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- PDB-2q14: Crystal structure of Phosphohydrolase (BT4208) from Bacteroides t... -

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Basic information

Entry
Database: PDB / ID: 2q14
TitleCrystal structure of Phosphohydrolase (BT4208) from Bacteroides thetaiotaomicron VPI-5482 at 2.20 A resolution
ComponentsPhosphohydrolase
KeywordsHYDROLASE / BT4208 / HD domain / Phosphohydrolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


dGTPase activity / dGTP catabolic process / nucleotide binding
Similarity search - Function
Growth Hormone; Chain: A; - #30 / HD-associated domain / HD associated region / Hypothetical protein af1432 / : / Hypothetical protein af1432 / HD domain profile. / HD domain / HD domain / Growth Hormone; Chain: A; ...Growth Hormone; Chain: A; - #30 / HD-associated domain / HD associated region / Hypothetical protein af1432 / : / Hypothetical protein af1432 / HD domain profile. / HD domain / HD domain / Growth Hormone; Chain: A; / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Phosphohydrolase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Phosphohydrolase (BT4208) from Bacteroides thetaiotaomicron VPI-5482 at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim / 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 / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 8 ... BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 8 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TETRAMER AS A SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)385,52828
Polymers381,3558
Non-polymers4,17320
Water29,2561624
1
A: Phosphohydrolase
B: Phosphohydrolase
C: Phosphohydrolase
D: Phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,86316
Polymers190,6784
Non-polymers2,18612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18310 Å2
ΔGint-62 kcal/mol
Surface area55570 Å2
MethodPISA
2
E: Phosphohydrolase
F: Phosphohydrolase
G: Phosphohydrolase
H: Phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,66512
Polymers190,6784
Non-polymers1,9878
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16480 Å2
ΔGint-32 kcal/mol
Surface area55540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.436, 137.504, 279.051
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91A
101B
111C
121D
131E
141F
151G
161H
171A
181B
191C
201D
211E
221F
231G
241H
251A
261B
271C
281D
291E
301F
311G
321H
331A
341B
351C
361D
371E
381F
391G
401H
411A
421B
431C
441D
451E
461F
471G
481H
491A
501B
511C
521D
531E
541F
551G
561H
571A
581B
591C
601D
611E
621F
631G
641H
651A
661B
671C
681D
691E
701F
711G
721H
731A
741B
751C
761D
771E
781F
791G
801H
811A
821B
831C
841D
851E
861F
871G
881H
891A
901B
911C
921D
931E
941F
951G
961H
971A
981B
991C
1001D
1011E
1021F
1031G
1041H
1051A
1061B
1071C
1081D
1091E
1101F
1111G
1121H
1131A
1141B
1151C
1161D
1171E
1181F
1191G
1201H
1211A
1221B
1231C
1241D
1251E
1261F
1271G
1281H
1291A
1301B
1311C
1321D
1331E
1341F
1351G
1361H
1371A
1381B
