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- PDB-1xxx: Crystal structure of Dihydrodipicolinate Synthase (DapA, Rv2753c)... -

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Basic information

Entry
Database: PDB / ID: 1xxx
TitleCrystal structure of Dihydrodipicolinate Synthase (DapA, Rv2753c) from Mycobacterium tuberculosis
ComponentsDihydrodipicolinate synthase
KeywordsLYASE / dihydrodipicolinate synthase / DapA / Rv2753c / Mycobacterium tuberculosis / lysine biosynthesis / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / plasma membrane / cytosol
Similarity search - Function
4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel ...4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / 4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsKefala, G. / Panjikar, S. / Janowski, R. / Weiss, M.S. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Biochem.J. / Year: 2008
Title: Crystal structure and kinetic study of dihydrodipicolinate synthase from Mycobacterium tuberculosis.
Authors: Kefala, G. / Evans, G.L. / Griffin, M.D. / Devenish, S.R. / Pearce, F.G. / Perugini, M.A. / Gerrard, J.A. / Weiss, M.S. / Dobson, R.C.
History
DepositionNov 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 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_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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE Author states that residue number one is indeed a VAL based on TB genome data base. THE ...SEQUENCE Author states that residue number one is indeed a VAL based on TB genome data base. THE CORRESPONDING CHAIN IDS BETWEEN PDB FILE AND THE PAPER ARE AS FOLLOWING: E->F, F->E, H->G, G->H

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase
C: Dihydrodipicolinate synthase
D: Dihydrodipicolinate synthase
E: Dihydrodipicolinate synthase
F: Dihydrodipicolinate synthase
G: Dihydrodipicolinate synthase
H: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,63632
Polymers248,9248
Non-polymers1,71224
Water28,5901587
1
A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase
C: Dihydrodipicolinate synthase
D: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,31816
Polymers124,4624
Non-polymers85612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11650 Å2
ΔGint-156 kcal/mol
Surface area37040 Å2
MethodPISA
2
E: Dihydrodipicolinate synthase
F: Dihydrodipicolinate synthase
G: Dihydrodipicolinate synthase
H: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,31816
Polymers124,4624
Non-polymers85612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11690 Å2
ΔGint-160 kcal/mol
Surface area37240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.790, 87.370, 139.850
Angle α, β, γ (deg.)90.00, 107.78, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91A
101B
111C
121D
131E
141F
151G
161H
171A
181B
191C
201D
211E
221F
231G
241H
251A
261B
271C
281D
291E
301F
311G
321H
331A
341B
351C
361D
371E
381F
391G
401H
411A
421B
431C
441D
451E
461F
471G
481H
491A
501B
511C
521D
531E
541F
551G
561H
571A
581B
591C
601D
611E
621F
631G
641H
651A
661B
671C
681D
691E
701F
711G
721H
731A
741B
751C
761D
771E
781F
791G
801H
811A
821B
831C
841D
851E
861F
871G
881H

