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- PDB-2c2b: Crystallographic structure of Arabidopsis thaliana Threonine synt... -

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Basic information

Entry
Database: PDB / ID: 2c2b
TitleCrystallographic structure of Arabidopsis thaliana Threonine synthase complexed with pyridoxal phosphate and S-adenosylmethionine
ComponentsTHREONINE SYNTHASE 1, CHLOROPLASTIC
KeywordsLYASE / THREONINE SYNTHESIS / ALLOSTERY / SYNTHASE
Function / homology
Function and homology information


threonine synthase / threonine synthase activity / threonine biosynthetic process / chloroplast stroma / chloroplast / pyridoxal phosphate binding / plasma membrane
Similarity search - Function
Threonine synthase-like / Serine/threonine dehydratase, pyridoxal-phosphate-binding site / Serine/threonine dehydratases pyridoxal-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / S-ADENOSYLMETHIONINE / Threonine synthase 1, chloroplastic
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMas-Droux, C. / Biou, V. / Dumas, R.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Allosteric Threonine Synthase: Reorganization of the Pyridoxal Phosphate Site Upon Asymmetric Activation Through S-Adenosylmethionine Binding to a Novel Site.
Authors: Mas-Droux, C. / Biou, V. / Dumas, R.
History
DepositionSep 27, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 11, 2015Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THREONINE SYNTHASE 1, CHLOROPLASTIC
B: THREONINE SYNTHASE 1, CHLOROPLASTIC
C: THREONINE SYNTHASE 1, CHLOROPLASTIC
D: THREONINE SYNTHASE 1, CHLOROPLASTIC
E: THREONINE SYNTHASE 1, CHLOROPLASTIC
F: THREONINE SYNTHASE 1, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)326,94427
Polymers320,3146
Non-polymers6,63121
Water5,639313
1
A: THREONINE SYNTHASE 1, CHLOROPLASTIC
B: THREONINE SYNTHASE 1, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,9819
Polymers106,7712
Non-polymers2,2107
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8400 Å2
ΔGint-58.4 kcal/mol
Surface area31520 Å2
MethodPISA
2
C: THREONINE SYNTHASE 1, CHLOROPLASTIC
D: THREONINE SYNTHASE 1, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,9819
Polymers106,7712
Non-polymers2,2107
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8430 Å2
ΔGint-60.1 kcal/mol
Surface area31480 Å2
MethodPISA
3
E: THREONINE SYNTHASE 1, CHLOROPLASTIC
F: THREONINE SYNTHASE 1, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,9819
Polymers106,7712
Non-polymers2,2107
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8430 Å2
ΔGint-58.4 kcal/mol
Surface area31870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.920, 110.846, 152.779
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31F
12B
22D
32E
13A
23C
33F

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERALAALA5AA40 - 47040 - 470
21SERSERALAALA5CC40 - 47040 - 470
31SERSERALAALA5FF40 - 47040 - 470
12SERSERALAALA5BB40 - 47040 - 470
22SERSERALAALA5DD40 - 47040 - 470
32SERSERALAALA5EE40 - 47040 - 470
13TRSTRSTRSTRS4AI800
23TRSTRSTRSTRS4CP800
33TRSTRSTRSTRS4FZ800

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(-0.49938, 0.86639, 0.00017), (-0.86639, -0.49938, -0.00063), (-0.00047, -0.00046, 1)32.06766, 55.19161, -50.8735
2given(0.50075, 0.86559, 0.00023), (0.86559, -0.50075, 0.00035), (0.00042, 2.0E-5, -1)32.0809, -55.6683, 101.83951
3given(-0.4998, 0.86614, 6.0E-5), (-0.86614, -0.4998, 0.00068), (0.00062, 0.00029, 1)32.11317, 55.10795, -50.94014
4given(0.5005, 0.86574, -0.00043), (0.86574, -0.5005, -0.00037), (-0.00054, -0.00019, -1)32.15505, -55.63955, 101.86627
DetailsTHE BIOLOGICAL UNIT OF ARABIDOPSIS THALIANA THREONINESYNTHASE (HOMODIMER) IN COMPLEX WITH SAM IS FORMED BY TWOASYMETRIC MONOMERS. IN ONE MONOMER THE ACTIVE SITECORRESPONDS TO AN INACTIVE FORM WHEREAS IN THE OTHERMONOMER, THE ACTIVE SITE CORRESPONDS TO AN ACTIVE FORM WITHA STANDARD PLP ORIENTATION FOR A TYPE II FAMILY PLPENZYMES.