1391C
1401D
1411E
1421F
1431G
1441H
1451A
1461B
1471C
1481D
1491E
1501F
1511G
1521H
1531A
1541B
1551C
1561D
1571E
1581F
1591G
1601H
1611A
1621B
1631C
1641D
1651E
1661F
1671G
1681H
12A
22B
32C
42D
52E
62F
72G
82H

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUARGARG5AA4 - 55 - 6
211ARGARGARGARG5BB56
311GLUGLUARGARG5CC4 - 55 - 6
411GLUGLUARGARG5DD4 - 55 - 6
511GLUGLUARGARG5EE4 - 55 - 6
611ARGARGARGARG5FF56
711GLUGLUARGARG5GG4 - 55 - 6
811ARGARGARGARG5HH56
921LYSLYSGLYGLY2AA6 - 147 - 15
1021LYSLYSGLYGLY2BB6 - 147 - 15
1121LYSLYSGLYGLY2CC6 - 147 - 15
1221LYSLYSGLYGLY2DD6 - 147 - 15
1321LYSLYSGLYGLY2EE6 - 147 - 15
1421LYSLYSGLYGLY2FF6 - 147 - 15
1521LYSLYSGLYGLY2GG6 - 147 - 15
1621LYSLYSGLYGLY2HH6 - 147 - 15
1731PHEPHEPHEPHE6AA1516
1831PHEPHEPHEPHE6BB1516
1931PHEPHEPHEPHE6CC1516
2031PHEPHEPHEPHE6DD1516
2131PHEPHEPHEPHE6EE1516
2231PHEPHEPHEPHE6FF1516
2331PHEPHEPHEPHE6GG1516
2431PHEPHEPHEPHE6HH1516
2541ILEILEVALVAL2AA16 - 2717 - 28
2641ILEILEVALVAL2BB16 - 2717 - 28
2741ILEILEVALVAL2CC16 - 2717 - 28
2841ILEILEVALVAL2DD16 - 2717 - 28
2941ILEILEVALVAL2EE16 - 2717 - 28
3041ILEILEVALVAL2FF16 - 2717 - 28
3141ILEILEVALVAL2GG16 - 2717 - 28
3241ILEILEVALVAL2HH16 - 2717 - 28
3351ARGARGARGARG6AA2829
3451ARGARGARGARG6BB2829
3551ARGARGARGARG6CC2829
3651ARGARGARGARG6DD2829
3751ARGARGARGARG6EE2829
3851ARGARGARGARG6FF2829
3951ARGARGARGARG6GG2829
4051ARGARGARGARG6HH2829
4161HISHISLYSLYS2AA29 - 7630 - 77
4261HISHISLYSLYS2BB29 - 7630 - 77
4361HISHISLYSLYS2CC29 - 7630 - 77
4461HISHISLYSLYS2DD29 - 7630 - 77
4561HISHISLYSLYS2EE29 - 7630 - 77
4661HISHISLYSLYS2FF29 - 7630 - 77
4761HISHISLYSLYS2GG29 - 7630 - 77
4861HISHISLYSLYS2HH29 - 7630 - 77
4971GLYGLYPHEPHE6AA77 - 7978 - 80
5071GLYGLYPHEPHE6BB77 - 7978 - 80
5171GLYGLYPHEPHE6CC77 - 7978 - 80
5271GLYGLYPHEPHE6DD77 - 7978 - 80
5371GLYGLYPHEPHE6EE77 - 7978 - 80
5471GLYGLYPHEPHE6FF77 - 7978 - 80
5571GLYGLYPHEPHE6GG77 - 7978 - 80
5671GLYGLYPHEPHE6HH77 - 7978 - 80
5781ILEILETHRTHR2AA80 - 17481 - 175
5881ILEILETHRTHR2BB80 - 17481 - 175
5981ILEILETHRTHR2CC80 - 17481 - 175
6081ILEILETHRTHR2DD80 - 17481 - 175
6181ILEILETHRTHR2EE80 - 17481 - 175
6281ILEILETHRTHR2FF80 - 17481 - 175
6381ILEILETHRTHR2GG80 - 17481 - 175
6481ILEILETHRTHR2HH80 - 17481 - 175
6591GLYGLYGLYGLY6AA175 - 182176 - 183
6691GLYGLYGLYGLY6BB175 - 182176 - 183
6791GLYGLYGLYGLY6CC175 - 182176 - 183
6891GLYGLYGLYGLY6DD175 - 182176 - 183
6991GLYGLYGLYGLY6EE175 - 182176 - 183
7091GLYGLYGLYGLY6FF175 - 182176 - 183
7191GLYGLYGLYGLY6GG175 - 182176 - 183
7291GLYGLYGLYGLY6HH175 - 182176 - 183
73101SERSERILEILE2AA183 - 204184 - 205
74101SERSERILEILE2BB183 - 204184 - 205
75101SERSERILEILE2CC183 - 204184 - 205
76101SERSERILEILE2DD183 - 204184 - 205
77101SERSERILEILE2EE183 - 204184 - 205
78101SERSERILEILE2FF183 - 204184 - 205
79101SERSERILEILE2GG183 - 204184 - 205
80101SERSERILEILE2HH183 - 204184 - 205
81111TYRTYRGLUGLU5AA205 - 208206 - 209
82111TYRTYRGLUGLU5BB205 - 208206 - 209
83111TYRTYRGLUGLU5CC205 - 208206 - 209
84111TYRTYRGLUGLU5DD205 - 208206 - 209
