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- PDB-5nue: Cytosolic Malate Dehydrogenase 1 (peroxide-treated) -

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Basic information

Entry
Database: PDB / ID: 5nue
TitleCytosolic Malate Dehydrogenase 1 (peroxide-treated)
Components(Malate dehydrogenase 1, ...) x 3
KeywordsOXIDOREDUCTASE / Dehydrogenase / Oxidized / Malate/Oxaloacetate / NAD+
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / apoplast / plasmodesma / plant-type vacuole / chloroplast stroma / response to zinc ion / tricarboxylic acid cycle / chloroplast ...malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / apoplast / plasmodesma / plant-type vacuole / chloroplast stroma / response to zinc ion / tricarboxylic acid cycle / chloroplast / mRNA binding / extracellular region / nucleus / plasma membrane / cytosol
Similarity search - Function
Malate dehydrogenase, NAD-dependent, cytosolic / Malate dehydrogenase, type 2 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain ...Malate dehydrogenase, NAD-dependent, cytosolic / Malate dehydrogenase, type 2 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 2-ETHOXYETHANOL / FORMIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / HYDROGEN PEROXIDE / Malate dehydrogenase 1, cytoplasmic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35000279615 Å
AuthorsYoung, D. / Messens, J. / Huang, J. / Reichheld, J.-P.
Funding support France, Belgium, 4items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique and the Agence Nationale de la RechercheANR-Blanc Cynthiol 12-BSV6-0011 France
VIB Belgium
Vrije Universiteit BrusselSPR34 Belgium
Research Foundation - Flanders (FWO) Belgium
CitationJournal: J. Exp. Bot. / Year: 2018
Title: Self-protection of cytosolic malate dehydrogenase against oxidative stress in Arabidopsis.
Authors: Huang, J. / Niazi, A.K. / Young, D. / Rosado, L.A. / Vertommen, D. / Bodra, N. / Abdelgawwad, M.R. / Vignols, F. / Wei, B. / Wahni, K. / Bashandy, T. / Bariat, L. / Van Breusegem, F. / ...Authors: Huang, J. / Niazi, A.K. / Young, D. / Rosado, L.A. / Vertommen, D. / Bodra, N. / Abdelgawwad, M.R. / Vignols, F. / Wei, B. / Wahni, K. / Bashandy, T. / Bariat, L. / Van Breusegem, F. / Messens, J. / Reichheld, J.P.
History
DepositionApr 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Apr 9, 2025Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Malate dehydrogenase 1, cytoplasmic
B: Malate dehydrogenase 1, cytoplasmic
C: Malate dehydrogenase 1, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,42044
Polymers106,9293
Non-polymers4,49141
Water17,997999
1
A: Malate dehydrogenase 1, cytoplasmic
B: Malate dehydrogenase 1, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,44331
Polymers71,2862
Non-polymers3,15729
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11260 Å2
ΔGint-103 kcal/mol
Surface area24100 Å2
MethodPISA
2
C: Malate dehydrogenase 1, cytoplasmic
hetero molecules

