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- PDB-7g00: Crystal Structure of human FABP1 in complex with 2-[[3-(5-tert-bu... -

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Basic information

Entry
Database: PDB / ID: 7g00
TitleCrystal Structure of human FABP1 in complex with 2-[[3-(5-tert-butyl-1,2,4-oxadiazol-3-yl)-4,5,6,7-tetrahydro-1-benzothiophen-2-yl]carbamoyl]cyclopentene-1-carboxylic acid
ComponentsFatty acid-binding protein, liver
KeywordsLIPID BINDING PROTEIN / FATTY ACID BINDING PROTEIN / CYTOPLASM / LIPID-BINDING / TRANSPORT / PROTEIN BINDING
Function / homology
Function and homology information


response to vitamin B3 / oleic acid binding / apical cortex / positive regulation of fatty acid beta-oxidation / bile acid binding / intestinal absorption / Heme degradation / long-chain fatty acid transmembrane transporter activity / heterocyclic compound binding / Triglyceride catabolism ...response to vitamin B3 / oleic acid binding / apical cortex / positive regulation of fatty acid beta-oxidation / bile acid binding / intestinal absorption / Heme degradation / long-chain fatty acid transmembrane transporter activity / heterocyclic compound binding / Triglyceride catabolism / antioxidant activity / peroxisomal matrix / fatty acid transport / Regulation of lipid metabolism by PPARalpha / fatty acid binding / phospholipid binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PPARA activates gene expression / Cytoprotection by HMOX1 / cellular response to hydrogen peroxide / cellular response to hypoxia / chromatin binding / negative regulation of apoptotic process / protein-containing complex / extracellular exosome / nucleoplasm / nucleus / cytosol
Similarity search - Function
Lipocalin / cytosolic fatty-acid binding protein family / Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin
Similarity search - Domain/homology
THIOCYANATE ION / Chem-WII / Fatty acid-binding protein, liver
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsEhler, A. / Benz, J. / Obst, U. / Neidhart, W. / Rudolph, M.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: To be published
Title: Crystal Structure of a human FABP1 complex
Authors: Obst, U. / Magnone, C. / Kuhn, B. / Rudolph, M.G.
History
DepositionApr 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fatty acid-binding protein, liver
B: Fatty acid-binding protein, liver
C: Fatty acid-binding protein, liver
D: Fatty acid-binding protein, liver
E: Fatty acid-binding protein, liver
F: Fatty acid-binding protein, liver
G: Fatty acid-binding protein, liver
H: Fatty acid-binding protein, liver
I: Fatty acid-binding protein, liver
J: Fatty acid-binding protein, liver
K: Fatty acid-binding protein, liver
L: Fatty acid-binding protein, liver
M: Fatty acid-binding protein, liver
N: Fatty acid-binding protein, liver
O: Fatty acid-binding protein, liver
P: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,71648
Polymers232,13816
Non-polymers7,57732
Water4,702261
1
A: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9823
Polymers14,5091
Non-polymers4742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0404
Polymers14,5091
Non-polymers5323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9242
Polymers14,5091
Non-polymers4161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9823
Polymers14,5091
Non-polymers4742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9823
Polymers14,5091
Non-polymers4742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9823
Polymers14,5091
Non-polymers4742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9823
Polymers14,5091
Non-polymers4742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9823
Polymers14,5091
Non-polymers4742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9823
Polymers14,5091
Non-polymers4742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0404
Polymers14,5091
Non-polymers5323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9242
Polymers14,5091
Non-polymers4161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9823
Polymers14,5091
Non-polymers4742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
M: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9823
Polymers14,5091
Non-polymers4742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
N: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9823
Polymers14,5091
Non-polymers4742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
O: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9823
Polymers14,5091
Non-polymers4742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
16
P: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9823
Polymers14,5091
Non-polymers4742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.698, 129.581, 115.914
Angle α, β, γ (deg.)90.000, 90.110, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 3:19 or resseq 21:24 or resseq...
21chain B and (resseq 3:19 or resseq 21:24 or resseq...
31chain C and (resseq 3:19 or resseq 21:24 or resseq...
41chain D and (resseq 3:19 or resseq 21:24 or resseq...
51chain E and (resseq 3:19 or resseq 21:24 or resseq...
61chain F and (resseq 3:19 or resseq 21:24 or resseq...
71chain G and (resseq 3:19 or resseq 21:24 or resseq...
81chain H and (resseq 3:19 or resseq 21:24 or resseq...
91chain I and (resseq 3:19 or resseq 21:24 or resseq...
101chain J and (resseq 3:19 or resseq 21:24 or resseq...
111chain K and (resseq 3:19 or resseq 21:24 or resseq...
121chain L and (resseq 3:19 or resseq 21:24 or resseq...
131chain M and (resseq 3:19 or resseq 21:24 or resseq...
141chain N and (resseq 3:19 or resseq 21:24 or resseq...
151chain O and (resseq 3:19 or resseq 21:24 or resseq...
161chain P and (resseq 3:19 or resseq 21:24 or resseq...

