[English] 日本語
Yorodumi
- PDB-1vkm: Crystal structure of an indigoidine synthase a (idga)-like protei... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vkm
TitleCrystal structure of an indigoidine synthase a (idga)-like protein (tm1464) from thermotoga maritima msb8 at 1.90 A resolution
Componentsconserved hypothetical protein TM1464
KeywordsBIOSYNTHETIC PROTEIN / Indigoidine synthase a-like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


nucleobase catabolic process / pseudouridylate synthase / pseudouridylate synthase activity / hydrolase activity, acting on glycosyl bonds / metal ion binding / cytoplasm
Similarity search - Function
Indigoidine synthase fold / Indigoidine synthase domain / Pseudouridine-5'-phosphate glycosidase / Indigoidine synthase A-like / Indigoidine synthase A like protein / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Unknown ligand / Pseudouridine-5'-phosphate glycosidase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2005
Title: Crystal structure of an indigoidine synthase A (IndA)-like protein (TM1464) from Thermotoga maritima at 1.90 A resolution reveals a new fold.
Authors: Levin, I. / Miller, M.D. / Schwarzenbacher, R. / McMullan, D. / Abdubek, P. / Ambing, E. / Biorac, T. / Cambell, J. / Canaves, J.M. / Chiu, H.J. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. ...Authors: Levin, I. / Miller, M.D. / Schwarzenbacher, R. / McMullan, D. / Abdubek, P. / Ambing, E. / Biorac, T. / Cambell, J. / Canaves, J.M. / Chiu, H.J. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Hale, J. / Hampton, E. / Han, G.W. / Haugen, J. / Hornsby, M. / Jaroszewski, L. / Karlak, C. / Klock, H.E. / Koesema, E. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / Morse, A. / Moy, K. / Nigoghossian, E. / Ouyang, J. / Page, R. / Quijano, K. / Reyes, R. / Robb, A. / Sims, E. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Vincent, J. / Wang, X. / West, B. / Wolf, G. / Xu, Q. / Zagnitko, O. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionJun 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_database_remark ...database_2 / pdbx_database_remark / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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_seq_id
Remark 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THERE ARE TWO TRIMERS PACKED IN THE ASYMMETRIC UNIT AS AN APPARENT D3 HEXAMER. THE PACKING INTERACTION BETWEEN THE TRIMERS IS MEDIATED BY THE PURIFICATION TAGS AND 6 MN IONS (ASSIGNED RESIDUE NUMBER 300) FROM EACH MONOMER. ASSIGNMENT OF THE C3 TRIMER AS THE BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE IS BASED ON THE FACT THAT ANOTHER CRYSTAL WITHOUT MN CONTAINS THE TRIMER AND NOT THE HEXAMER AND THAT THE PRIMARY INTERACTION BETWEEN TRIMERS INVOLVES THE PURIFICATION TAG.
Remark 999SEQUENCE CLONING ARTIFACT: THIS GENE USES AN ALTERNATE INITIATION CODON THAT RESULTS IN A VALINE AT ...SEQUENCE CLONING ARTIFACT: THIS GENE USES AN ALTERNATE INITIATION CODON THAT RESULTS IN A VALINE AT POSITION 1 WHEN EXPRESSED AS A FUSION WITH THE PURIFICATION TAG

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: conserved hypothetical protein TM1464
B: conserved hypothetical protein TM1464
C: conserved hypothetical protein TM1464
D: conserved hypothetical protein TM1464
E: conserved hypothetical protein TM1464
F: conserved hypothetical protein TM1464
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,86739