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPSERSERAA7 - 2410 - 27
21ASPASPSERSERBB7 - 2410 - 27
31ASPASPSERSERCC7 - 2410 - 27
41ASPASPSERSERDD7 - 2410 - 27
51ASPASPSERSEREE7 - 2410 - 27
61ASPASPSERSERFF7 - 2410 - 27
71ASPASPSERSERGG7 - 2410 - 27
81ASPASPSERSERHH7 - 2410 - 27
92SERSERALAALAAA28 - 3431 - 37
102SERSERALAALABB28 - 3431 - 37
112SERSERALAALACC28 - 3431 - 37
122SERSERALAALADD28 - 3431 - 37
132SERSERALAALAEE28 - 3431 - 37
142SERSERALAALAFF28 - 3431 - 37
152SERSERALAALAGG28 - 3431 - 37
162SERSERALAALAHH28 - 3431 - 37
173ALAALAILEILEAA38 - 6741 - 70
183ALAALAILEILEBB38 - 6741 - 70
193ALAALAILEILECC38 - 6741 - 70
203ALAALAILEILEDD38 - 6741 - 70
213ALAALAILEILEEE38 - 6741 - 70
223ALAALAILEILEFF38 - 6741 - 70
233ALAALAILEILEGG38 - 6741 - 70
243ALAALAILEILEHH38 - 6741 - 70
254CYSCYSLEULEUAA102 - 125105 - 128
264CYSCYSLEULEUBB102 - 125105 - 128
274CYSCYSLEULEUCC102 - 125105 - 128
284CYSCYSLEULEUDD102 - 125105 - 128
294CYSCYSLEULEUEE102 - 125105 - 128
304CYSCYSLEULEUFF102 - 125105 - 128
314CYSCYSLEULEUGG102 - 125105 - 128
324CYSCYSLEULEUHH102 - 125105 - 128
335ALAALAPHEPHEAA127 - 129130 - 132
345ALAALAPHEPHEBB127 - 129130 - 132
355ALAALAPHEPHECC127 - 129130 - 132
365ALAALAPHEPHEDD127 - 129130 - 132
375ALAALAPHEPHEEE127 - 129130 - 132
385ALAALAPHEPHEFF127 - 129130 - 132
395ALAALAPHEPHEGG127 - 129130 - 132
405ALAALAPHEPHEHH127 - 129130 - 132
416ALAALATHRTHRAA131 - 136134 - 139
426ALAALATHRTHRBB131 - 136134 - 139
436ALAALATHRTHRCC131 - 136134 - 139
446ALAALATHRTHRDD131 - 136134 - 139
456ALAALATHRTHREE131 - 136134 - 139
466ALAALATHRTHRFF131 - 136134 - 139
476ALAALATHRTHRGG131 - 136134 - 139
486ALAALATHRTHRHH131 - 136134 - 139
497LEULEUALAALAAA138 - 162141 - 165
507LEULEUALAALABB138 - 162141 - 165
517LEULEUALAALACC138 - 162141 - 165
527LEULEUALAALADD138 - 162141 - 165
537LEULEUALAALAEE138 - 162141 - 165
547LEULEUALAALAFF138 - 162141 - 165
557LEULEUALAALAGG138 - 162141 - 165
567LEULEUALAALAHH138 - 162141 - 165
578HISHISASPASPAA164 - 176167 - 179
588HISHISASPASPBB164 - 176167 - 179
598HISHISASPASPCC164 - 176167 - 179
608HISHISASPASPDD164 - 176167 - 179
618HISHISASPASPEE164 - 176167 - 179
628HISHISASPASPFF164 - 176167 - 179
638HISHISASPASPGG164 - 176167 - 179
648HISHISASPASPHH164 - 176167 - 179
659HISHISGLYGLYAA178 - 194181 - 197
669HISHISGLYGLYBB178 - 194181 - 197
679HISHISGLYGLYCC178 - 194181 - 197
689HISHISGLYGLYDD178 - 194181 - 197
699HISHISGLYGLYEE178 - 194181 - 197
709HISHISGLYGLYFF178 - 194181 - 197
719HISHISGLYGLYGG178 - 194181 - 197
729HISHISGLYGLYHH178 - 194181 - 197
7310ASPASPLEULEUAA196 - 222199 - 225
7410ASPASPLEULEUBB196 - 222199 - 225
7510ASPASPLEULEUCC196 - 222199 - 225
7610ASPASPLEULEUDD196 - 222199 - 225
7710ASPASPLEULEUEE196 - 222199 - 225
7810ASPASPLEULEUFF196 - 222199 - 225
7910ASPASPLEULEUGG196 - 222199 - 225
8010ASPASPLEULEUHH196 - 222199 - 225
8111ASNASNTHRTHRAA241 - 282244 - 285
8211ASNASNTHRTHRBB241 - 282244 - 285
8311ASNASNTHRTHRCC241 - 282244 - 285
8411ASNASNTHRTHRDD241 - 282244 - 285
8511ASNASNTHRTHREE241 - 282244 - 285
8611ASNASNTHRTHRFF241 - 282244 - 285
8711ASNASNTHRTHRGG241 - 282244 - 285
8811ASNASNTHRTHRHH241 - 282244 - 285
DetailsDapA occurs as a tetramer. The asymmetric unit contains two tetramers ABCD and EFGH.

