. / Michalska, K. / Maltseva, N.I. / Jedrzejczak, R. / McCarren, P. / Nag, P.P. / Joachimiak, A. / Satchell, K.
History
DepositionJun 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.2Oct 11, 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_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tryptophan synthase alpha chain
B: Tryptophan synthase beta chain
G: Tryptophan synthase alpha chain
H: Tryptophan synthase beta chain
E: Tryptophan synthase alpha chain
F: Tryptophan synthase beta chain
C: Tryptophan synthase alpha chain
D: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)293,91569
Polymers287,6568
Non-polymers6,25961
Water13,709761
1
A: Tryptophan synthase alpha chain
B: Tryptophan synthase beta chain
C: Tryptophan synthase alpha chain
D: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,91133
Polymers143,8284
Non-polymers3,08329
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Tryptophan synthase alpha chain
H: Tryptophan synthase beta chain
E: Tryptophan synthase alpha chain
F: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,00436
Polymers143,8284
Non-polymers3,17532
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.093, 159.396, 165.226
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Tryptophan synthase ... , 2 types, 8 molecules AGECBHFD

#1: Protein
Tryptophan synthase alpha chain


Mass: 28579.449 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: trpA, Rv1613, MTCY01B2.05 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFY1, tryptophan synthase
#2: Protein
Tryptophan synthase beta chain


Mass: 43334.598 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: trpB, Rv1612, MTCY01B2.04 / Plasmid: pMCSG81 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFX9, tryptophan synthase

-
Non-polymers , 10 types, 822 molecules

#3: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical...
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical
ChemComp-P1T / 2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID


Mass: 318.220 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H15N2O7P
#6: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cs
#7: Chemical
ChemComp-HDJ / (2R,3S,4R)-3-(2',6'-difluoro-4'-methyl[1,1'-biphenyl]-4-yl)-4-(fluoromethyl)azetidine-2-carbonitrile


Mass: 316.320 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H15F3N2
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#9: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#10: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#11: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 761 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 8% Tacsimate, pH 8.0, 20% PEG3350, 100 mM sodium malonate, pH 7.0
PH range: 7.0~8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.691→30 Å / Num. obs: 98448 / % possible obs: 99.3 % / Redundancy: 6.3 % / Biso Wilson estimate: 43.2 Å2 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.07 / Rrim(I) all: 0.178 / Χ2: 0.775 / Net I/σ(I): 4.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.691-2.755.10.74546480.610.3520.8270.68994.5
2.75-2.85.40.63547200.7270.2940.7030.69397
2.8-2.855.50.61548100.7530.2830.680.71997.7
2.85-2.915.70.57848320.7770.2630.6380.71898.4
2.91-2.975.80.56248570.7790.2550.6190.71199.2
2.97-3.0460.50448890.8380.2280.5550.70299.7
3.04-3.126.10.45949040.8550.2060.5050.72399.5
3.12-3.25.70.39249180.8810.1820.4340.73799.8
3.2-3.295.90.35448970.9180.160.390.74999.9
3.29-3.470.29649400.9590.1210.320.742100
3.4-3.5270.25549110.970.1040.2760.754100
3.52-3.6670.19949590.9810.0810.2150.746100
3.66-3.836.90.16849340.9860.0690.1810.777100
3.83-4.036.80.13849550.990.0570.1490.79399.9
4.03-4.286.70.11549590.9930.0480.1250.79199.9
4.28-4.616.20.09149690.9950.0390.0990.82499.8
4.61-5.076.10.08449870.9950.0370.0920.831100
5.07-5.870.10550230.9940.0430.1130.811100
5.8-7.36.70.08350710.9960.0350.090.829100
7.3-306.20.04852650.9980.0210.0521.07399.8