Polymers202,3056
Non-polymers1,56233
Water17,727984
1
A: conserved hypothetical protein TM1464
B: conserved hypothetical protein TM1464
C: conserved hypothetical protein TM1464
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,96420
Polymers101,1523
Non-polymers81217
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11060 Å2
ΔGint-53 kcal/mol
Surface area32650 Å2
MethodPISA
2
D: conserved hypothetical protein TM1464
E: conserved hypothetical protein TM1464
F: conserved hypothetical protein TM1464
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,90219
Polymers101,1523
Non-polymers75016
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11470 Å2
ΔGint-47 kcal/mol
Surface area32490 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28720 Å2
ΔGint-118 kcal/mol
Surface area58960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.958, 130.799, 138.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71A
81B
91C
101D
111E
121F
131A
141B
151C
161D
171E
181F
191A
201B
211C
221D
231E
241F
251A
261B
271C
281D
291E
301F
311A
321B
331C
341D
351E
361F
371A
381B
391C
401D
411E
421F
431A
441B
451C
461D
471E
481F
491A
501B
511C
521D
531E
541F
551A
561B
571C
581D
591E
601F
611A
621B
631C
641D
651E
661F
671A
681B
691C
701D
711E
721F
731A
741B
751C
761D
771E
781F
791A
801B
811C
821D
831E
841F
851A
861B
871C
881D
891E
901F
911A
921B
931C
941D
951E
961F

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSILEILE5AA-7 - -65 - 6
21LYSLYSILEILE5BB-7 - -65 - 6
31LYSLYSILEILE5CC-7 - -65 - 6
41LYSLYSILEILE5DD-7 - -65 - 6
51LYSLYSILEILE5EE-7 - -65 - 6
61LYSLYSILEILE5FF-7 - -65 - 6
72HISHISSERSER2AA-5 - 57 - 17
82HISHISSERSER2BB-5 - 57 - 17
92HISHISSERSER2CC-5 - 57 - 17
102HISHISSERSER2DD-5 - 57 - 17
112HISHISSERSER2EE-5 - 57 - 17
122HISHISSERSER2FF-5 - 57 - 17
133ARGARGPROPRO5AA6 - 1218 - 24
143ARGARGPROPRO5BB6 - 1218 - 24
153ARGARGPROPRO5CC6 - 1218 - 24
163ARGARGPROPRO5DD6 - 1218 - 24
173ARGARGPROPRO5EE6 - 1218 - 24
183ARGARGPROPRO5FF6 - 1218 - 24
194VALVALPHEPHE2AA13 - 2125 - 33
204VALVALPHEPHE2BB13 - 2125 - 33
214VALVALPHEPHE2CC13 - 2125 - 33
224VALVALPHEPHE2DD13 - 2125 - 33
234VALVALPHEPHE2EE13 - 2125 - 33
244VALVALPHEPHE2FF13 - 2125 - 33
255VALVALARGARG5AA22 - 3534 - 47
265VALVALARGARG5BB22 - 3534 - 47
275VALVALARGARG5CC22 - 3534 - 47
285VALVALARGARG5DD22 - 3534 - 47
295VALVALARGARG5EE22 - 3534 - 47
305VALVALARGARG5FF22 - 3534 - 47
316ARGARGILEILE2AA36 - 4048 - 52
326ARGARGILEILE2BB36 - 4048 - 52
336ARGARGILEILE2CC36 - 4048 - 52
346ARGARGILEILE2DD36 - 4048 - 52
356ARGARGILEILE2EE36 - 4048 - 52
366ARGARGILEILE2FF36 - 4048 - 52
377SERSERLYSLYS5AA41 - 4453 - 56
387SERSERLYSLYS5BB41 - 4453 - 56
397SERSERLYSLYS5CC41 - 4453 - 56
407SERSERLYSLYS5DD41 - 4453 - 56
417SERSERLYSLYS5EE41 - 4453 - 56
427SERSERLYSLYS5FF41 - 4453 - 56
438GLYGLYMSEMSE2AA45 - 7057 - 82
448GLYGLYMSEMSE2BB45 - 7057 - 82
458GLYGLYMSEMSE2CC45 - 7057 - 82
468GLYGLYMSEMSE2DD45 - 7057 - 82
478GLYGLYMSEMSE2EE45 - 7057 - 82
488GLYGLYMSEMSE2FF45 - 7057 - 82
499MSEMSEASPASP5AA71 - 7683 - 88
509MSEMSEASPASP5BB71 - 7683 - 88
519MSEMSEASPASP5CC71 - 7683 - 88
529MSEMSEASPASP5DD71 - 7683 - 88
539MSEMSEASPASP5EE71 - 7683 - 88
549MSEMSEASPASP5FF71 - 7683 - 88
5510LYSLYSSERSER2AA77 - 17989 - 191
5610LYSLYSSERSER2BB77 - 17989 - 191
5710LYSLYSSERSER2CC77 - 17989 - 191
5810LYSLYSSERSER2DD77 - 17989 - 191
5910LYSLYSSERSER2EE77 - 17989 - 191
6010LYSLYSSERSER2FF77 - 17989 - 191
