[English] 日本語
Yorodumi
- PDB-6yei: Arabidopsis thaliana glutamate dehydrogenase isoform 1 in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yei
TitleArabidopsis thaliana glutamate dehydrogenase isoform 1 in complex with NAD
ComponentsGlutamate dehydrogenase 1
KeywordsOXIDOREDUCTASE / glutamate dehydrogenase / 2-oxoglutarate / NAD / amino acid metabolism
Function / homology
Function and homology information


response to absence of light / glutamate dehydrogenase [NAD(P)+] activity / glutamate catabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / : / cobalt ion binding / plastid / copper ion binding ...response to absence of light / glutamate dehydrogenase [NAD(P)+] activity / glutamate catabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / : / cobalt ion binding / plastid / copper ion binding / mitochondrion / zinc ion binding / ATP binding
Similarity search - Function
Glutamate dehydrogenase / Leucine Dehydrogenase, chain A, domain 1 / NAD(P) binding domain of glutamate dehydrogenase / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal ...Glutamate dehydrogenase / Leucine Dehydrogenase, chain A, domain 1 / NAD(P) binding domain of glutamate dehydrogenase / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glutamate dehydrogenase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsRuszkowski, M. / Grzechowiak, M. / Jaskolski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreSONATA 2018/31/D/NZ1/03630 Poland
CitationJournal: Front Plant Sci / Year: 2020
Title: Structural Studies of Glutamate Dehydrogenase (Isoform 1) FromArabidopsis thaliana, an Important Enzyme at the Branch-Point Between Carbon and Nitrogen Metabolism.
Authors: Grzechowiak, M. / Sliwiak, J. / Jaskolski, M. / Ruszkowski, M.
History
DepositionMar 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: 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
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.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.value / _struct_conn.pdbx_dist_value / _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.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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamate dehydrogenase 1
B: Glutamate dehydrogenase 1
C: Glutamate dehydrogenase 1
D: Glutamate dehydrogenase 1
E: Glutamate dehydrogenase 1
F: Glutamate dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,97441
Polymers269,1256
Non-polymers6,84935
Water13,637757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32810 Å2
ΔGint-257 kcal/mol
Surface area84490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.843, 99.811, 317.948
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

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
11ALAALAPHEPHE(chain 'A' and (resid 6 through 32 or resid 34...AA6 - 329 - 35
12GLUGLUTHRTHR(chain 'A' and (resid 6 through 32 or resid 34...AA34 - 12537 - 128
13LYSLYSLEULEU(chain 'A' and (resid 6 through 32 or resid 34...AA127 - 179130 - 182
14ASPASPASNASN(chain 'A' and (resid 6 through 32 or resid 34...AA182 - 312185 - 315
15PROPROTRPTRP(chain 'A' and (resid 6 through 32 or resid 34...AA314 - 409317 - 412
26ALAALAPHEPHE(chain 'B' and (resid 6 through 32 or resid 34...BB6 - 329 - 35
27GLUGLUTHRTHR(chain 'B' and (resid 6 through 32 or resid 34...BB34 - 12537 - 128
28LYSLYSLEULEU(chain 'B' and (resid 6 through 32 or resid 34...BB127 - 179130 - 182
29ASPASPASNASN(chain 'B' and (resid 6 through 32 or resid 34...BB182 - 312185 - 315
210PROPROTRPTRP(chain 'B' and (resid 6 through 32 or resid 34...BB314 - 409317 - 412
311ALAALAPHEPHE(chain 'C' and (resid 6 through 32 or resid 34...CC6 - 329 - 35
312GLUGLUTHRTHR(chain 'C' and (resid 6 through 32 or resid 34...CC34 - 12537 - 128
313LYSLYSLEULEU(chain 'C' and (resid 6 through 32 or resid 34...CC127 - 179130 - 182
314ASPASPASNASN(chain 'C' and (resid 6 through 32 or resid 34...CC182 - 312185 - 315
315PROPROTRPTRP(chain 'C' and (resid 6 through 32 or resid 34...CC314 - 409317 - 412
416ALAALAPHEPHE(chain 'D' and (resid 6 through 32 or resid 34...DD6 - 329 - 35
417GLUGLUTHRTHR(chain 'D' and (resid 6 through 32 or resid 34...DD34 - 12537 - 128
418LYSLYSLEULEU(chain 'D' and (resid 6 through 32 or resid 34...DD127 - 179130 - 182
419ASPASPASNASN(chain 'D' and (resid 6 through 32 or resid 34...DD182 - 312185 - 315
420PROPROTRPTRP(chain 'D' and (resid 6 through 32 or resid 34...DD314 - 409317 - 412
521ALAALAPHEPHE(chain 'E' and (resid 6 through 32 or resid 34...EE6 - 329 - 35
522GLUGLUTHRTHR(chain 'E' and (resid 6 through 32 or resid 34...EE34 - 12537 - 128
523LYSLYSLEULEU(chain 'E' and (resid 6 through 32 or resid 34...EE127 - 179130 - 182
524ASPASPASNASN(chain 'E' and (resid 6 through 32 or resid 34...EE182 - 312185 - 315
525PROPROTRPTRP(chain 'E' and (resid 6 through 32 or resid 34...EE314 - 409317 - 412
626ALAALAPHEPHE(chain 'F' and (resid 6 through 32 or resid 34...FF6 - 329 - 35
627GLUGLUTHRTHR(chain 'F' and (resid 6 through 32 or resid 34...FF34 - 12537 - 128
628LYSLYSLEULEU(chain 'F' and (resid 6 through 32 or resid 34...FF127 - 179130 - 182
629ASPASPASNASN(chain 'F' and (resid 6 through 32 or resid 34...FF182 - 312185 - 315
630PROPROTRPTRP(chain 'F' and (resid 6 through 32 or resid 34...FF314 - 409317 - 412

