[English] 日本語
Yorodumi
- PDB-5ahj: Yeast 20S proteasome in complex with Macyranone A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ahj
TitleYeast 20S proteasome in complex with Macyranone A
Components
  • (PROTEASOME SUBUNIT ALPHA TYPE- ...) x 6
  • (PROTEASOME SUBUNIT BETA TYPE- ...) x 6
  • 20S PROTEASOMEProteasome
  • PROBABLE PROTEASOME SUBUNIT ALPHA TYPE-7
KeywordsHYDROLASE / PROTEASOME / NATURAL PRODUCT / TARGET IDENTIFICATION / INHIBITION / BINDING ANALYSIS
Function / homology
Function and homology information


proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ub-specific processing proteases / proteasome storage granule / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex ...proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ub-specific processing proteases / proteasome storage granule / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / Neutrophil degranulation / proteasome complex / proteasomal protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol / cytoplasm
Similarity search - Function
Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. ...Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-7IM / Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 ...Chem-7IM / Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsEtzbach, L. / Plaza, A. / Dubiella, C. / Groll, M. / Kaiser, M. / Mueller, R.
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Macyranones: Structure, Biosynthesis, and Binding Mode of an Unprecedented Epoxyketone that Targets the 20S Proteasome.
Authors: Keller, L. / Plaza, A. / Dubiella, C. / Groll, M. / Kaiser, M. / Muller, R.
History
DepositionFeb 6, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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_conn_type / 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_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.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.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.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_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEASOME SUBUNIT ALPHA TYPE-2
B: PROTEASOME SUBUNIT ALPHA TYPE-3
C: PROTEASOME SUBUNIT ALPHA TYPE-4
D: PROTEASOME SUBUNIT ALPHA TYPE-5
E: PROTEASOME SUBUNIT ALPHA TYPE-6
F: PROBABLE PROTEASOME SUBUNIT ALPHA TYPE-7
G: PROTEASOME SUBUNIT ALPHA TYPE-1
H: PROTEASOME SUBUNIT BETA TYPE-2
I: PROTEASOME SUBUNIT BETA TYPE-3
J: PROTEASOME SUBUNIT BETA TYPE-4
K: PROTEASOME SUBUNIT BETA TYPE-5
L: PROTEASOME SUBUNIT BETA TYPE-6
M: PROTEASOME SUBUNIT BETA TYPE-7
N: 20S PROTEASOME
O: PROTEASOME SUBUNIT ALPHA TYPE-2
P: PROTEASOME SUBUNIT ALPHA TYPE-3
Q: PROTEASOME SUBUNIT ALPHA TYPE-4
R: PROTEASOME SUBUNIT ALPHA TYPE-5
S: PROTEASOME SUBUNIT ALPHA TYPE-6
T: PROBABLE PROTEASOME SUBUNIT ALPHA TYPE-7
U: PROTEASOME SUBUNIT ALPHA TYPE-1
V: PROTEASOME SUBUNIT BETA TYPE-2
W: PROTEASOME SUBUNIT BETA TYPE-3
X: PROTEASOME SUBUNIT BETA TYPE-4
Y: PROTEASOME SUBUNIT BETA TYPE-5
Z: PROTEASOME SUBUNIT BETA TYPE-6
a: PROTEASOME SUBUNIT BETA TYPE-7
b: 20S PROTEASOME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)732,90747
Polymers728,54028
Non-polymers4,36719
Water5,999333
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area119890 Å2
ΔGint-460.8 kcal/mol
Surface area213370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.670, 300.700, 143.990
Angle α, β, γ (deg.)90.00, 112.52, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21O
12B
22P
13C
23Q
14D
24R
15E
25S
16F
26T
17G
27U
18H
28V
19I
29W
110J
210X
111K
211Y
112L
212Z
113M
213a
114N
214b

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 300
2111O1 - 300
1121B1 - 300
2121P1 - 300
1131C1 - 300
2131Q1 - 300
1141D1 - 300
2141R1 - 300
1151E1 - 300
2151S1 - 300
1161F1 - 300
2161T1 - 300
1171G1 - 300
2171U1 - 300
1181H1 - 300
2181V1 - 300
1191I1 - 300
2191W1 - 300
11101J1 - 300
21101X1 - 300
11111K1 - 300
21111Y1 - 300
11121L1 - 300
21121Z1 - 300
11131M1 - 300
21131a1 - 300
11141N1 - 300
21141b1 - 300

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999402, -0.00502, 0.03421), (-0.001103, -0.984273, -0.176651), (0.034559, -0.176583, 0.983679)66.29247, -289.35196, -26.48555