6111ARGARGARGARG5AA180 - 185192 - 197
6211ARGARGARGARG5BB180 - 185192 - 197
6311ARGARGARGARG5CC180 - 185192 - 197
6411ARGARGARGARG5DD180 - 185192 - 197
6511ARGARGARGARG5EE180 - 185192 - 197
6611ARGARGARGARG5FF180 - 185192 - 197
6712VALVALPROPRO2AA186 - 216198 - 228
6812VALVALPROPRO2BB186 - 216198 - 228
6912VALVALPROPRO2CC186 - 216198 - 228
7012VALVALPROPRO2DD186 - 216198 - 228
7112VALVALPROPRO2EE186 - 216198 - 228
7212VALVALPROPRO2FF186 - 216198 - 228
7313VALVALLEULEU5AA217 - 265229 - 277
7413VALVALLEULEU5BB217 - 265229 - 277
7513VALVALLEULEU5CC217 - 265229 - 277
7613VALVALLEULEU5DD217 - 265229 - 277
7713VALVALLEULEU5EE217 - 265229 - 277
7813VALVALLEULEU5FF217 - 265229 - 277
7914ALAALALEULEU2AA266 - 282278 - 294
8014ALAALALEULEU2BB266 - 282278 - 294
8114ALAALALEULEU2CC266 - 282278 - 294
8214ALAALALEULEU2DD266 - 282278 - 294
8314ALAALALEULEU2EE266 - 282278 - 294
8414ALAALALEULEU2FF266 - 282278 - 294
8515LYSLYSARGARG5AA283 - 284295 - 296
8615LYSLYSARGARG5BB283 - 284295 - 296
8715LYSLYSARGARG5CC283 - 284295 - 296
8815LYSLYSARGARG5DD283 - 284295 - 296
8915LYSLYSARGARG5EE283 - 284295 - 296
9015LYSLYSARGARG5FF283 - 284295 - 296
9116MNMNUNLUNL2AG - J300 - 600
9216MNMNUNLUNL2BL - N300 - 600
9316MNMNUNLUNL2CR - U300 - 600
9416MNMNUNLUNL2DX - Z300 - 600
9516MNMNUNLUNL2ECA - FA300 - 600
9616MNMNUNLUNL2FJA - MA300 - 600
DetailsBIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAIN(S). SEE FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THERE ARE TWO TRIMERS PACKED IN THE ASYMMETRIC UNIT AS AN APPARENT D3 HEXAMER. THE PACKING INTERACTION BETWEEN THE TRIMERS IS MEDIATED BY THE PURIFICATION TAGS AND 6 MN IONS (ASSIGNED RESIDUE NUMBER 300) FROM EACH MONOMER. ASSIGNMENT OF THE C3 TRIMER AS THE BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE IS BASED ON THE FACT THAT ANOTHER CRYSTAL WITHOUT MN CONTAINS THE TRIMER AND NOT THE HEXAMER AND THAT THE PRIMARY INTERACTION BETWEEN TRIMERS INVOLVES THE PURIFICATION TAG. GENERATING THE BIOMOLECULE COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. BIOMOLECULE: 1 APPLY THE FOLLOWING TO CHAINS: A, B, C BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 BIOMOLECULE: 2 APPLY THE FOLLOWING TO CHAINS: D, E, F BIOMT1 2 1.000000 0.000000 0.000000 0.00000 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 BIOMT3 2 0.000000 0.000000 1.000000 0.00000

-
Components

#1: Protein
conserved hypothetical protein TM1464


Mass: 33717.480 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: possibly involved in carbohydrate metabolism / Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM1464 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1H5
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 6 / Source method: obtained synthetically
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 984 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.0640.36
2237.91
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.4
Details: 7% PEG 1000, 0.045M HEPES_Na, 0.055M HEPES, 0.01M MANGANESE (II) CHLORIDE, pH 7.4, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONALS 8.2.111
SYNCHROTRONALS 8.2.221.0000, 0.9797, 0.9795
Detector
TypeIDDetectorDate
ADSC1CCDOct 12, 2003
ADSC2CCDOct 12, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double Crystal Si(111)SINGLE WAVELENGTHMx-ray1
2Double Crystal Si(111)MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97971
30.97951