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5TCJ
Resolution: 2.691→29.899 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.32
RfactorNum. reflection% reflection
Rfree0.2024 1955 1.99 %
Rwork0.1555 --
obs0.1564 98346 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 185.5 Å2 / Biso mean: 41.9582 Å2 / Biso min: 1.07 Å2
Refinement stepCycle: final / Resolution: 2.691→29.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19112 0 352 762 20226
Biso mean--53.7 39.36 -
Num. residues----2597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00219928
X-RAY DIFFRACTIONf_angle_d0.75127037
X-RAY DIFFRACTIONf_chiral_restr0.0423016
X-RAY DIFFRACTIONf_plane_restr0.0043600
X-RAY DIFFRACTIONf_dihedral_angle_d17.36611698
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6913-2.75860.3591200.25856434655493
2.7586-2.83310.33811250.22936714683998
2.8331-2.91640.25851500.21266696684698
2.9164-3.01050.24781410.213468847025100
3.0105-3.1180.28561340.204868436977100
3.118-3.24270.25591520.190868777029100
3.2427-3.390.23261650.172368697034100
3.39-3.56850.2061290.159269137042100
3.5685-3.79170.19781610.140769237084100
3.7917-4.08380.18021410.13169477088100
4.0838-4.49350.16451440.116369377081100
4.4935-5.14090.13911200.114170207140100
5.1409-6.46610.16361530.144570377190100
6.4661-29.90130.16021200.139672977417100
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)
10.0987-0.04780.08720.1143-0.05160.07020.13950.0229-0.03090.0627-0.0545-0.1459-0.01320.04510.00090.1760.01730.01740.28120.05090.371789.2945-13.083621.8847
20.048-0.01190.05630.0082-0.01890.063-0.0819-0.00580.13960.0623-0.0471-0.1977-0.20780.1824-0.02030.1746-0.05080.02480.27220.06790.396987.2855-1.373821.2376
30.0657-0.04040.02280.0310.01010.0350.00470.2530.05940.0711-0.0326-0.109-0.0269-0.0281-00.24180.02420.03450.30320.07240.326879.2641-8.08899.0901
40.0679-0.0328-0.04210.01010.01530.0235-0.00120.223-0.3675-0.0397-0.1676-0.15620.19840.0822-0.00410.26940.07990.00780.3188-0.02070.436189.2209-23.921515.1051
50.0082-0.0121-0.01760.025-0.0070.0372-0.01170.15510.0059-0.06860.05860.1432-0.14270.02560.00030.15190.01550.00190.20.04360.157558.0095-5.344411.2925
60.00980.0608-0.06930.0974-0.10540.11160.0359-0.04-0.0272-0.07860.00980.0246-0.0539-0.08610.00020.14120.01390.01230.1281-0.00740.126942.5184-10.24126.2343
70.07460.00890.01190.0295-0.00890.02230.0777-0.2032-0.16750.0347-0.1037-0.1541-0.00170.025-00.16330.0117-0.00970.22490.06510.235959.124-17.85429.2086
80.19580.1244-0.18630.29640.07340.22950.0501-0.03960.02450.0242-0.0143-0.0372-0.07920.025900.152-0.00380.00070.16640.01840.128851.22072.43933.193
90.12210.02410.08380.2651-0.11330.11870.18150.0351-0.1188-0.10340.01280.29540.0836-0.04790.0460.11860.03710.00820.2146-0.0420.3461-20.913314.52419.4822
100.0249-0.0095-0.00870.05060.04330.04720.1312-0.04450.01410.0181-0.01570.1372-0.0550.049-00.17950.02630.01150.2748-0.00270.2804-12.062322.195312.185
110.02710.00270.00290.0116-0.01980.03090.051-0.0828-0.25480.12460.02960.1271-0.09120.068600.2824-0.04940.03910.2485-0.03450.3002-8.596918.407722.417
120.2174-0.1083-0.10720.10930.02510.0720.0357-0.3077-0.24490.03070.0850.3420.10940.0408-0.00540.2031-0.0465-0.00790.31130.0550.4885-22.22155.899618.8924
130.0504-0.00690.03240.04260.02090.03620.0128-0.1369-0.0285-0.0240.0174-0.0035-0.14050.09470.00080.1217-0.02570.02380.217-0.01990.122511.29146.455719.8697
140.1734-0.0965-0.16350.46560.12230.43970.0343-0.0272-0.0119-0.0782-0.04610.032-0.056-0.004500.1071-0.011200.132-0.00810.117316.97793.39280.468
150.02020.01990.04320.06480.05830.0707-0.27840.2482-0.1147-0.62030.1833-0.10080.15090.0311-0.07670.9992-0.27830.21880.3857-0.2220.198635.4491-38.5477-49.1031
160.53910.02650.3269-0.00080.02260.2152-0.32450.1586-0.1386-0.43920.0072-0.26620.275-0.044-0.42130.7374-0.0420.34050.2163-0.08880.318144.6209-41.8458-38.7779