85111TYRTYRGLUGLU5EE205 - 208206 - 209
86111TYRTYRGLUGLU5FF205 - 208206 - 209
87111TYRTYRGLUGLU5GG205 - 208206 - 209
88111TYRTYRGLUGLU5HH205 - 208206 - 209
89121ASNASNMSEMSE2AA209 - 217210 - 218
90121ASNASNMSEMSE2BB209 - 217210 - 218
91121ASNASNMSEMSE2CC209 - 217210 - 218
92121ASNASNMSEMSE2DD209 - 217210 - 218
93121ASNASNMSEMSE2EE209 - 217210 - 218
94121ASNASNMSEMSE2FF209 - 217210 - 218
95121ASNASNMSEMSE2GG209 - 217210 - 218
96121ASNASNMSEMSE2HH209 - 217210 - 218
97131TYRTYRTYRTYR3AA218219
98131TYRTYRTYRTYR3BB218219
99131TYRTYRTYRTYR3CC218219
100131TYRTYRTYRTYR3DD218219
101131TYRTYRTYRTYR3EE218219
102131TYRTYRTYRTYR3FF218219
103131TYRTYRTYRTYR3GG218219
104131TYRTYRTYRTYR3HH218219
105141TRPTRPASNASN2AA219 - 320220 - 321
106141TRPTRPASNASN2BB219 - 320220 - 321
107141TRPTRPASNASN2CC219 - 320220 - 321
108141TRPTRPASNASN2DD219 - 320220 - 321
109141TRPTRPASNASN2EE219 - 320220 - 321
110141TRPTRPASNASN2FF219 - 320220 - 321
111141TRPTRPASNASN2GG219 - 320220 - 321
112141TRPTRPASNASN2HH219 - 320220 - 321
113151SERSERALAALA3AA321 - 322322 - 323
114151SERSERALAALA3BB321 - 322322 - 323
115151SERSERALAALA3CC321 - 322322 - 323
116151SERSERALAALA3DD321 - 322322 - 323
117151SERSERALAALA3EE321 - 322322 - 323
118151SERSERALAALA3FF321 - 322322 - 323
119151SERSERALAALA3GG321 - 322322 - 323
120151SERSERALAALA3HH321 - 322322 - 323
121161GLUGLUTHRTHR2AA323 - 354324 - 355
122161GLUGLUTHRTHR2BB323 - 354324 - 355
123161GLUGLUTHRTHR2CC323 - 354324 - 355
124161GLUGLUTHRTHR2DD323 - 354324 - 355
125161GLUGLUTHRTHR2EE323 - 354324 - 355
126161GLUGLUTHRTHR2FF323 - 354324 - 355
127161GLUGLUTHRTHR2GG323 - 354324 - 355
128161GLUGLUTHRTHR2HH323 - 354324 - 355
129171PROPROSERSER6AA355 - 356356 - 357
130171PROPROSERSER6BB355 - 356356 - 357
131171PROPROSERSER6CC355 - 356356 - 357
132171PROPROSERSER6DD355 - 356356 - 357
133171PROPROSERSER6EE355 - 356356 - 357
134171PROPROSERSER6FF355 - 356356 - 357
135171PROPROSERSER6GG355 - 356356 - 357
136171PROPROSERSER6HH355 - 356356 - 357
137181ILEILEASNASN2AA357 - 360358 - 361
138181ILEILEILEILE2BB357358
139181ILEILEASNASN2CC357 - 360358 - 361
140181ILEILEILEILE2DD357358
141181ILEILEASNASN2EE357 - 360358 - 361
142181ILEILEILEILE2FF357358
143181ILEILEASNASN2GG357 - 360358 - 361
144181SERSERSERSER2HH356357
145191MSEMSESERSER5AA361 - 368362 - 369
146191MSEMSESERSER5BB361 - 368362 - 369
147191MSEMSESERSER5CC361 - 368362 - 369
148191MSEMSESERSER5DD361 - 368362 - 369
149191MSEMSESERSER5EE361 - 368362 - 369
150191MSEMSESERSER5FF361 - 368362 - 369
151191MSEMSESERSER5GG361 - 368362 - 369
152191MSEMSESERSER5HH361 - 368362 - 369
153201ILEILESERSER2AA369 - 385370 - 386
154201ILEILESERSER2BB369 - 385370 - 386
155201ILEILESERSER2CC369 - 385370 - 386
156201ILEILESERSER2DD369 - 385370 - 386
157201ILEILESERSER2EE369 - 385370 - 386
158201ILEILESERSER2FF369 - 385370 - 386
159201ILEILESERSER2GG369 - 385370 - 386
160201ILEILESERSER2HH369 - 385370 - 386
161211ASPASPARGARG5AA386 - 406387 - 407
162211ASPASPLEULEU5BB386 - 407387 - 408