ReflectionResolution: 1.9→75.23 Å / Num. obs: 130700 / % possible obs: 99.1 % / Redundancy: 4.7 % / Biso Wilson estimate: 32.57 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 13.7
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 1.9 / Num. unique all: 9022 / % possible all: 93.3

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SOLVEphasing
SHARPphasing
REFMAC5.2.0000refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→75.23 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 6.256 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.134
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AN UNKNOWN LIGAND (UNL) IS BOUND TO EACH MONOMER. THE LIGAND HAS A HEAVIER ATOM AT ONE END WHOSE GEOMETRY IS CONSISTENT WITH A PHOSPHATE OR ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AN UNKNOWN LIGAND (UNL) IS BOUND TO EACH MONOMER. THE LIGAND HAS A HEAVIER ATOM AT ONE END WHOSE GEOMETRY IS CONSISTENT WITH A PHOSPHATE OR SULFATE. THE ELECTRON DENSITY SUGGESTS THE LIGAND MAY BE A GLYCEROL-3- PHOSPHATE ANALOG. HOWEVER, THE UNL IS LARGER THAN GLYCEROL- 3-PHOSPHATE WITH DENSITY EXTENDING BEYOND THE CARBON 1 ATOM OF GLYCEROL-3-PHOSPHATE. THE MANGANESE ASSIGNMENT HAS BEEN MADE BASED ON ANOMALOUS DIFFERENCE FOURIER, X-RAY FLUORESCENCE, GEOMETRY AND THE ABSENCE OF SIMILAR PEAKS IN ANOTHER CRYSTAL FORM WITHOUT MANGANESE ADDED. THERE ARE 12 WELL RESOLVED MN IONS, ONE ASSOCIATED WITH THE UNL AND ONE ASSOCIATED WITH THE PURIFICATION TAG OF EACH MONOMER. THERE ARE 4 MN IONS MODELED IN THE SOLVENT THAT ARE LIKELY ONLY PARTIALLY OCCUPIED. THERE IS EXTRA DENSITY AROUND ILE 85, IN CHAINS A, E AND F, THAT IS NOT FULLY ACCOUNTED FOR WITH THE MODELED ALTERNATE CONFORMATIONS. ELEVEN MOLECULES OF 1,2 ETHANEDIOL, USED FOR CRYSTAL CRYOPROTECTION, WERE MODELED IN THE SOLVENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.19959 6577 5 %RANDOM
Rwork0.15384 ---
obs0.15618 124050 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.631 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.64 Å20 Å2
3---0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.9→75.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13623 0 138 984 14745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02214126
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213868
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.99619042
X-RAY DIFFRACTIONr_angle_other_deg0.846332234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.83951812
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.36323.692558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69152802
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.16515113
X-RAY DIFFRACTIONr_chiral_restr0.0890.22281
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215200
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022621
X-RAY DIFFRACTIONr_nbd_refined0.2180.22764
X-RAY DIFFRACTIONr_nbd_other0.1750.214251
X-RAY DIFFRACTIONr_nbtor_other0.0830.28586
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0530.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2590.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.220
X-RAY DIFFRACTIONr_mcbond_it2.05839104
X-RAY DIFFRACTIONr_mcbond_other0.66833615
X-RAY DIFFRACTIONr_mcangle_it2.688514330
X-RAY DIFFRACTIONr_scbond_it5.30885478
X-RAY DIFFRACTIONr_scangle_it7.294114679
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1176tight positional0.10.1
2B1176tight positional0.080.1
3C1176tight positional0.070.1