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
11PHEPHEMETMETchain A and (resseq 3:19 or resseq 21:24 or resseq...AA3 - 196 - 22
12METMETILEILEchain A and (resseq 3:19 or resseq 21:24 or resseq...AA1 - 1274 - 130
13METMETILEILEchain A and (resseq 3:19 or resseq 21:24 or resseq...AA1 - 1274 - 130
14METMETILEILEchain A and (resseq 3:19 or resseq 21:24 or resseq...AA1 - 1274 - 130
15METMETILEILEchain A and (resseq 3:19 or resseq 21:24 or resseq...AA1 - 1274 - 130
16ILEILEILEILEchain A and (resseq 3:19 or resseq 21:24 or resseq...AA118 - 127121 - 130
21PHEPHEMETMETchain B and (resseq 3:19 or resseq 21:24 or resseq...BB3 - 196 - 22
22ALAALALEULEUchain B and (resseq 3:19 or resseq 21:24 or resseq...BB21 - 2424 - 27
23ILEILEGLNGLNchain B and (resseq 3:19 or resseq 21:24 or resseq...BB29 - 4332 - 46
24PHEPHEASNASNchain B and (resseq 3:19 or resseq 21:24 or resseq...BB48 - 9751 - 100
25VALVALGLYGLYchain B and (resseq 3:19 or resseq 21:24 or resseq...BB101 - 116104 - 119
26ILEILEILEILEchain B and (resseq 3:19 or resseq 21:24 or resseq...BB118 - 127121 - 130
31PHEPHEMETMETchain C and (resseq 3:19 or resseq 21:24 or resseq...CC3 - 196 - 22
32METMETILEILEchain C and (resseq 3:19 or resseq 21:24 or resseq...CC1 - 1274 - 130
33METMETILEILEchain C and (resseq 3:19 or resseq 21:24 or resseq...CC1 - 1274 - 130
34METMETILEILEchain C and (resseq 3:19 or resseq 21:24 or resseq...CC1 - 1274 - 130
35METMETILEILEchain C and (resseq 3:19 or resseq 21:24 or resseq...CC1 - 1274 - 130
36ILEILEILEILEchain C and (resseq 3:19 or resseq 21:24 or resseq...CC118 - 127121 - 130
41PHEPHEMETMETchain D and (resseq 3:19 or resseq 21:24 or resseq...DD3 - 196 - 22
42ALAALALEULEUchain D and (resseq 3:19 or resseq 21:24 or resseq...DD21 - 2424 - 27
43ILEILEGLNGLNchain D and (resseq 3:19 or resseq 21:24 or resseq...DD29 - 4332 - 46
44PHEPHEASNASNchain D and (resseq 3:19 or resseq 21:24 or resseq...DD48 - 9751 - 100
45VALVALGLYGLYchain D and (resseq 3:19 or resseq 21:24 or resseq...DD101 - 116104 - 119
46ILEILEILEILEchain D and (resseq 3:19 or resseq 21:24 or resseq...DD118 - 127121 - 130
51PHEPHEMETMETchain E and (resseq 3:19 or resseq 21:24 or resseq...EE3 - 196 - 22
52SERSERILEILEchain E and (resseq 3:19 or resseq 21:24 or resseq...EE-1 - 1272 - 130
53SERSERILEILEchain E and (resseq 3:19 or resseq 21:24 or resseq...EE-1 - 1272 - 130
54SERSERILEILEchain E and (resseq 3:19 or resseq 21:24 or resseq...EE-1 - 1272 - 130
55SERSERILEILEchain E and (resseq 3:19 or resseq 21:24 or resseq...EE-1 - 1272 - 130
56ILEILEILEILEchain E and (resseq 3:19 or resseq 21:24 or resseq...EE118 - 127121 - 130
61PHEPHEMETMETchain F and (resseq 3:19 or resseq 21:24 or resseq...FF3 - 196 - 22
62ALAALALEULEUchain F and (resseq 3:19 or resseq 21:24 or resseq...FF21 - 2424 - 27