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Glutamate dehydrogenase 1 / / GDH 1


Mass: 44854.219 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GDH1, At5g18170, MRG7.13 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3)
References: UniProt: Q43314, glutamate dehydrogenase [NAD(P)+]

-
Non-polymers , 7 types, 792 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 757 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.89 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 15% w/v PEG 6000, 100 mM MES pH 6.5, 10% (v/v) MPD

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.02→70.3 Å / Num. obs: 164077 / % possible obs: 95.7 % / Redundancy: 7.4 % / Biso Wilson estimate: 35.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.028 / Net I/σ(I): 17.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) all% possible all
2.02-2.147.30.8042.581940.7810.44964.8
5.94-70.36.90.02748.882040.9990.01599.8

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1b26

1b26


Resolution: 2.02→70.26 Å / SU ML: 0.1996 / Cross valid method: FREE R-VALUE / Phase error: 22.4684
Details: Hydrogen atoms at riding positions were added during refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1646 1 %random
Rwork0.1604 ---
obs0.1607 164061 83.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 53.86 Å2
Refinement stepCycle: LAST / Resolution: 2.02→70.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18639 0 448 757 19844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007919509
X-RAY DIFFRACTIONf_angle_d0.952726442
X-RAY DIFFRACTIONf_chiral_restr0.05842953
X-RAY DIFFRACTIONf_plane_restr0.00673390
X-RAY DIFFRACTIONf_dihedral_angle_d15.219411691
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.46394366292-0.2459794094120.7306174803870.761182149536-0.4073450892572.54760786573-0.0214605204829-0.04672959186250.2514135868950.0986582947659-0.03096770076550.0791926676828-0.256635579003-0.162209375810.08387032949020.2054602624070.031993711994-0.0009256201946180.212740312382-0.07845476725650.28022417867613.887365071316.9433237204135.565780885
21.89410477502-0.873120400845-1.087397736241.493715496620.915699836361.46069168482-0.0475425353982-0.2305476212980.007582369994620.272127276372-0.05189085582210.1559897557440.0505937315851-0.1003769521790.1087274702240.281537843053-0.03119852368310.02674659769690.242311996897-0.05453734886140.2205055252263.3347779058811.2655541568155.296617936
32.884755842340.0768924943572-1.157488522516.42261911079-3.17803959084.551206686340.1031776309330.1124680162070.8204868080580.3689730415340.2129756235710.247197978619-1.06935494546-0.448962906772-0.272377947980.4791071726750.1340555137930.02792814349830.2837687499780.008205780917990.45425284152216.962523077837.3300372795115.297567585
42.57144404247-0.4260775846161.516818225471.67314360826-0.7983801667734.59778250849-0.081119116673-0.2375807540280.1981543770070.123450926830.0751500429501-0.0581402581752-0.4662659327560.164260565410.04252008598070.2252965850690.01649108369850.01047798512140.240975086691-0.08838536933040.28301559640132.494208088721.817484745128.272300526
52.47413483023-1.024049076130.8285207193571.73440197717-0.7208267127612.97804005486-0.0131121257962-0.1071222584590.2124695914330.04408593302940.0397557524947-0.158975689876-0.139568661160.144193946981-0.02093090196760.172908066588-0.009202576180020.01243191735090.172386550069-0.06956775626430.25647560402235.581671314820.024635749122.314782807
61.46091283121.04133152079-0.8541137616637.17289373478-2.989547127262.50543166918-0.02240105184990.09276843894030.0372720282234-0.2404862335150.0733013698279-0.488117857911-0.1521159043120.1117877018440.01485590613120.298332558024-0.00849335980440.03488370655580.280889293785-0.09509781289790.28796206090242.39162018626.6805965796105.724331255
