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- PDB-2v5h: Controlling the storage of nitrogen as arginine: the complex of P... -

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Basic information

Entry
Database: PDB / ID: 2v5h
TitleControlling the storage of nitrogen as arginine: the complex of PII and acetylglutamate kinase from Synechococcus elongatus PCC 7942
Components
  • ACETYLGLUTAMATE KINASE
  • NITROGEN REGULATORY PROTEIN P-II
KeywordsTRANSCRIPTION / AMINO-ACID BIOSYNTHESIS / TRANSCRIPTION REGULATION / TRANSFERASE / CYANOBACTERIA / N-ACETYL-L-GLUTAMATE KINASE / PII SIGNAL PROTEIN / NUCLEOTIDE-BINDING / ACETYLGLUTAMATE / PHOSPHORYLATION / AMINO ACID KINASE / GLNB / KINASE / TRIMER / HEXAMER / ATP-BINDING / ARGININE INHIBITION / ARGININE BIOSYNTHESIS
Function / homology
Function and homology information


acetylglutamate kinase / acetylglutamate kinase activity / arginine biosynthetic process via ornithine / regulation of nitrogen utilization / enzyme regulator activity / phosphorylation / nucleotide binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
N-Acetyl-L-glutamate kinase, cyclic / Acetylglutamate kinase ArgB / Nitrogen regulatory protein P-II, urydylation site / P-II protein uridylation site. / Acetylglutamate kinase family / Glutamate/acetylglutamate kinase / Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / Nitrogen regulatory protein P-II ...N-Acetyl-L-glutamate kinase, cyclic / Acetylglutamate kinase ArgB / Nitrogen regulatory protein P-II, urydylation site / P-II protein uridylation site. / Acetylglutamate kinase family / Glutamate/acetylglutamate kinase / Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / Nitrogen regulatory protein P-II / Nitrogen regulatory protein PII / P-II protein family profile. / Carbamate kinase / Acetylglutamate kinase-like / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-ACETYL-L-GLUTAMATE / Nitrogen regulatory protein P-II / Acetylglutamate kinase
Similarity search - Component
Biological speciesSYNECHOCOCCUS ELONGATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsLlacer, J.L. / Marco-Marin, C. / Gil-Ortiz, F. / Fita, I. / Rubio, V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: The Crystal Structure of the Complex of Pii and Acetylglutamate Kinase Reveals How Pii Controls the Storage of Nitrogen as Arginine.
Authors: Llacer, J.L. / Contreras, A. / Forchhammer, K. / Marco-Marin, C. / Gil-Ortiz, F. / Maldonado, R. / Fita, I. / Rubio, V.
History
DepositionJul 4, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 10, 2014Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description
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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACETYLGLUTAMATE KINASE
B: ACETYLGLUTAMATE KINASE
C: ACETYLGLUTAMATE KINASE
D: ACETYLGLUTAMATE KINASE
E: ACETYLGLUTAMATE KINASE
F: ACETYLGLUTAMATE KINASE
G: NITROGEN REGULATORY PROTEIN P-II
H: NITROGEN REGULATORY PROTEIN P-II
I: NITROGEN REGULATORY PROTEIN P-II
J: NITROGEN REGULATORY PROTEIN P-II
K: NITROGEN REGULATORY PROTEIN P-II
L: NITROGEN REGULATORY PROTEIN P-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,98831
Polymers281,41012
Non-polymers1,57819
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42610 Å2
ΔGint-292.5 kcal/mol
Surface area83790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.379, 161.027, 91.562
Angle α, β, γ (deg.)90.00, 106.53, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11I
21J
31K
41L
12A
22B
32E
42F
13F
23E
33C
43D
14A
24F
15G
25H
35I
45J
55K
65L
16B