C: Malate dehydrogenase 1, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,95426
Polymers71,2862
Non-polymers2,66824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556x,-y,-z+11
Buried area10220 Å2
ΔGint-110 kcal/mol
Surface area24750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.598, 118.374, 148.489
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11C-797-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALYSLYS(chain 'A' and (resid 2 through 3 or resid 6...AA2 - 32 - 3
12VALVALALAALA(chain 'A' and (resid 2 through 3 or resid 6...AA6 - 146 - 14
13ILEILEPROPRO(chain 'A' and (resid 2 through 3 or resid 6...AA17 - 2317 - 23
14ILEILEILEILE(chain 'A' and (resid 2 through 3 or resid 6...AA2525
15METMETGLYGLY(chain 'A' and (resid 2 through 3 or resid 6...AA30 - 3230 - 32
16GLNGLNHISHIS(chain 'A' and (resid 2 through 3 or resid 6...AA35 - 4035 - 40
17LEULEUALAALA(chain 'A' and (resid 2 through 3 or resid 6...AA42 - 4742 - 47
18ALAALALEULEU(chain 'A' and (resid 2 through 3 or resid 6...AA50 - 5150 - 51
19GLYGLYLYSLYS(chain 'A' and (resid 2 through 3 or resid 6...AA53 - 5553 - 55
110GLUGLULEULEU(chain 'A' and (resid 2 through 3 or resid 6...AA57 - 5857 - 58
111ASPASPVALVAL(chain 'A' and (resid 2 through 3 or resid 6...AA60 - 8660 - 86
112VALVALARGARG(chain 'A' and (resid 2 through 3 or resid 6...AA88 - 9388 - 93
113GLUGLUGLUGLU(chain 'A' and (resid 2 through 3 or resid 6...AA9595
114GLUGLUVALVAL(chain 'A' and (resid 2 through 3 or resid 6...AA98 - 10298 - 102
115LYSLYSVALVAL(chain 'A' and (resid 2 through 3 or resid 6...AA105 - 107105 - 107
116ILEILELEULEU(chain 'A' and (resid 2 through 3 or resid 6...AA109 - 117109 - 117
117HISHISALAALA(chain 'A' and (resid 2 through 3 or resid 6...AA120 - 121120 - 121
118CYSCYSCYSCYS(chain 'A' and (resid 2 through 3 or resid 6...AA125125
119VALVALASNASN(chain 'A' and (resid 2 through 3 or resid 6...AA127 - 132127 - 132
120ALAALAILEILE(chain 'A' and (resid 2 through 3 or resid 6...AA134 - 140134 - 140
121GLUGLUPROPRO(chain 'A' and (resid 2 through 3 or resid 6...AA143 - 146143 - 146
122ILEILEPROPRO(chain 'A' and (resid 2 through 3 or resid 6...AA148 - 149148 - 149
123ASNASNGLNGLN(chain 'A' and (resid 2 through 3 or resid 6...AA152 - 167152 - 167
124GLUGLUSERSER(chain 'A' and (resid 2 through 3 or resid 6...AA170 - 189170 - 189
125SERSERASNASN(chain 'A' and (resid 2 through 3 or resid 6...AA191 - 197191 - 197
126ALAALALYSLYS(chain 'A' and (resid 2 through 3 or resid 6...AA199 - 208199 - 208
127VALVALASPASP(chain 'A' and (resid 2 through 3 or resid 6...AA210 - 221210 - 221
128PHEPHEILEILE(chain 'A' and (resid 2 through 3 or resid 6...AA224 - 225224 - 225
129THRTHRILEILE(chain 'A' and (resid 2 through 3 or resid 6...AA227 - 235227 - 235
130LYSLYSARGARG(chain 'A' and (resid 2 through 3 or resid 6...AA237 - 239237 - 239
131SERSERALAALA(chain 'A' and (resid 2 through 3 or resid 6...AA246 - 247246 - 247
132ALAALAILEILE(chain 'A' and (resid 2 through 3 or resid 6...AA251 - 255251 - 255
133ASPASPTYRTYR(chain 'A' and (resid 2 through 3 or resid 6...AA257 - 273257 - 273
134ASPASPPROPRO(chain 'A' and (resid 2 through 3 or resid 6...AA275 - 281275 - 281
135GLYGLYASNASN(chain 'A' and (resid 2 through 3 or resid 6...AA283 - 294283 - 294
136TRPTRPTRPTRP(chain 'A' and (resid 2 through 3 or resid 6...AA297297
137ILEILEASPASP(chain 'A' and (resid 2 through 3 or resid 6...AA299 - 306299 - 306
138VALVALARGARG(chain 'A' and (resid 2 through 3 or resid 6...AA308 - 310308 - 310
139LYSLYSTHRTHR(chain 'A' and (resid 2 through 3 or resid 6...AA312 - 316312 - 316