73.025351422650.7641917800280.3657150039793.87642146234-0.06718203434192.89955603572-0.02375594217130.1436351755520.591076950822-0.07845644842570.327489638348-1.05763436555-0.6614429321510.860042033896-0.2861421082530.498066562765-0.140868488340.1225668758270.492990602097-0.1987435267890.79191108538252.69484121143.5764198806105.05205791
84.81498213667-0.3143562292220.6442176539182.341988663520.6696507495292.57810965353-0.100816036226-0.2666440464620.618978300640.2655067958870.289257973192-1.08205243455-0.8112460280591.0930075347-0.1692518079850.614094065443-0.205688045750.01598704804140.736058298749-0.2919588225961.0210407931256.948322768745.5484597822111.756949017
92.28289796384-1.075979125280.4335576021863.000377886331.670014746051.48755573115-0.139965715831-0.4707581304691.24763915070.356685067510.0513606798276-0.204975696723-1.267256654510.2804455054920.03743010513310.897878565016-0.09667125057240.1067746292830.353118933439-0.1594573974190.76081341393540.592171666552.2292762406112.416479442
101.65188889984-0.1935641986610.4077701786517.085524022940.7452704362481.446735279760.0306964247942-0.1427388511080.425124789337-0.005586222298360.01289879203750.065753270927-0.4902214149150.0198579396375-0.05922764392340.3489690159370.009931385349230.09254090637610.235623237095-0.04809154794070.32402406256436.551418433134.4358803672107.637575292
114.3402612222-4.39801343482-1.086573374514.727341735941.0572935712.952382832230.5502002996580.5731865400080.29677064481-1.20677367467-0.2641332862320.110413889859-0.351610670711-0.175175700893-0.2234463534920.446506091179-0.04095265216330.02336241904240.2935785576070.01676579492750.41690745678133.495881410132.804913818597.6689076369
123.443588723562.18691349106-0.7166011895536.151034670840.3982545101392.358448340420.07282874410240.09552331535620.736726804674-0.317594318037-0.00698210003690.556639016941-0.477065282867-0.163625667182-0.1118240338490.3402899409740.126921484158-0.02539072320670.2446009940380.01799411291490.32250848139119.411371135733.7103224711107.098209978
131.570378647970.945895497357-0.1423829006251.794402197750.4157705887842.23742592728-0.0604133636225-0.0375480728533-0.2968343825270.1458950765950.0947092662587-0.2480579208760.5314999792070.295443401146-0.06363340748840.313648798440.117404703811-0.04166361495860.221428728688-0.04033804273250.29937220884337.3980770065-15.5013121866131.503486659
141.691363196750.2826142993260.04335659134783.245617925640.3987976690342.41604978052-0.0124797332833-0.46194661-0.6316897731531.027104611660.0777769404956-0.9038485573620.9524850253190.289599996389-0.01151354659110.8292041828780.140424165487-0.1743768961720.3653026612870.08430116006780.64388171866530.4396480954-28.5260719598149.435370443
155.243480512790.283248521998-2.404116800952.17031243767-1.364162673811.797646681080.240149251175-0.222709610639-0.7461373773610.374228562602-0.161449874079-0.9333601753080.4154771801061.045921234680.09597106479120.2183966759590.143523921365-0.06437868716530.639878722306-0.114889170880.57843880104160.1562685391-3.49696958829118.464112514
160.8395605241490.250656672465-0.3859079829931.678156183690.2870379749651.387452432940.009330384199810.0749291366355-0.16111675951-0.08959651597040.0117943684358-0.1185651777060.2284841228270.117312145684-0.0006977013576070.2405914034810.0794642677351-0.02622742835890.241129722346-0.08547990870660.30028980877341.2146138399-11.4288402703104.482697911
172.66370326496-0.115744446962-0.4397544838663.008526496481.328125147823.86492348453-0.01678410196970.124859394525-0.262230597724-0.2321344193440.628794676362-1.040324237620.8998917345081.17106888976-0.2916071522620.5763524403620.1670090008440.1389100465220.645111068134-0.2961688340080.70684752070564.4020742221-10.838778509486.6716649739