163211ASPASPARGARG5CC386 - 406387 - 407
164211ASPASPARGARG5DD386 - 406387 - 407
165211ASPASPARGARG5EE386 - 406387 - 407
166211ASPASPLEULEU5FF386 - 407387 - 408
167211ASPASPARGARG5GG386 - 406387 - 407
168211ASPASPARGARG5HH386 - 406387 - 407
112ADPADPADPADP1AJ501
212ADPADPADPADP1BM501
312ADPADPADPADP1CP501
412ADPADPADPADP1DS501
512ADPADPADPADP1EU501
612ADPADPADPADP1FW501
712ADPADPADPADP1GX501
812ADPADPADPADP1HAA501

NCS ensembles :
ID
1
2
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Phosphohydrolase


Mass: 47669.426 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Species: Bacteroides thetaiotaomicron / Strain: E50, DSM 2079, NCTC 10582, VPI-5482 / Gene: BT_4208 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A013

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Non-polymers , 5 types, 1644 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1624 / 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: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: NANODROP, 15.0% PEG 8000, 8.0% Ethylene glycol, 0.1M Bicine pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97925, 0.97939, 0.94926
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 11, 2006 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979251
20.979391
30.949261
ReflectionResolution: 2.2→49.029 Å / Num. obs: 224828 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.164 / Net I/σ(I): 5.73
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.2-2.430.8061.65661115606189.3
2.43-2.530.65827098918853199.9
2.53-2.650.5432.37161719006199.8
2.65-2.790.41536877518251199.8
2.79-2.960.3193.86734017827199.8
2.96-3.190.244.86945918439199.7
3.19-3.510.1556.66886318303199.5
3.51-4.010.0969.26826318155199.2
4.01-5.040.07211.66927018456199.1
5.04-49.0290.06911.96940018859196.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→49.029 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.581 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.205
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. DUE TO BOOKKEEPING ERROR, THE CRYSTALLIZATION CONDITIONS PROVIDED IN PDB FILE MAY BE NOT RELIABLE. 4. THE ADP MOLECULES ARE ASSIGNED BASED ON THE ELECTRON DENSITY, THEIR INTERACTION WITH THE PROTEIN AND SIMILARITY OF THE PROTEIN TO A HOMOLOG (PDB ID: 2HEK). THE OCCUPANCY IS REDUCED TO 0.6. THE DENSITIES FOR ADP MOLECULES ARE POOR. 5. GOL, EDO AND CL ARE PRESENT IN CRYSTALLIZATION/CRYO BUFFER.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 11153 5 %RANDOM
Rwork0.207 ---
obs0.21 221971 98.75 %-
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: 26.737 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å20 Å20 Å2
2---1.03 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25568 0 261 1624 27453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02226624
X-RAY DIFFRACTIONr_bond_other_d0.0020.0217678
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.96936142
X-RAY DIFFRACTIONr_angle_other_deg0.958343199