140GLUGLULEULEU(chain 'A' and (resid 2 through 3 or resid 6...AA319 - 320319 - 320
141GLUGLULYSLYS(chain 'A' and (resid 2 through 3 or resid 6...AA323 - 324323 - 324
142LEULEULEULEU(chain 'A' and (resid 2 through 3 or resid 6...AA326326
143SERSERSERSER(chain 'A' and (resid 2 through 3 or resid 6...AA332332
244ALAALALYSLYS(chain 'B' and (resid 2 through 3 or resid 6...BB2 - 32 - 3
245VALVALALAALA(chain 'B' and (resid 2 through 3 or resid 6...BB6 - 146 - 14
246ILEILEPROPRO(chain 'B' and (resid 2 through 3 or resid 6...BB17 - 2317 - 23
247ILEILEILEILE(chain 'B' and (resid 2 through 3 or resid 6...BB2525
248METMETGLYGLY(chain 'B' and (resid 2 through 3 or resid 6...BB30 - 3230 - 32
249GLNGLNHISHIS(chain 'B' and (resid 2 through 3 or resid 6...BB35 - 4035 - 40
250LEULEUALAALA(chain 'B' and (resid 2 through 3 or resid 6...BB42 - 4742 - 47
251ALAALALEULEU(chain 'B' and (resid 2 through 3 or resid 6...BB50 - 5150 - 51
252GLYGLYLYSLYS(chain 'B' and (resid 2 through 3 or resid 6...BB53 - 5553 - 55
253GLUGLULEULEU(chain 'B' and (resid 2 through 3 or resid 6...BB57 - 5857 - 58
254ASPASPVALVAL(chain 'B' and (resid 2 through 3 or resid 6...BB60 - 8660 - 86
255VALVALARGARG(chain 'B' and (resid 2 through 3 or resid 6...BB88 - 9388 - 93
256GLUGLUGLUGLU(chain 'B' and (resid 2 through 3 or resid 6...BB9595
257GLUGLUVALVAL(chain 'B' and (resid 2 through 3 or resid 6...BB98 - 10298 - 102
258LYSLYSVALVAL(chain 'B' and (resid 2 through 3 or resid 6...BB105 - 107105 - 107
259ILEILELEULEU(chain 'B' and (resid 2 through 3 or resid 6...BB109 - 117109 - 117
260HISHISALAALA(chain 'B' and (resid 2 through 3 or resid 6...BB120 - 121120 - 121
261CYSCYSCYSCYS(chain 'B' and (resid 2 through 3 or resid 6...BB125125
262VALVALASNASN(chain 'B' and (resid 2 through 3 or resid 6...BB127 - 132127 - 132
263ALAALAILEILE(chain 'B' and (resid 2 through 3 or resid 6...BB134 - 140134 - 140
264GLUGLUPROPRO(chain 'B' and (resid 2 through 3 or resid 6...BB143 - 146143 - 146
265ILEILEPROPRO(chain 'B' and (resid 2 through 3 or resid 6...BB148 - 149148 - 149
266ASNASNGLNGLN(chain 'B' and (resid 2 through 3 or resid 6...BB152 - 167152 - 167
267GLUGLUSERSER(chain 'B' and (resid 2 through 3 or resid 6...BB170 - 189170 - 189
268SERSERASNASN(chain 'B' and (resid 2 through 3 or resid 6...BB191 - 197191 - 197
269ALAALALYSLYS(chain 'B' and (resid 2 through 3 or resid 6...BB199 - 208199 - 208
270VALVALASPASP(chain 'B' and (resid 2 through 3 or resid 6...BB210 - 221210 - 221
271PHEPHEILEILE(chain 'B' and (resid 2 through 3 or resid 6...BB224 - 225224 - 225
272THRTHRILEILE(chain 'B' and (resid 2 through 3 or resid 6...BB227 - 235227 - 235
273LYSLYSARGARG(chain 'B' and (resid 2 through 3 or resid 6...BB237 - 239237 - 239
274SERSERALAALA(chain 'B' and (resid 2 through 3 or resid 6...BB246 - 247246 - 247
275ALAALAILEILE(chain 'B' and (resid 2 through 3 or resid 6...BB251 - 255251 - 255
276ASPASPTYRTYR(chain 'B' and (resid 2 through 3 or resid 6...BB257 - 273257 - 273
277ASPASPPROPRO(chain 'B' and (resid 2 through 3 or resid 6...BB275 - 281275 - 281
278GLYGLYASNASN(chain 'B' and (resid 2 through 3 or resid 6...BB283 - 294283 - 294
279TRPTRPTRPTRP(chain 'B' and (resid 2 through 3 or resid 6...BB297297
280ILEILEASPASP(chain 'B' and (resid 2 through 3 or resid 6...BB299 - 306299 - 306
281VALVALARGARG(chain 'B' and (resid 2 through 3 or resid 6...BB308 - 310308 - 310
282LYSLYSTHRTHR(chain 'B' and (resid 2 through 3 or resid 6...BB312 - 316312 - 316
283GLUGLULEULEU(chain 'B' and (resid 2 through 3 or resid 6...BB319 - 320319 - 320
284GLUGLULYSLYS(chain 'B' and (resid 2 through 3 or resid 6...BB323 - 324323 - 324