26C
36D
46E
17A
27B
37C
47D
57E
67F
18A
28B
38C
48D
58F
19B
29C
39D
49E
59F
110A
210B
310C
410E
510F
111A
211C
311D
411E
511F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114I108 - 112
2114J108 - 112
3114K108 - 112
4114L108 - 112
1121A45
2121B45
3121E45
4121F45
1134F289 - 301
2134E289 - 301
3134C289 - 301
4134D289 - 301
1141A144
2141F144
1151G48 - 100
2151H48 - 100
3151I48 - 100
4151J48 - 100
5151K48 - 100
6151L48 - 100
1251G1 - 36
2251H1 - 36
3251I1 - 36
4251J1 - 36
5251K1 - 36
6251L1 - 36
1351G102 - 107
2351H102 - 107
3351I102 - 107
4351J102 - 107
5351K102 - 107
6351L102 - 107
1454G43 - 47
2454H43 - 47
3454I43 - 47
4454J43 - 47
5454K43 - 47
6454L43 - 47
1556G37 - 42
2556H37 - 42
3556I37 - 42
4556J37 - 42
5556K37 - 42
6556L37 - 42
1653G101
2653H101
3653I101
4653J101
5653K101
6653L101
1164B144
2164C144
3164D144
4164E144
1171A16 - 44
2171B16 - 44
3171C16 - 44
4171D16 - 44
5171E16 - 44
6171F16 - 44
1271A46 - 72
2271B46 - 72
3271C46 - 72
4271D46 - 72
5271E46 - 72
6271F46 - 72
1371A74 - 83
2371B74 - 83
3371C74 - 83
4371D74 - 83
5371E74 - 83
6371F74 - 83
1473A84
2473B84
3473C84
4473D84
5473E84
6473F84
1571A85 - 87
2571B85 - 87
3571C85 - 87
4571D85 - 87
5571E85 - 87
6571F85 - 87
1674A89
2674B89
3674C89
4674D89
5674E89
6674F89
1771A90
2771B90
3771C90
4771D90
5771E90
6771F90
1872A91
2872B91
3872C91
4872D91
5872E91
6872F91
1971A92 - 93
2971B92 - 93
3971C92 - 93
4971D92 - 93
5971E92 - 93
6971F92 - 93
11071A95 - 98
21071B95 - 98
31071C95 - 98
41071D95 - 98
51071E95 - 98
61071F95 - 98
11171A100 - 143
21171B100 - 143
31171C100 - 143
41171D100 - 143
51171E100 - 143
61171F100 - 143
11271A145 - 150
21271B145 - 150
31271C145 - 150
41271D145 - 150
51271E145 - 150
61271F145 - 150
11371A152 - 160
21371B152 - 160
31371C152 - 160
41371D152 - 160
51371E152 - 160
61371F152 - 160
11471A162 - 164
21471B162 - 164
31471C162 - 164
41471D162 - 164
51471E162 - 164
61471F162 - 164
11572A165 - 166
21572B165 - 166
31572C165 - 166
41572D165 - 166
51572E165 - 166
61572F165 - 166
11671A167 - 178
21671B167 - 178
31671C167 - 178
41671D167 - 178
51671E167 - 178
61671F167 - 178
11772A179
21772B179
31772C179
41772D179
51772E179
61772F179
11871A180 - 207
21871B180 - 207
31871C180 - 207
41871D180 - 207
51871E180 - 207
61871F180 - 207
11971A209 - 210
21971B209 - 210
31971C209 - 210
41971D209 - 210
51971E209 - 210
61971F209 - 210
12073A211
22073B211
32073C211
42073D211
52073E211
62073F211
12171A212 - 214
22171B212 - 214
32171C212 - 214
42171D212 - 214
52171E212 - 214
62171F212 - 214
12274A215 - 223
22274B215 - 223
32274C215 - 223
42274D215 - 223
52274E215 - 223
62274F215 - 223
12371A224 - 233
22371B224 - 233
32371C224 - 233
42371D224 - 233
52371E224 - 233
62371F224 - 233
12473A234
22473B234
32473C234
42473D234
52473E234
62473F234
12571A235 - 253
22571B235 - 253
32571C235 - 253
42571D235 - 253
52571E235 - 253
62571F235 - 253
12671A262 - 289
22671B262 - 289
32671C262 - 289
42671D262 - 289
52671E262 - 289
62671F262 - 289
12773A73
22773B73
32773C73
42773D73
52773E73
62773F73
12872A254
22872B254
32872C254
42872D254
52872E254
62872F254
12971A255 - 260
22971B255 - 260
32971C255 - 260
42971D255 - 260
52971E255 - 260
62971F255 - 260
13076A10 - 13
23076B10 - 13
33076C10 - 13
43076D10 - 13
53076E10 - 13
63076F10 - 13
1181A208
2181B208
3181C208
4181D208
5181F208
1192B88
2192C88
3192D88
4192E88
5192F88
1291B99
2291C99
3291D99
4291E99
5291F99
1391B261
2391C261
3391D261
4391E261
5391F261
1491B151
2491C151
3491D151
4491E151
5491F151
11101A94
21101B94
31101C94
41101E94
51101F94
11111A161
21111C161
31111D161
41111E161
51111F161