182.95616051557-0.2251160400320.1265925836731.144369656160.3838662304043.402478478710.01021275551210.1618687814250.0840796826122-0.1582962886990.154707016856-0.359736804345-0.2542705768690.553823588713-0.1315873887870.2113283115780.01597523489620.03921793424570.235205123411-0.08127530443340.32377576679651.99264034285.0963296298102.449691555
191.08525790709-0.873530127622-0.8414609730141.930301240940.4733875513241.808435207680.04198229628240.163683837395-0.150824463679-0.225213695978-0.0386582212430.2647860292750.216760315088-0.374127254333-0.01541166118390.268138728637-0.0965226628684-0.04349359589410.404833674118-0.1156100928550.3036548527752.59202932608-13.6530184097111.771649046
202.21233092359-1.630744964380.9678669603793.39190791464-1.799088122173.538898347920.278717476228-0.189222381876-1.14023177445-0.4545573859590.4476993496951.54296349881.28866358594-1.24040713297-0.07800482503960.667719881802-0.511941059575-0.2151881159750.728408894290.03232860237831.02701132679-12.1395912321-24.196416872127.441050635
211.129438079060.292805100318-0.2599357821091.346074888920.4428535765611.49014987331-0.01604535095740.2153302912110.0498003071574-0.242745480729-0.03990897243850.227031626009-0.0379482437096-0.3682265686110.05746135743930.2218136216280.047528586768-0.07398441351660.382804418761-0.01157236504570.2357549156589.195533838624.3963363220697.5809491672
222.92225852016-0.9725890499260.1904190906271.867059006840.2672699673392.46232763771-0.09630291013620.546110359050.31382734257-0.5072784522590.0457064175045-0.0317340976157-0.354916652122-0.2630723757920.04723194794490.603081020525-0.0525396249828-0.1302224377520.5943972680040.1268287696630.3676694386629.5755469096118.647210415174.2283036509
235.87684965245-1.15671639375-0.2360999106667.548267368950.9951352666180.152837893675-0.2152532127830.2673884051640.463712313297-0.2552411218020.1493990352570.548226722309-0.326544509279-0.3426633709060.0709107885740.603196885370.111466595016-0.1607185774580.6205634331680.187569612990.391763516084-0.69796858961922.715811167677.6140380709
241.61687449798-0.03031164821571.533055719051.14034704484-0.1017872868242.44809364969-0.08134196331490.474277765698-0.120520465127-0.6222995417240.1791175282160.213081607736-0.0112984147257-0.0935070260459-0.09135723321270.407712862252-0.0398681348457-0.04171123174470.503606847749-0.01797946410920.2806685135415.84912122713.3427144263680.4810149155
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 161 )
2X-RAY DIFFRACTION2chain 'A' and (resid 162 through 410 )
3X-RAY DIFFRACTION3chain 'B' and (resid 6 through 32 )
4X-RAY DIFFRACTION4chain 'B' and (resid 33 through 76 )
5X-RAY DIFFRACTION5chain 'B' and (resid 77 through 161 )
6X-RAY DIFFRACTION6chain 'B' and (resid 162 through 200 )
7X-RAY DIFFRACTION7chain 'B' and (resid 201 through 249 )
8X-RAY DIFFRACTION8chain 'B' and (resid 250 through 287 )
9X-RAY DIFFRACTION9chain 'B' and (resid 288 through 308 )
10X-RAY DIFFRACTION10chain 'B' and (resid 309 through 358 )
11X-RAY DIFFRACTION11chain 'B' and (resid 359 through 384 )
12X-RAY DIFFRACTION12chain 'B' and (resid 385 through 411 )
13X-RAY DIFFRACTION13chain 'C' and (resid 4 through 161 )
14X-RAY DIFFRACTION14chain 'C' and (resid 162 through 410 )
15X-RAY DIFFRACTION15chain 'D' and (resid 5 through 32 )
16X-RAY DIFFRACTION16chain 'D' and (resid 33 through 200 )
17X-RAY DIFFRACTION17chain 'D' and (resid 201 through 338 )
18X-RAY DIFFRACTION18chain 'D' and (resid 339 through 411 )
19X-RAY DIFFRACTION19chain 'E' and (resid 5 through 161 )
20X-RAY DIFFRACTION20chain 'E' and (resid 162 through 410 )
21X-RAY DIFFRACTION21chain 'F' and (resid 1 through 183 )
22X-RAY DIFFRACTION22chain 'F' and (resid 184 through 249 )
23X-RAY DIFFRACTION23chain 'F' and (resid 250 through 287 )
24X-RAY DIFFRACTION24chain 'F' and (resid 288 through 410 )

+
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