285LEULEULEULEU(chain 'B' and (resid 2 through 3 or resid 6...BB326326
286SERSERSERSER(chain 'B' and (resid 2 through 3 or resid 6...BB332332
387ALAALALYSLYS(chain 'C' and (resid 2 through 3 or resid 6...CC2 - 32 - 3
388VALVALALAALA(chain 'C' and (resid 2 through 3 or resid 6...CC6 - 146 - 14
389ILEILEPROPRO(chain 'C' and (resid 2 through 3 or resid 6...CC17 - 2317 - 23
390ILEILEILEILE(chain 'C' and (resid 2 through 3 or resid 6...CC2525
391METMETGLYGLY(chain 'C' and (resid 2 through 3 or resid 6...CC30 - 3230 - 32
392GLNGLNHISHIS(chain 'C' and (resid 2 through 3 or resid 6...CC35 - 4035 - 40
393LEULEUALAALA(chain 'C' and (resid 2 through 3 or resid 6...CC42 - 4742 - 47
394ALAALALEULEU(chain 'C' and (resid 2 through 3 or resid 6...CC50 - 5150 - 51
395GLYGLYLYSLYS(chain 'C' and (resid 2 through 3 or resid 6...CC53 - 5553 - 55
396GLUGLULEULEU(chain 'C' and (resid 2 through 3 or resid 6...CC57 - 5857 - 58
397ASPASPVALVAL(chain 'C' and (resid 2 through 3 or resid 6...CC60 - 8660 - 86
398VALVALARGARG(chain 'C' and (resid 2 through 3 or resid 6...CC88 - 9388 - 93
399GLUGLUGLUGLU(chain 'C' and (resid 2 through 3 or resid 6...CC9595
3100GLUGLUVALVAL(chain 'C' and (resid 2 through 3 or resid 6...CC98 - 10298 - 102
3101LYSLYSVALVAL(chain 'C' and (resid 2 through 3 or resid 6...CC105 - 107105 - 107
3102ILEILELEULEU(chain 'C' and (resid 2 through 3 or resid 6...CC109 - 117109 - 117
3103HISHISALAALA(chain 'C' and (resid 2 through 3 or resid 6...CC120 - 121120 - 121
3104CYSCYSCYSCYS(chain 'C' and (resid 2 through 3 or resid 6...CC125125
3105VALVALASNASN(chain 'C' and (resid 2 through 3 or resid 6...CC127 - 132127 - 132
3106ALAALAILEILE(chain 'C' and (resid 2 through 3 or resid 6...CC134 - 140134 - 140
3107GLUGLUPROPRO(chain 'C' and (resid 2 through 3 or resid 6...CC143 - 146143 - 146
3108ILEILEPROPRO(chain 'C' and (resid 2 through 3 or resid 6...CC148 - 149148 - 149
3109ASNASNGLNGLN(chain 'C' and (resid 2 through 3 or resid 6...CC152 - 167152 - 167
3110GLUGLUSERSER(chain 'C' and (resid 2 through 3 or resid 6...CC170 - 189170 - 189
3111SERSERASNASN(chain 'C' and (resid 2 through 3 or resid 6...CC191 - 197191 - 197
3112ALAALALYSLYS(chain 'C' and (resid 2 through 3 or resid 6...CC199 - 208199 - 208
3113VALVALASPASP(chain 'C' and (resid 2 through 3 or resid 6...CC210 - 221210 - 221
3114PHEPHEILEILE(chain 'C' and (resid 2 through 3 or resid 6...CC224 - 225224 - 225
3115THRTHRILEILE(chain 'C' and (resid 2 through 3 or resid 6...CC227 - 235227 - 235
3116LYSLYSARGARG(chain 'C' and (resid 2 through 3 or resid 6...CC237 - 239237 - 239
3117SERSERALAALA(chain 'C' and (resid 2 through 3 or resid 6...CC246 - 247246 - 247
3118ALAALAILEILE(chain 'C' and (resid 2 through 3 or resid 6...CC251 - 255251 - 255
3119ASPASPTYRTYR(chain 'C' and (resid 2 through 3 or resid 6...CC257 - 273257 - 273
3120ASPASPPROPRO(chain 'C' and (resid 2 through 3 or resid 6...CC275 - 281275 - 281
3121GLYGLYASNASN(chain 'C' and (resid 2 through 3 or resid 6...CC283 - 294283 - 294
3122TRPTRPTRPTRP(chain 'C' and (resid 2 through 3 or resid 6...CC297297
3123ILEILEASPASP(chain 'C' and (resid 2 through 3 or resid 6...CC299 - 306299 - 306
3124VALVALARGARG(chain 'C' and (resid 2 through 3 or resid 6...CC308 - 310308 - 310
3125LYSLYSTHRTHR(chain 'C' and (resid 2 through 3 or resid 6...CC312 - 316312 - 316
3126GLUGLULEULEU(chain 'C' and (resid 2 through 3 or resid 6...CC319 - 320319 - 320
3127GLUGLULYSLYS(chain 'C' and (resid 2 through 3 or resid 6...CC323 - 324323 - 324
3128LEULEULEULEU(chain 'C' and (resid 2 through 3 or resid 6...CC326326
3129SERSERSERSER(chain 'C' and (resid 2 through 3 or resid 6...CC332332