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11

NCS oper:
IDCodeMatrixVector
1given(-0.399, 0.379, 0.835), (0.405, -0.744, 0.531), (0.823, 0.55, 0.143)0.45982, -21.56274, 9.85157
2given(-0.804, -0.506, -0.311), (-0.496, 0.283, 0.821), (-0.327, 0.815, -0.479)38.84369, -14.56789, 46.34348
3given(0.479, -0.766, 0.429), (-0.769, -0.601, -0.216), (0.423, -0.226, -0.877)-3.14198, 18.71328, 44.80878
4given(-0.131, 0.99, 0.045), (-0.11, 0.031, -0.993), (-0.985, -0.135, 0.105)17.94614, 29.15375, 41.2959
5given(-0.126, -0.117, -0.985), (0.99, 0.046, -0.132), (0.061, -0.992, 0.11)46.23878, -13.10571, 23.56084
6given(0.47079, -0.76529, 0.43897), (-0.76721, -0.60079, -0.22459), (0.43561, -0.23104, -0.86998)-3.66628, 19.25593, 44.10998

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Components

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Protein , 2 types, 12 molecules ABCDEFGHIJKL

#1: Protein
ACETYLGLUTAMATE KINASE / / NAG KINASE / AGK / N-ACETYL-L-GLUTAMATE 5-PHOSPHOTRANSFERASE


Mass: 34492.391 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (bacteria) / Strain: PCC 7942 / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q6V1L5, acetylglutamate kinase
#2: Protein
NITROGEN REGULATORY PROTEIN P-II / PII PROTEIN / PII SIGNAL TRANSDUCING PROTEIN


Mass: 12409.347 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (bacteria) / Strain: PCC 7942 / Plasmid: PET-22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P0A3F4

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Non-polymers , 5 types, 206 molecules

#3: Chemical
ChemComp-NLG / N-ACETYL-L-GLUTAMATE / N-Acetylglutamic acid


Mass: 189.166 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H11NO5
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCATALYTIC ACTIVITY: ATP + N-ACETYL-L-GLUTAMATE = ADP + N-ACETYL-L- GLUTAMATE 5-PHOSPHATE P-II ...CATALYTIC ACTIVITY: ATP + N-ACETYL-L-GLUTAMATE = ADP + N-ACETYL-L- GLUTAMATE 5-PHOSPHATE P-II INDIRECTLY CONTROLS THE TRANSCRIPTION OF THE GS GENE (GLNA)
Sequence detailsN-TERMINALLY HIS-TAGGED (N-TERMINAL EXTRA SEQUENCE MGSSHHHHHHSSGLVPRGSH) CORRESPONDING TO A PET15B ...N-TERMINALLY HIS-TAGGED (N-TERMINAL EXTRA SEQUENCE MGSSHHHHHHSSGLVPRGSH) CORRESPONDING TO A PET15B N-TERMINAL EXTRA HIS-TAG

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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: 2.3 Å3/Da / Density % sol: 45.1 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1 M TRIS-HCL PH 8.5, 0.15 M SODIUM ACETATE, 20% (WT/VOL) POLYETHYLENE GLYCOL 4K, 20 MM ACETYLGLUTAMATE.

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID14-310.978
SYNCHROTRONESRF BM162
Detector
TypeIDDetectorDateDetails
ADSC CCD1CCDMar 21, 2006RD COATED FLAT MIRROR AND RD COATED TOROIDAL MIRROR
MARRESEARCH2CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI111SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.75→87.71 Å / Num. obs: 65178 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 61.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.9
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2 / % possible all: 100