4D1176tight positional0.070.1
5E1176tight positional0.110.1
6F1176tight positional0.070.1
1A2291medium positional0.360.7
2B2291medium positional0.330.7
3C2291medium positional0.320.7
4D2291medium positional0.270.7
5E2291medium positional0.340.7
6F2291medium positional0.310.7
1A743loose positional0.725
2B743loose positional0.875
3C743loose positional0.755
4D743loose positional0.825
5E743loose positional1.225
6F743loose positional0.625
1A1176tight thermal0.621
2B1176tight thermal0.521
3C1176tight thermal0.581
4D1176tight thermal0.571
5E1176tight thermal0.651
6F1176tight thermal0.561
1A2291medium thermal1.684
2B2291medium thermal1.394
3C2291medium thermal1.634
4D2291medium thermal1.544
5E2291medium thermal2.024
6F2291medium thermal1.654
1A743loose thermal3.2610
2B743loose thermal2.5910
3C743loose thermal2.8710
4D743loose thermal2.8910
5E743loose thermal3.4810
6F743loose thermal2.9810
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 480 5.33 %
Rwork0.216 8532 -
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)
11.52570.05620.76821.27060.08311.32560.071-0.2943-0.09410.1576-0.0573-0.05910.173-0.1809-0.0136-0.1532-0.04790.022-0.07880.008-0.117920.379-20.60325.513
21.2407-0.41180.27281.009-0.3180.81070.0493-0.03530.1517-0.0274-0.0473-0.2278-0.05070.0609-0.002-0.1957-0.03080.0396-0.1362-0.0173-0.063432.505-8.07316.97
31.7353-0.548-0.18012.2695-0.60092.10960.1824-0.05280.73530.05540.0901-0.24-0.6375-0.0103-0.27250.03460.00840.1613-0.115-0.03010.192416.77120.52312.835
41.1875-0.0895-0.23322.271-0.04131.28120.17660.33440.4504-0.4905-0.0469-0.1888-0.2519-0.0017-0.12970.05220.04390.1696-0.0530.11570.04417.07413.321-5.087
51.59220.54330.12151.79760.33370.4946-0.01340.31030.1653-0.22490.01320.2858-0.0056-0.12340.0002-0.06250.0207-0.03250.01970.0287-0.0913-6.239-10.348-7.364
61.98850.49450.43940.99250.30330.91680.03420.3402-0.1669-0.24830.0562-0.04950.09620.0923-0.0904-0.05710.03060.0111-0.0366-0.054-0.134310.243-20.675-6.03
71.1125-0.05270.35313.5768-0.09831.30460.01270.33230.0904-0.7635-0.12190.283-0.1627-0.17490.10920.02810.0504-0.0628-0.0391-0.0064-0.144-26.7089.15210.66
81.1590.07940.09821.48840.25961.2547-0.00230.01210.2478-0.1633-0.09290.1719-0.1923-0.15050.0952-0.13040.0504-0.0241-0.1357-0.0151-0.1226-27.45718.88927.514
92.7860.92592.2152.46082.17643.38650.6214-0.0869-0.95370.78430.0719-0.4261.09850.0956-0.69320.22770.0578-0.2739-0.11720.02790.1602-11.86-23.32934.953
101.88550.0280.90872.07361.32121.84310.2271-0.278-0.3750.4466-0.16520.18040.5069-0.3209-0.0619-0.0442-0.0874-0.0088-0.08990.0439-0.0624-29.288-15.18832.696
111.1439-0.13180.36861.36610.39912.77410.088-0.08990.3020.13170.1163-0.366-0.22230.6322-0.2043-0.136-0.0364-0.00060.0221-0.0826-0.02111.78916.80342.443
120.92710.25330.24761.01851.06922.16790.1114-0.2037-0.01830.39040.0666-0.14830.38080.1464-0.178-0.03930.0208-0.0657-0.0498-0.0061-0.1659-9.1754.54352.683
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA-7 - 1105 - 122
21AG300
32AA111 - 284123 - 296
42AH400
52AW600
63BB-7 - 1105 - 122
73BI300
84BB111 - 284123 - 296
94BJ400
104BX600
115CC-7 - 1105 - 122
125CK300
136CC111 - 284123 - 296
146CL400
156CY600
167DD-7 - 1105 - 122
177DM300
188DD111 - 284123 - 296
198DN400
208DZ600
219EE-7 - 1105 - 122
229EO300
2310EE111 - 284123 - 296
2410EP400
2510EAA600
2611FF-7 - 1105 - 122
2711FQ300
2812FF111 - 284123 - 296
2912FR400
3012FBA600

+
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