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Components

#1: Protein
Dihydrodipicolinate synthase / DHDPS


Mass: 31115.477 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: dapA / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RP
References: UniProt: P63945, UniProt: P9WP25*PLUS, dihydrodipicolinate synthase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1587 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.32 %
Crystal growTemperature: 292 K / pH: 8.5
Details: 100 mM Tris-HCl, 28 % PEG 4000, 170 mM MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.981
DetectorType: MARRESEARCH / Detector: CCD / Date: May 7, 2004
RadiationMonochromator: DOUBLE CRYSTAL (SI111, SI220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981 Å / Relative weight: 1
ReflectionResolution: 2.28→99 Å / Num. obs: 99893 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.085 / Net I/σ(I): 27.98
Reflection shellResolution: 2.28→2.32 Å / Rmerge(I) obs: 0.192 / Mean I/σ(I) obs: 12.53 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O5K
Resolution: 2.28→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.927 / SU B: 10.125 / SU ML: 0.139 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.311 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: TLS REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1987 2 %RANDOM
Rwork0.148 ---
obs0.149 97308 100 %-
all-99362 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å2-1.07 Å2
2--1.44 Å20 Å2
3----1.38 Å2
Refinement stepCycle: LAST / Resolution: 2.28→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17072 0 80 1587 18739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02217408
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.98423708
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49652356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97123.462624
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.805152664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.90115128
X-RAY DIFFRACTIONr_chiral_restr0.0960.22872
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213032
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.210615
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.212512
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.21851
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.248
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9431.511970
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.532.518604
X-RAY DIFFRACTIONr_scbond_it4.04955971
X-RAY DIFFRACTIONr_scangle_it5.89105104
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1517 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.070.05
2Btight positional0.060.05
3Ctight positional0.070.05
4Dtight positional0.070.05
5Etight positional0.060.05
6Ftight positional0.050.05
7Gtight positional0.070.05
8Htight positional0.060.05
1Atight thermal0.971.5
2Btight thermal0.931.5
3Ctight thermal0.941.5
4Dtight thermal0.91.5
5Etight thermal0.831.5
6Ftight thermal0.771.5
7Gtight thermal0.931.5
8Htight thermal0.891.5
LS refinement shellResolution: 2.28→2.34 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 145 -
Rwork0.165 7137 -
obs--100 %
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)
11.1294-0.0668-0.05420.87940.15491.3174-0.0697-0.07750.09560.09560.060.042-0.139-0.12020.0097-0.16250.02470.0006-0.13430.0027-0.0842.709244.683668.3558
31.69810.1254-0.02620.55860.00420.683-0.0432-0.0255-0.157-0.03950.04530.03330.1192-0.0432-0.002-0.15930.01230.0208-0.13420.0218-0.06534.0745-3.233579.412
51.2817-0.1696-0.22810.8806-0.04842.0971-0.0175-0.0117-0.0586-0.0511-0.04640.0463-0.1572-0.41210.0640.12570.1118-0.0597-0.0072-0.0369-0.1157-25.1786-23.0114-14.8957
71.29560.18850.26731.4131-0.09351.0322-0.0741-0.03380.0951-0.0319-0.0428-0.0227-0.1527-0.080.1169-0.11580.0082-0.0096-0.1321-0.0118-0.1215-8.7285-17.291931.0321
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 3008 - 303
2X-RAY DIFFRACTION3CC5 - 3008 - 303
3X-RAY DIFFRACTION5EE6 - 3009 - 303
4X-RAY DIFFRACTION7GG6 - 3009 - 303

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