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Components

#1: Protein
THREONINE SYNTHASE 1, CHLOROPLASTIC / / THREONINE SYNTHASE / TS / PROTEIN METHIONINE OVER-ACCUMULATOR 2


Mass: 53385.590 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PET23D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9S7B5, threonine synthase
#2: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H10NO6P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE CORRESPONDS TO THE MATURE SEQUENCE WITHOUT THE TRANSIT PEPTIDE

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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: 5.3 Å3/Da / Density % sol: 76.4 %
Crystal growpH: 6.5
Details: 10 MM CACL2, 15% (W/V) PEG 2000 MONOMETHYL ETHER, 1 MM PLP, 5MM SAM, 100 MM BISTRIS PH 6.5 BUFFER

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 30, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 93317 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.7
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E5X
Resolution: 2.6→29.89 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / SU B: 25.549 / SU ML: 0.272 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.812 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-35 AND 480-486 ARE DISORDERED IN MONOMERS A, C AND F RESIDUS 1-34, 344-362 AND 482-486 ARE DISORDERED IN MONOMERS B, D AND E.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 4904 5 %RANDOM
Rwork0.206 ---
obs0.208 93254 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å2-0.26 Å2
2---0.12 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20207 0 438 313 20958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02221143
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9611.97628733
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.40552608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56424.224883
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.487153403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.29415102
X-RAY DIFFRACTIONr_chiral_restr0.060.23160
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0215932
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1740.210204
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.214637
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2719
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.2118
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.733213378
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.296321002
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.83249015
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.79767731
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1724medium positional0.090.5
12C1724medium positional0.070.5
13F1724medium positional0.070.5
21B1648medium positional0.070.5
22D1648medium positional0.080.5
23E1648medium positional0.070.5
31A8medium positional0.480.5
32C8medium positional0.440.5
33F8medium positional0.560.5
11A1612loose positional0.315
12C1612loose positional0.35
13F1612loose positional0.355
21B1550loose positional0.265
22D1550loose positional0.245
23E1550loose positional0.245
11A1724medium thermal0.142
12C1724medium thermal0.152
13F1724medium thermal0.152
21B1648medium thermal0.142
22D1648medium thermal0.142
23E1648medium thermal0.142
31A8medium thermal0.062
32C8medium thermal0.092
33F8medium thermal0.132
11A1612loose thermal0.8110
12C1612loose thermal0.910
13F1612loose thermal0.8510
21B1550loose thermal0.8610
22D1550loose thermal0.8510
23E1550loose thermal0.8510
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.347 356
Rwork0.3 6882
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)
11.5691-0.30751.44811.86042.06926.1114-0.17010.22780.0097-0.07070.1346-0.2239-0.79741.20090.0355-0.1289-0.33680.0084-0.09150.1066-0.167652.0149.87882.433
21.9355-0.04970.31991.52642.08886.27-0.04990.4295-0.1168-0.4585-0.05670.0959-0.47780.36790.1066-0.0368-0.07560.0233-0.15140.0095-0.228138.57135.26645.596