63ILEILEGLNGLNchain F and (resseq 3:19 or resseq 21:24 or resseq...FF29 - 4332 - 46
64PHEPHEASNASNchain F and (resseq 3:19 or resseq 21:24 or resseq...FF48 - 9751 - 100
65VALVALGLYGLYchain F and (resseq 3:19 or resseq 21:24 or resseq...FF101 - 116104 - 119
66ILEILEILEILEchain F and (resseq 3:19 or resseq 21:24 or resseq...FF118 - 127121 - 130
71PHEPHEMETMETchain G and (resseq 3:19 or resseq 21:24 or resseq...GG3 - 196 - 22
72METMETILEILEchain G and (resseq 3:19 or resseq 21:24 or resseq...GG1 - 1274 - 130
73METMETILEILEchain G and (resseq 3:19 or resseq 21:24 or resseq...GG1 - 1274 - 130
74METMETILEILEchain G and (resseq 3:19 or resseq 21:24 or resseq...GG1 - 1274 - 130
75METMETILEILEchain G and (resseq 3:19 or resseq 21:24 or resseq...GG1 - 1274 - 130
76ILEILEILEILEchain G and (resseq 3:19 or resseq 21:24 or resseq...GG118 - 127121 - 130
81PHEPHEMETMETchain H and (resseq 3:19 or resseq 21:24 or resseq...HH3 - 196 - 22
82ALAALALEULEUchain H and (resseq 3:19 or resseq 21:24 or resseq...HH21 - 2424 - 27
83ILEILEGLNGLNchain H and (resseq 3:19 or resseq 21:24 or resseq...HH29 - 4332 - 46
84PHEPHEASNASNchain H and (resseq 3:19 or resseq 21:24 or resseq...HH48 - 9751 - 100
85VALVALGLYGLYchain H and (resseq 3:19 or resseq 21:24 or resseq...HH101 - 116104 - 119
86ILEILEILEILEchain H and (resseq 3:19 or resseq 21:24 or resseq...HH118 - 127121 - 130
91PHEPHEMETMETchain I and (resseq 3:19 or resseq 21:24 or resseq...II3 - 196 - 22
92METMETILEILEchain I and (resseq 3:19 or resseq 21:24 or resseq...II1 - 1274 - 130
93METMETILEILEchain I and (resseq 3:19 or resseq 21:24 or resseq...II1 - 1274 - 130
94METMETILEILEchain I and (resseq 3:19 or resseq 21:24 or resseq...II1 - 1274 - 130
95METMETILEILEchain I and (resseq 3:19 or resseq 21:24 or resseq...II1 - 1274 - 130
96ILEILEILEILEchain I and (resseq 3:19 or resseq 21:24 or resseq...II118 - 127121 - 130
101PHEPHEMETMETchain J and (resseq 3:19 or resseq 21:24 or resseq...JJ3 - 196 - 22
102ALAALALEULEUchain J and (resseq 3:19 or resseq 21:24 or resseq...JJ21 - 2424 - 27
103ILEILEGLNGLNchain J and (resseq 3:19 or resseq 21:24 or resseq...JJ29 - 4332 - 46
104PHEPHEASNASNchain J and (resseq 3:19 or resseq 21:24 or resseq...JJ48 - 9751 - 100
105VALVALGLYGLYchain J and (resseq 3:19 or resseq 21:24 or resseq...JJ101 - 116104 - 119
106ILEILEILEILEchain J and (resseq 3:19 or resseq 21:24 or resseq...JJ118 - 127121 - 130
111PHEPHEMETMETchain K and (resseq 3:19 or resseq 21:24 or resseq...KK3 - 196 - 22
112METMETILEILEchain K and (resseq 3:19 or resseq 21:24 or resseq...KK1 - 1274 - 130
113METMETILEILEchain K and (resseq 3:19 or resseq 21:24 or resseq...KK1 - 1274 - 130
114METMETILEILEchain K and (resseq 3:19 or resseq 21:24 or resseq...KK1 - 1274 - 130