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Components

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Malate dehydrogenase 1, ... , 3 types, 3 molecules ABC

#1: Protein Malate dehydrogenase 1, cytoplasmic / Cytosolic NAD-dependent malate dehydrogenase 1 / cNAD-MDH1 / Cytosolic malate dehydrogenase 1 / Cytosolic MDH1


Mass: 35610.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residue 56 oxidized to methionine sulfoxide / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Cell: cytoplasmic / Gene: MDH1, At1g04410, F19P19.13 / Plasmid: pDEST17 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P93819, malate dehydrogenase
#2: Protein Malate dehydrogenase 1, cytoplasmic / Cytosolic NAD-dependent malate dehydrogenase 1 / cNAD-MDH1 / Cytosolic malate dehydrogenase 1 / Cytosolic MDH1


Mass: 35674.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MDH1, At1g04410, F19P19.13 / Plasmid: pDEST17 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P93819, malate dehydrogenase
#3: Protein Malate dehydrogenase 1, cytoplasmic / Cytosolic NAD-dependent malate dehydrogenase 1 / cNAD-MDH1 / Cytosolic malate dehydrogenase 1 / Cytosolic MDH1


Mass: 35642.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MDH1, At1g04410, F19P19.13 / Plasmid: pDEST17 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P93819, malate dehydrogenase

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Non-polymers , 10 types, 1040 molecules

#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: H2O2
#8: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#9: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#10: Chemical ChemComp-ETX / 2-ETHOXYETHANOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#11: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#12: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 999 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.66 Å3/Da / Density % sol: 53.87 % / Description: 100 um x 200 um
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.5 M ammonium sulfate, 0.1 M Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen cryostream
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980105 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980105 Å / Relative weight: 1
ReflectionResolution: 1.35→92.561 Å / Num. obs: 236503 / % possible obs: 99.96 % / Redundancy: 13.6 % / Biso Wilson estimate: 14.47098422 Å2 / CC1/2: 0.973 / Rrim(I) all: 0.1092 / Net I/σ(I): 5.56
Reflection shellResolution: 1.35→1.398 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 0.63 / CC1/2: 0.369 / Rpim(I) all: 0.798 / Rrim(I) all: 2.934 / % possible all: 99.98