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.64753275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56624.3481242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.206154626
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.215147
X-RAY DIFFRACTIONr_chiral_restr0.0820.24108
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0229385
X-RAY DIFFRACTIONr_gen_planes_other0.0020.025386
X-RAY DIFFRACTIONr_nbd_refined0.2190.26199
X-RAY DIFFRACTIONr_nbd_other0.1960.219237
X-RAY DIFFRACTIONr_nbtor_refined0.1830.213102
X-RAY DIFFRACTIONr_nbtor_other0.0880.213671
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.21433
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.070.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1930.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.210
X-RAY DIFFRACTIONr_mcbond_it1.686316654
X-RAY DIFFRACTIONr_mcbond_other0.38336548
X-RAY DIFFRACTIONr_mcangle_it2.673526148
X-RAY DIFFRACTIONr_scbond_it4.784811342
X-RAY DIFFRACTIONr_scangle_it6.276119967
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2054TIGHT POSITIONAL0.10.1
12B2054TIGHT POSITIONAL0.130.1
13C2054TIGHT POSITIONAL0.130.1
14D2054TIGHT POSITIONAL0.150.1
15E2054TIGHT POSITIONAL0.10.1
16F2054TIGHT POSITIONAL0.090.1
17G2054TIGHT POSITIONAL0.10.1
18H2054TIGHT POSITIONAL0.10.1
11A2602MEDIUM POSITIONAL0.530.5
12B2602MEDIUM POSITIONAL0.580.5
13C2602MEDIUM POSITIONAL0.560.5
14D2602MEDIUM POSITIONAL0.610.5
15E2602MEDIUM POSITIONAL0.530.5
16F2602MEDIUM POSITIONAL0.560.5
17G2602MEDIUM POSITIONAL0.550.5
18H2602MEDIUM POSITIONAL0.540.5
11A321LOOSE POSITIONAL1.675
12B321LOOSE POSITIONAL1.775
13C321LOOSE POSITIONAL1.735
14D321LOOSE POSITIONAL1.855
15E321LOOSE POSITIONAL25
16F321LOOSE POSITIONAL1.735
17G321LOOSE POSITIONAL1.655
18H321LOOSE POSITIONAL1.765
11A2054TIGHT THERMAL0.190.5
12B2054TIGHT THERMAL0.180.5
13C2054TIGHT THERMAL0.170.5
14D2054TIGHT THERMAL0.170.5
15E2054TIGHT THERMAL0.130.5
16F2054TIGHT THERMAL0.180.5
17G2054TIGHT THERMAL0.170.5
18H2054TIGHT THERMAL0.220.5
11A2602MEDIUM THERMAL1.492
12B2602MEDIUM THERMAL1.262
13C2602MEDIUM THERMAL1.22
14D2602MEDIUM THERMAL1.272
15E2602MEDIUM THERMAL1.042
16F2602MEDIUM THERMAL1.312
17G2602MEDIUM THERMAL1.32
18H2602MEDIUM THERMAL1.552
11A321LOOSE THERMAL7.0610
12B321LOOSE THERMAL5.3510
13C321LOOSE THERMAL5.1710
14D321LOOSE THERMAL5.9610
15E321LOOSE THERMAL4.8910
16F321LOOSE THERMAL5.510
17G321LOOSE THERMAL5.7210
18H321LOOSE THERMAL7.0910
21A37TIGHT POSITIONAL0.030.1
22B37TIGHT POSITIONAL0.030.1
23C37TIGHT POSITIONAL0.040.1
24D37TIGHT POSITIONAL0.040.1
25E37TIGHT POSITIONAL0.040.1
26F37TIGHT POSITIONAL0.050.1
27G37TIGHT POSITIONAL0.040.1
28H37TIGHT POSITIONAL0.040.1
21A37TIGHT THERMAL0.040.5
22B37TIGHT THERMAL0.040.5
23C37TIGHT THERMAL0.040.5
24D37TIGHT THERMAL0.040.5
25E37TIGHT THERMAL0.030.5
26F37TIGHT THERMAL0.050.5
27G37TIGHT THERMAL0.040.5
28H37TIGHT THERMAL0.040.5
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 743 -
Rwork0.309 14175 -
obs-14918 90.46 %

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