115METMETILEILEchain K and (resseq 3:19 or resseq 21:24 or resseq...KK1 - 1274 - 130
116ILEILEILEILEchain K and (resseq 3:19 or resseq 21:24 or resseq...KK118 - 127121 - 130
121PHEPHEMETMETchain L and (resseq 3:19 or resseq 21:24 or resseq...LL3 - 196 - 22
122ALAALALEULEUchain L and (resseq 3:19 or resseq 21:24 or resseq...LL21 - 2424 - 27
123ILEILEGLNGLNchain L and (resseq 3:19 or resseq 21:24 or resseq...LL29 - 4332 - 46
124PHEPHEASNASNchain L and (resseq 3:19 or resseq 21:24 or resseq...LL48 - 9751 - 100
125VALVALGLYGLYchain L and (resseq 3:19 or resseq 21:24 or resseq...LL101 - 116104 - 119
126ILEILEILEILEchain L and (resseq 3:19 or resseq 21:24 or resseq...LL118 - 127121 - 130
131PHEPHEMETMETchain M and (resseq 3:19 or resseq 21:24 or resseq...MM3 - 196 - 22
132SERSERILEILEchain M and (resseq 3:19 or resseq 21:24 or resseq...MM-1 - 1272 - 130
133SERSERILEILEchain M and (resseq 3:19 or resseq 21:24 or resseq...MM-1 - 1272 - 130
134SERSERILEILEchain M and (resseq 3:19 or resseq 21:24 or resseq...MM-1 - 1272 - 130
135SERSERILEILEchain M and (resseq 3:19 or resseq 21:24 or resseq...MM-1 - 1272 - 130
136ILEILEILEILEchain M and (resseq 3:19 or resseq 21:24 or resseq...MM118 - 127121 - 130
141PHEPHEMETMETchain N and (resseq 3:19 or resseq 21:24 or resseq...NN3 - 196 - 22
142ALAALALEULEUchain N and (resseq 3:19 or resseq 21:24 or resseq...NN21 - 2424 - 27
143ILEILEGLNGLNchain N and (resseq 3:19 or resseq 21:24 or resseq...NN29 - 4332 - 46
144PHEPHEASNASNchain N and (resseq 3:19 or resseq 21:24 or resseq...NN48 - 9751 - 100
145VALVALGLYGLYchain N and (resseq 3:19 or resseq 21:24 or resseq...NN101 - 116104 - 119
146ILEILEILEILEchain N and (resseq 3:19 or resseq 21:24 or resseq...NN118 - 127121 - 130
151PHEPHEMETMETchain O and (resseq 3:19 or resseq 21:24 or resseq...OO3 - 196 - 22
152METMETILEILEchain O and (resseq 3:19 or resseq 21:24 or resseq...OO1 - 1274 - 130
153METMETILEILEchain O and (resseq 3:19 or resseq 21:24 or resseq...OO1 - 1274 - 130
154METMETILEILEchain O and (resseq 3:19 or resseq 21:24 or resseq...OO1 - 1274 - 130
155METMETILEILEchain O and (resseq 3:19 or resseq 21:24 or resseq...OO1 - 1274 - 130
156ILEILEILEILEchain O and (resseq 3:19 or resseq 21:24 or resseq...OO118 - 127121 - 130
161PHEPHEMETMETchain P and (resseq 3:19 or resseq 21:24 or resseq...PP3 - 196 - 22
162ALAALALEULEUchain P and (resseq 3:19 or resseq 21:24 or resseq...PP21 - 2424 - 27
163ILEILEGLNGLNchain P and (resseq 3:19 or resseq 21:24 or resseq...PP29 - 4332 - 46
164PHEPHEASNASNchain P and (resseq 3:19 or resseq 21:24 or resseq...PP48 - 9751 - 100
165VALVALGLYGLYchain P and (resseq 3:19 or resseq 21:24 or resseq...PP101 - 116104 - 119
166ILEILEILEILEchain P and (resseq 3:19 or resseq 21:24 or resseq...PP118 - 127121 - 130