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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 2JJ4
Resolution: 2.75→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.905 / SU B: 28.08 / SU ML: 0.263 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3297 5.1 %RANDOM
Rwork0.2 ---
obs0.202 61827 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: 38.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20.09 Å2
2---0.25 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17828 0 96 187 18111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02218204
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.97724614
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39652374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97223.864766
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.875153194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.31115168
X-RAY DIFFRACTIONr_chiral_restr0.0960.22898
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213594
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.28370
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.212505
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2675
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3890.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3941.511749
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.796218917
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.41936516
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5734.55697
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
21A9tight positional0.030.05
22B9tight positional0.030.05
23E9tight positional0.040.05
24F9tight positional0.030.05
41A9tight positional0.040.05
42F9tight positional0.040.05
51G724tight positional0.030.05
52H724tight positional0.030.05
53I724tight positional0.030.05
54J724tight positional0.040.05
55K724tight positional0.050.05
56L724tight positional0.040.05
71A1826tight positional0.040.05
72B1826tight positional0.040.05
73C1826tight positional0.030.05
74D1826tight positional0.030.05
75E1826tight positional0.040.05
76F1826tight positional0.030.05
81A7tight positional0.030.05
82B7tight positional0.020.05
83C7tight positional0.020.05
84D7tight positional0.030.05
85F7tight positional0.020.05
91B32tight positional0.040.05
92C32tight positional0.030.05
93D32tight positional0.030.05
94E32tight positional0.040.05
95F32tight positional0.020.05
101A7tight positional0.020.05
102B7tight positional0.020.05
103C7tight positional0.020.05
104E7tight positional0.010.05
105F7tight positional0.020.05
111A9tight positional0.150.05
112C9tight positional0.150.05
113D9tight positional0.140.05
114E9tight positional0.210.05
115F9tight positional0.210.05
11I8medium positional0.290.5
12J8medium positional0.290.5
13K8medium positional0.440.5
14L8medium positional0.260.5
31F17medium positional0.240.5
32E17medium positional0.290.5
33C17medium positional0.320.5
34D17medium positional0.450.5
51G50medium positional0.510.5
52H50medium positional0.290.5
53I50medium positional0.520.5
54J50medium positional0.530.5
55K50medium positional0.460.5
56L50medium positional0.410.5
61B9medium positional0.270.5
62C9medium positional0.610.5
63D9medium positional0.840.5
64E9medium positional0.280.5
71A87medium positional0.940.5
72B87medium positional0.820.5
73C87medium positional0.590.5
74D87medium positional0.630.5
75E87medium positional0.540.5
76F87medium positional0.580.5
91B6medium positional0.410.5
92C6medium positional0.440.5
93D6medium positional0.570.5
94E6medium positional0.210.5
95F6medium positional0.230.5
51G11loose positional0.85
52H11loose positional1.365
53I11loose positional0.745
54J11loose positional0.725
55K11loose positional0.765
56L11loose positional1.115
71A36loose positional1.565
72B36loose positional2.55
73C36loose positional1.115
74D36loose positional1.135
75E36loose positional1.285
76F36loose positional1.155
21A9tight thermal0.030.5
22B9tight thermal0.070.5
23E9tight thermal0.040.5
24F9tight thermal0.060.5
41A9tight thermal0.050.5
42F9tight thermal0.050.5
51G724tight thermal0.060.5
52H724tight thermal0.060.5
53I724tight thermal0.050.5
54J724tight thermal0.060.5
55K724tight thermal0.070.5
56L724tight thermal0.070.5
71A1826tight thermal0.080.5
72B1826tight thermal0.070.5