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35000279615→92.5612886735 Å / SU ML: 0.163547634761 / Cross valid method: FREE R-VALUE / σ(F): 1.32522207677 / Phase error: 19.3646044324
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.179506294341 12401 4.98260247664 %
Rwork0.146297730068 236485 -
obs0.147967919778 248886 99.9213110542 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.3464790462 Å2
Refinement stepCycle: LAST / Resolution: 1.35000279615→92.5612886735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7454 0 283 999 8736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01378131529378471
X-RAY DIFFRACTIONf_angle_d1.4132965480611621
X-RAY DIFFRACTIONf_chiral_restr0.1024878580111341
X-RAY DIFFRACTIONf_plane_restr0.008548986203171483
X-RAY DIFFRACTIONf_dihedral_angle_d15.69489762423326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.36530.3534770925484150.3291972311787742X-RAY DIFFRACTION99.6335654086
1.3653-1.38140.339133700014080.3111337641647777X-RAY DIFFRACTION99.7805680848
1.3814-1.39830.3417938762344120.3046699052527811X-RAY DIFFRACTION99.85428051
1.3983-1.4160.325571749513890.2852612478167826X-RAY DIFFRACTION99.8905642023
1.416-1.43460.3050356264344150.2626751673757872X-RAY DIFFRACTION99.8794745089
1.4346-1.45420.2784718902753900.2602562091797800X-RAY DIFFRACTION99.9633833761
1.4542-1.4750.2851640907243810.2482736482397857X-RAY DIFFRACTION99.9757281553
1.475-1.4970.2758027369814330.2363601775527818X-RAY DIFFRACTION99.9515445185
1.497-1.52040.2515531752233900.2165036185477801X-RAY DIFFRACTION99.9755889174
1.5204-1.54540.2648958041624350.2046022239747852X-RAY DIFFRACTION99.951754915
1.5454-1.5720.2484226737174160.1859796234917813X-RAY DIFFRACTION99.9757016158
1.572-1.60060.2161076683233970.1734826857787819X-RAY DIFFRACTION99.9878301083
1.6006-1.63140.200034286044110.1577038243947841X-RAY DIFFRACTION99.9515503876
1.6314-1.66470.1973767772144290.1462218940467876X-RAY DIFFRACTION99.9879605105
1.6647-1.70090.1747291159474150.1348923662117851X-RAY DIFFRACTION100
1.7009-1.74050.1796108941563810.1360017267827868X-RAY DIFFRACTION100
1.7405-1.7840.1779721533774170.1323359713697814X-RAY DIFFRACTION99.9878522838
1.784-1.83220.1713084797434230.1227106829357876X-RAY DIFFRACTION99.9518246417
1.8322-1.88620.1694879965764290.1265625392667852X-RAY DIFFRACTION99.9879256218
1.8862-1.9470.1717449970824110.1198035490517901X-RAY DIFFRACTION99.9639206254
1.947-2.01660.1719795709834260.1166444075377866X-RAY DIFFRACTION99.9397372544
2.0166-2.09740.1565889588913510.1169523567557918X-RAY DIFFRACTION99.9516499456
2.0974-2.19280.1659888234334200.1177319754427893X-RAY DIFFRACTION99.8798510153
2.1928-2.30850.1524234808864290.1170493241047913X-RAY DIFFRACTION99.8205097523
2.3085-2.45310.1567714613664290.1244260278647891X-RAY DIFFRACTION99.8559769563
2.4531-2.64250.1708446256533910.1292599695317965X-RAY DIFFRACTION99.8446648345
2.6425-2.90850.1622258972684330.1372893544597953X-RAY DIFFRACTION99.9046938289
2.9085-3.32930.1564872556534520.1399840800287957X-RAY DIFFRACTION99.9049542592
3.3293-4.19460.1413581099994460.1236298504628074X-RAY DIFFRACTION99.9882642882
4.1946-92.77960.1657369744234270.1445080789138388X-RAY DIFFRACTION99.9206529132

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