170.08650.02980.12720.32350.01020.3508-0.32210.3861-0.033-0.89840.1749-0.2660.25330.1935-0.2320.9137-0.37590.29850.5933-0.050.122644.9023-28.1021-51.9465
180.009-0.0022-0.00460.00690.00870.007-0.07950.0323-0.0834-0.18020.0965-0.0770.06780.188800.34190.11610.0830.32130.00060.314646.8857-33.8042-18.659
190.01410.0129-0.02090.0326-0.02210.02450.0049-0.11150.031-0.06720.0425-0.2496-0.03940.109-0.00010.15590.0180.04470.23140.00540.200747.7086-14.7876-15.7078
200.1731-0.1009-0.11910.4380.05340.36-0.0445-0.0051-0.0219-0.1035-0.04310.01920.1245-0.0586-00.1678-0.01410.02470.111-0.01720.15329.9264-24.5516-12.8482
210.03110.0084-0.03720.0102-0.00160.03150.0119-0.0484-0.0817-0.03740.05350.10130.1737-0.1494-00.1856-0.0433-0.00560.21350.00870.194817.102-22.9552-5.3759
220.23540.108-0.01630.35860.09130.04130.0174-0.0747-0.04880.6069-0.03950.0236-0.1476-0.15370.05260.5489-0.02670.17470.29570.01780.215410.1298-29.792882.6532
230.0858-0.0631-0.01790.0631-0.02010.0495-0.03160.0229-0.00240.2969-0.03950.1733-0.074-0.0182-0.00030.2677-0.04430.09130.19510.02350.292810.7234-34.579671.9071
240.0219-0.0016-0.00030.00810.00210.0195-0.0546-0.015-0.03940.0170.04330.1416-0.210.0243-0.00010.2781-0.0130.14570.2075-0.02550.35820.4074-25.948669.0046
250.29940.2033-0.18590.1472-0.13260.13980.1613-0.03010.17770.6271-0.05730.3713-0.2293-0.15940.1680.7613-0.01990.17060.2134-0.11570.190510.0437-18.322482.9402
260.0168-0.0054-0.00980.00260.00070.0061-0.05130.0641-0.1060.0397-0.07050.0804-0.1052-0.128900.1605-0.0461-0.00510.3755-0.03730.24616.2735-22.924849.4075
270.24690.1899-0.09970.2997-0.04410.18040.01920.00110.01570.0198-0.038-0.0068-0.0243-0.090700.1222-0.00650.00430.1720.00520.145824.0141-16.088644.2206
280.03160.058-0.07650.1068-0.02510.1919-0.0523-0.0555-0.0337-0.0211-0.0146-0.02760.23440.011200.1829-0.00990.02650.16390.02550.202827.9244-32.36742.5946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 85 )A8 - 85
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 126 )A86 - 126
3X-RAY DIFFRACTION3chain 'A' and (resid 127 through 197 )A127 - 197
4X-RAY DIFFRACTION4chain 'A' and (resid 198 through 267 )A198 - 267
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 50 )B5 - 50
6X-RAY DIFFRACTION6chain 'B' and (resid 51 through 140 )B51 - 140
7X-RAY DIFFRACTION7chain 'B' and (resid 141 through 210 )B141 - 210
8X-RAY DIFFRACTION8chain 'B' and (resid 211 through 408 )B211 - 408
9X-RAY DIFFRACTION9chain 'G' and (resid 9 through 85 )G9 - 85
10X-RAY DIFFRACTION10chain 'G' and (resid 86 through 142 )G86 - 142
11X-RAY DIFFRACTION11chain 'G' and (resid 143 through 165 )G143 - 165
12X-RAY DIFFRACTION12chain 'G' and (resid 166 through 267 )G166 - 267
13X-RAY DIFFRACTION13chain 'H' and (resid 4 through 50 )H4 - 50
14X-RAY DIFFRACTION14chain 'H' and (resid 51 through 407 )H51 - 407
15X-RAY DIFFRACTION15chain 'E' and (resid 9 through 97 )E9 - 97
16X-RAY DIFFRACTION16chain 'E' and (resid 98 through 165 )E98 - 165
17X-RAY DIFFRACTION17chain 'E' and (resid 166 through 265 )E166 - 265
18X-RAY DIFFRACTION18chain 'F' and (resid 9 through 31 )F9 - 31
19X-RAY DIFFRACTION19chain 'F' and (resid 32 through 64 )F32 - 64
20X-RAY DIFFRACTION20chain 'F' and (resid 65 through 379 )F65 - 379
21X-RAY DIFFRACTION21chain 'F' and (resid 380 through 407 )F380 - 407
22X-RAY DIFFRACTION22chain 'C' and (resid 8 through 69 )C8 - 69
23X-RAY DIFFRACTION23chain 'C' and (resid 70 through 142 )C70 - 142
24X-RAY DIFFRACTION24chain 'C' and (resid 143 through 165 )C143 - 165
25X-RAY DIFFRACTION25chain 'C' and (resid 166 through 266 )C166 - 266
26X-RAY DIFFRACTION26chain 'D' and (resid 9 through 31 )D9 - 31
27X-RAY DIFFRACTION27chain 'D' and (resid 32 through 271 )D32 - 271
28X-RAY DIFFRACTION28chain 'D' and (resid 272 through 407 )D272 - 407

+
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