73C1826tight thermal0.070.5
74D1826tight thermal0.070.5
75E1826tight thermal0.070.5
76F1826tight thermal0.060.5
81A7tight thermal0.130.5
82B7tight thermal0.080.5
83C7tight thermal0.050.5
84D7tight thermal0.070.5
85F7tight thermal0.060.5
91B32tight thermal0.10.5
92C32tight thermal0.070.5
93D32tight thermal0.060.5
94E32tight thermal0.070.5
95F32tight thermal0.050.5
101A7tight thermal0.040.5
102B7tight thermal0.050.5
103C7tight thermal0.030.5
104E7tight thermal0.040.5
105F7tight thermal0.040.5
111A9tight thermal0.140.5
112C9tight thermal0.070.5
113D9tight thermal0.040.5
114E9tight thermal0.070.5
115F9tight thermal0.040.5
11I8medium thermal0.762
12J8medium thermal0.482
13K8medium thermal1.382
14L8medium thermal0.422
31F17medium thermal0.282
32E17medium thermal0.572
33C17medium thermal0.962
34D17medium thermal0.692
51G50medium thermal0.52
52H50medium thermal0.362
53I50medium thermal0.632
54J50medium thermal0.462
55K50medium thermal0.642
56L50medium thermal0.682
61B9medium thermal0.232
62C9medium thermal0.272
63D9medium thermal0.662
64E9medium thermal0.822
71A87medium thermal0.642
72B87medium thermal0.442
73C87medium thermal0.362
74D87medium thermal0.812
75E87medium thermal0.472
76F87medium thermal0.272
91B6medium thermal0.192
92C6medium thermal0.542
93D6medium thermal0.382
94E6medium thermal0.292
95F6medium thermal0.592
51G11loose thermal0.6810
52H11loose thermal1.5810
53I11loose thermal1.7710
54J11loose thermal1.310
55K11loose thermal110
56L11loose thermal2.0910
71A36loose thermal2.1810
72B36loose thermal1.8710
73C36loose thermal2.310
74D36loose thermal1.6210
75E36loose thermal1.0810
76F36loose thermal1.2810
LS refinement shellResolution: 2.75→2.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 224 -
Rwork0.323 4563 -
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)
11.7770.0796-0.17322.3412-0.80422.48850.1286-0.1530.13650.2655-0.1672-0.1267-0.2480.14040.0386-0.1164-0.0338-0.0462-0.2333-0.0172-0.157729.93727.12544.641
21.90650.2963-0.30772.66210.75792.0123-0.0028-0.2061-0.12860.1759-0.0872-0.1780.20270.16310.09-0.1266-0.0002-0.0518-0.18780.0723-0.175935.876-6.3555.922
32.38140.08260.44171.4672-0.08113.02770.03070.01830.15690.0784-0.10050.2298-0.1178-0.470.0699-0.19140.06930.00610.0087-0.0607-0.1065-12.81914.9937.36
43.0545-0.179-0.14921.7755-0.19791.5135-0.08470.2953-0.3826-0.0657-0.06170.16530.2067-0.16660.1465-0.0625-0.110.0525-0.1274-0.18510.02299.372-30.2512.166
51.8830.60530.16272.70040.16122.9025-0.15140.2195-0.1899-0.20710.0053-0.27120.12620.26220.1461-0.14070.0120.0753-0.1755-0.003-0.097742.682-17.48212.555
62.7844-0.3623-0.53542.09370.28152.0751-0.10540.45180.0149-0.21840.01430.1546-0.0828-0.40090.091-0.11780.0688-0.07780.1067-0.003-0.1828-4.57411.4652.885
72.57-1.4740.20824.5892-2.00141.823-0.1114-0.4066-0.20210.42060.02980.2620.0177-0.48220.0817-0.0304-0.04160.09440.0134-0.06160.0498-6.919-13.17454.861
86.30142.85231.88012.17590.02841.32580.1214-0.2129-0.58230.3897-0.09650.05250.2413-0.3141-0.025-0.0078-0.03150.0849-0.01730.0529-0.02048.544-24.56855.618
92.1929-0.0177-1.63662.81291.4014.3429-0.11530.0675-0.59030.1324-0.07830.24420.2279-0.41880.19350.0668-0.0950.05860.0007-0.03810.1325-5.828-27.38742.367
105.71240.74850.04381.0703-0.79761.55610.07390.5154-0.005-0.2521-0.1012-0.1521-0.1612-0.03670.02740.04020.0261-0.0399-0.04720.0537-0.125327.1720.09-3.453
111.7463-1.0202-0.96015.2714-0.42760.8885-0.0610.28330.08-0.23880.0428-0.4429-0.03920.1180.0181-0.07820.04590.0318-0.03730.0921-0.126243.526155.15
121.39320.84060.31941.96790.87115.5871-0.0470.24190.362-0.2171-0.0424-0.0731-0.3651-0.04330.0895-0.15510.0370.0399-0.15370.0547-0.052333.71630.52911.681
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 291
2X-RAY DIFFRACTION1A1292
3X-RAY DIFFRACTION2B8 - 296
4X-RAY DIFFRACTION2B1297
5X-RAY DIFFRACTION3C8 - 291
6X-RAY DIFFRACTION3C1292
7X-RAY DIFFRACTION4D8 - 293
8X-RAY DIFFRACTION4D1294
9X-RAY DIFFRACTION5E8 - 293
10X-RAY DIFFRACTION5E1294
11X-RAY DIFFRACTION6F6 - 292
12X-RAY DIFFRACTION6F1293
13X-RAY DIFFRACTION7G1 - 111
14X-RAY DIFFRACTION8H1 - 108
15X-RAY DIFFRACTION9I1 - 111
16X-RAY DIFFRACTION10J1 - 110
17X-RAY DIFFRACTION11K1 - 108
18X-RAY DIFFRACTION12L1 - 109

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