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Components

#1: Protein
Fatty acid-binding protein, liver / Fatty acid-binding protein 1 / Liver-type fatty acid-binding protein / L-FABP


Mass: 14508.641 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP1, FABPL / Plasmid: PET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07148
#2: Chemical
ChemComp-WII / 2-{[(3P)-3-(5-tert-butyl-1,2,4-oxadiazol-3-yl)-4,5,6,7-tetrahydro-1-benzothiophen-2-yl]carbamoyl}cyclopent-1-ene-1-carboxylic acid


Mass: 415.506 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C21H25N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: protein in 25mM Tris/HCl pH 7.5 100mM NaCl, see also PMID 27658368

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99987 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.6→46.62 Å / Num. obs: 70716 / % possible obs: 98.9 % / Redundancy: 3.461 % / Biso Wilson estimate: 55.05 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.104 / Χ2: 0.862 / Net I/σ(I): 9.87 / Num. measured all: 244750 / Scaling rejects: 20
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.673.5541.0331.3118415525151820.5731.21698.7
2.67-2.743.5160.8631.5517824513850700.6741.01998.7
2.74-2.823.3630.6981.8416686503349610.7270.83298.6
2.82-2.913.4250.5222.516308482047620.8340.6298.8
2.91-33.5020.4013.2316294470946530.8930.47398.8
3-3.113.5970.3034.3316228455745110.9340.35699
3.11-3.223.5590.2335.3915526440143630.9590.27599.1
3.22-3.363.4750.1617.2714552422741880.9820.1999.1
3.36-3.513.3170.1119.6513398407640390.990.13299.1
3.51-3.683.3950.0911.7713031387138380.9930.10799.1
3.68-3.883.5820.07813.613060368536460.9960.09198.9
3.88-4.113.5250.06116.5212232350334700.9970.07299.1
4.11-4.393.4320.04919.2611198329232630.9970.05899.1
4.39-4.753.2820.04221.169834305229960.9980.0598.2
4.75-5.23.4620.04221.669630282527820.9980.0598.5
5.2-5.813.4860.0421.828871256825450.9980.04799.1
5.81-6.713.3330.04418.967473226222420.9980.05299.1
6.71-8.223.4040.03321.966494192019080.9990.0499.4
8.22-11.633.4080.02724.495050149914820.9990.03298.9
11.63-46.6233.2470.02324.8826468408150.9990.02897

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_989refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 2.6→46.623 Å / FOM work R set: 0.7532 / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.84 / Stereochemistry target values: ML
Details: clear electron density for ligand and a thiocyanate ion from the crystallization mixture. co-crystallized complex. pseudo-orthorhombic but cannot refine - have to drop symmetry to p21 with beta=90.1deg.
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 3578 5.06 %RANDOM
Rwork0.2073 67082 --
obs0.2091 70660 98.84 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.046 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso max: 158.07 Å2 / Biso mean: 53.92 Å2 / Biso min: 25.01 Å2
Baniso -1Baniso -2Baniso -3
1--1.0673 Å20 Å2-0.3875 Å2
2--8.0747 Å2-0 Å2
3----7.0074 Å2
Refinement stepCycle: final / Resolution: 2.6→46.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16008 0 512 261 16781
Biso mean--55.93 45.94 -
Num. residues----2043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816718
X-RAY DIFFRACTIONf_angle_d1.10722415
X-RAY DIFFRACTIONf_chiral_restr0.0622538
X-RAY DIFFRACTIONf_plane_restr0.0042817
X-RAY DIFFRACTIONf_dihedral_angle_d15.5176379
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A877X-RAY DIFFRACTIONPOSITIONAL0.037
12B877X-RAY DIFFRACTIONPOSITIONAL0.037
13C877X-RAY DIFFRACTIONPOSITIONAL0.047
14D877X-RAY DIFFRACTIONPOSITIONAL0.061
15E877X-RAY DIFFRACTIONPOSITIONAL0.055
16F877X-RAY DIFFRACTIONPOSITIONAL0.047
17G877X-RAY DIFFRACTIONPOSITIONAL0.062
18H877X-RAY DIFFRACTIONPOSITIONAL0.069
19I877X-RAY DIFFRACTIONPOSITIONAL0.022
110J877X-RAY DIFFRACTIONPOSITIONAL0.039
111K877X-RAY DIFFRACTIONPOSITIONAL0.048
112L877X-RAY DIFFRACTIONPOSITIONAL0.062
113M877X-RAY DIFFRACTIONPOSITIONAL0.07
114N877X-RAY DIFFRACTIONPOSITIONAL0.047
115O877X-RAY DIFFRACTIONPOSITIONAL0.061
116P877X-RAY DIFFRACTIONPOSITIONAL0.055
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.63420.40841280.35832615274399
2.6342-2.67030.38041260.35122504263099
2.6703-2.70840.3931330.352627276099
2.7084-2.74890.35441360.33362531266798
2.7489-2.79180.38131270.34952581270899
2.7918-2.83760.39921440.3142535267999
2.8376-2.88650.29851360.30312594273099
2.8865-2.9390.32811290.27742577270699
2.939-2.99550.31811290.28052597272699
2.9955-3.05660.34031340.27252574270899
3.0566-3.12310.31691490.27172576272599
3.1231-3.19570.34261350.26542531266699
3.1957-3.27560.28451460.24032615276199
3.2756-3.36410.27531210.23372564268599
3.3641-3.46310.25831400.22942597273799
3.4631-3.57480.23561470.21432569271699
3.5748-3.70260.25981490.20972611276099
3.7026-3.85070.22151560.19562548270499
3.8507-4.02590.23261260.18392584271099
4.0259-4.2380.2221450.17182629277499
4.238-4.50340.21091130.15942597271099
4.5034-4.85070.19031390.15932593273299
4.8507-5.33820.21061300.1522607273799
5.3382-6.10920.17091590.14872616277599
6.1092-7.69140.17741590.156925942753100
7.6914-46.63010.16821420.16382516265894

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