32.83662.07622.1962.35932.09915.6918-0.1682-0.69110.5739-0.0744-0.54930.5123-0.5774-1.34420.7175-0.16490.0298-0.04480.0199-0.1641-0.092928.12446.76590.31
42.2247-0.48010.48562.31680.05392.5474-0.23830.35730.0969-0.6514-0.29290.6054-1.0777-1.27050.53120.41070.3495-0.31430.2987-0.1734-0.004718.05749.32148.745
52.02890.44690.73671.40710.76495.5008-0.51040.09560.4993-0.5033-0.09470.1775-2.38180.17580.60510.876-0.0537-0.2804-0.30960.0491-0.034337.52964.19269.139
61.7713-0.1979-0.60921.60180.77935.9373-0.09710.2052-0.1681-0.0826-0.17190.16780.8328-0.94620.269-0.1448-0.16210.0304-0.1897-0.0744-0.178927.94327.17465.983
71.9235-0.42120.60651.4251-1.99675.8910.0154-0.0319-0.1638-0.3725-0.09360.03481.5297-0.0430.07820.10910.18640.1047-0.3437-0.04-0.157549.456-14.77131.492
81.50280.10141.35341.5951-1.44256.5631-0.0410.41780.1157-0.5531-0.06660.06630.63250.28310.1076-0.10580.11090.0113-0.0872-0.0119-0.219943.3864.129-5.315
90.9782-0.7020.8124.4411-2.37824.7569-0.11490.04030.16040.6805-0.5796-0.7257-0.86371.1320.6945-0.1007-0.0679-0.0994-0.03180.1407-0.096558.5967.43439.4
102.7657-0.17840.12681.1818-0.42352.3325-0.1670.60530.5005-0.4412-0.4155-0.3497-0.60171.46560.5826-0.0072-0.12310.02780.66440.3730.006865.81714.878-2.162
111.0062-0.11110.41172.2123-1.36475.9693-0.02210.2134-0.0267-0.4559-0.6422-0.45351.39642.15790.6644-0.0610.61040.24910.62420.2194-0.056668.926-9.46818.202
121.96620.14261.08721.5361-0.07715.987-0.21940.16140.2206-0.0808-0.06130.0729-1.2668-0.23050.2807-0.09030.1349-0.0589-0.24160.0322-0.171841.71117.36515.055
131.6863-0.6737-2.61441.7806-0.73656.15140.0959-0.3450.10140.075-0.1978-0.1152-0.8321.41030.1019-0.4297-0.1635-0.02890.17850.0471-0.1677101.328-35.62719.444
141.48780.0384-2.1561.85870.58966.84010.0022-0.5369-0.02060.3859-0.09230.1268-0.11170.57950.0901-0.26040.03380.01220.0308-0.0063-0.21181.979-39.92756.241
153.88281.2246-2.33241.2078-0.6015.4521-0.70370.3187-0.6825-0.31220.0803-0.2521.443-0.19610.6234-0.0669-0.050.2116-0.1156-0.0363-0.097986.687-54.76711.569
162.0874-0.6542-0.4962.56480.24732.5732-0.3752-0.5544-0.54950.5277-0.1550.28651.69290.2250.53020.57820.23160.32570.11590.193-0.028683.853-64.72353.088
171.81260.2625-1.17641.2735-0.30935.7775-0.3761-0.5952-0.3721-0.0132-0.2496-0.30641.09082.21420.6257-0.11630.54160.14570.66170.259-0.0442106.493-55.28232.74
181.22710.0962-0.5051.86920.68985.8018-0.1133-0.0438-0.03070.236-0.14460.24050.4569-1.26790.2579-0.3585-0.02090.09660.034-0.0559-0.158269.655-45.09335.863
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 132
2X-RAY DIFFRACTION2B36 - 132
3X-RAY DIFFRACTION3A163 - 271
4X-RAY DIFFRACTION3B450 - 481
5X-RAY DIFFRACTION4B163 - 271
6X-RAY DIFFRACTION4A450 - 480
7X-RAY DIFFRACTION5A133 - 162
8X-RAY DIFFRACTION5A272 - 343
9X-RAY DIFFRACTION5A363 - 449
10X-RAY DIFFRACTION6B133 - 162
11X-RAY DIFFRACTION6B272 - 343
12X-RAY DIFFRACTION6B363 - 449
13X-RAY DIFFRACTION7C37 - 132
14X-RAY DIFFRACTION8D36 - 132
15X-RAY DIFFRACTION9C163 - 271
16X-RAY DIFFRACTION9D450 - 481
17X-RAY DIFFRACTION10D163 - 271
18X-RAY DIFFRACTION10C450 - 480
19X-RAY DIFFRACTION11C133 - 162
20X-RAY DIFFRACTION11C272 - 346
21X-RAY DIFFRACTION11C363 - 449
22X-RAY DIFFRACTION12D133 - 162
23X-RAY DIFFRACTION12D272 - 343
24X-RAY DIFFRACTION12D363 - 449
25X-RAY DIFFRACTION13F36 - 132
26X-RAY DIFFRACTION14E36 - 132
27X-RAY DIFFRACTION15F163 - 271
28X-RAY DIFFRACTION15E450 - 480
29X-RAY DIFFRACTION16E163 - 271
30X-RAY DIFFRACTION16F450 - 480
31X-RAY DIFFRACTION17F133 - 162
32X-RAY DIFFRACTION17F272 - 346
33X-RAY DIFFRACTION17F363 - 449
34X-RAY DIFFRACTION18E133 - 162
35X-RAY DIFFRACTION18E272 - 343
36X-RAY DIFFRACTION18E363 - 449

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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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