-
Components

-
PROTEASOME SUBUNIT ALPHA TYPE- ... , 6 types, 12 molecules AOBPCQDRESGU

#1: Protein PROTEASOME SUBUNIT ALPHA TYPE-2 / / MACROPAIN SUBUNIT Y7 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT Y7 / PROTEASOME COMPONENT Y7 / ...MACROPAIN SUBUNIT Y7 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT Y7 / PROTEASOME COMPONENT Y7 / PROTEINASE YSCE SUBUNIT 7


Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P23639, proteasome endopeptidase complex
#2: Protein PROTEASOME SUBUNIT ALPHA TYPE-3 / / MACROPAIN SUBUNIT Y13 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT Y13 / PROTEASOME COMPONENT Y13 ...MACROPAIN SUBUNIT Y13 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT Y13 / PROTEASOME COMPONENT Y13 / PROTEINASE YSCE SUBUNIT 13


Mass: 28748.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P23638, proteasome endopeptidase complex
#3: Protein PROTEASOME SUBUNIT ALPHA TYPE-4 / / MACROPAIN SUBUNIT PRE6 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PRE6 / PROTEASOME COMPONENT ...MACROPAIN SUBUNIT PRE6 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PRE6 / PROTEASOME COMPONENT PRE6 / PROTEINASE YSCE SUBUNIT PRE6


Mass: 28478.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P40303, proteasome endopeptidase complex
#4: Protein PROTEASOME SUBUNIT ALPHA TYPE-5 / / MACROPAIN SUBUNIT PUP2 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PUP2 / PROTEASOME COMPONENT ...MACROPAIN SUBUNIT PUP2 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PUP2 / PROTEASOME COMPONENT PUP2 / PROTEINASE YSCE SUBUNIT PUP2


Mass: 28649.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P32379, proteasome endopeptidase complex
#5: Protein PROTEASOME SUBUNIT ALPHA TYPE-6 / / MACROPAIN SUBUNIT PRE5 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PRE5 / PROTEASOME COMPONENT ...MACROPAIN SUBUNIT PRE5 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PRE5 / PROTEASOME COMPONENT PRE5 / PROTEINASE YSCE SUBUNIT PRE5


Mass: 25634.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P40302, proteasome endopeptidase complex
#7: Protein PROTEASOME SUBUNIT ALPHA TYPE-1 / / MACROPAIN SUBUNIT C7-ALPHA / MULTICATALYTIC ENDOPEPTIDASE COMPLEX C7 / PROTEASOME COMPONENT C7- ...MACROPAIN SUBUNIT C7-ALPHA / MULTICATALYTIC ENDOPEPTIDASE COMPLEX C7 / PROTEASOME COMPONENT C7-ALPHA / PROTEASOME COMPONENT Y8 / PROTEINASE YSCE SUBUNIT 7 / SCL1 SUPPRESSOR PROTEIN


Mass: 28033.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P21243, proteasome endopeptidase complex

-
Protein , 2 types, 4 molecules FTNb

#6: Protein PROBABLE PROTEASOME SUBUNIT ALPHA TYPE-7 / MACROPAIN SUBUNIT C1 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C1 / PROTEASOME COMPONENT C1 / ...MACROPAIN SUBUNIT C1 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C1 / PROTEASOME COMPONENT C1 / PROTEINASE YSCE SUBUNIT 1


Mass: 31575.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P21242, proteasome endopeptidase complex
#14: Protein 20S PROTEASOME / Proteasome / MACROPAIN SUBUNIT PRE3 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PRE3 / PROTEASOME COMPONENT ...MACROPAIN SUBUNIT PRE3 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PRE3 / PROTEASOME COMPONENT PRE3 / PROTEINASE YSCE SUBUNIT PRE3


Mass: 21517.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P38624, proteasome endopeptidase complex

-
PROTEASOME SUBUNIT BETA TYPE- ... , 6 types, 12 molecules HVIWJXKYLZMa

#8: Protein PROTEASOME SUBUNIT BETA TYPE-2 / PSMB2 / MACROPAIN SUBUNIT PUP1 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PUP1 / PROTEASOME COMPONENT ...MACROPAIN SUBUNIT PUP1 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PUP1 / PROTEASOME COMPONENT PUP1 / PROTEINASE YSCE SUBUNIT PUP1


Mass: 25114.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P25043, proteasome endopeptidase complex
#9: Protein PROTEASOME SUBUNIT BETA TYPE-3 / PSMB3 / MACROPAIN SUBUNIT PUP3 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PUP3 / PROTEASOME COMPONENT PUP3


Mass: 22627.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P25451, proteasome endopeptidase complex
#10: Protein PROTEASOME SUBUNIT BETA TYPE-4 / PSMB4 / MACROPAIN SUBUNIT C11 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C11 / PROTEASOME COMPONENT C11 ...MACROPAIN SUBUNIT C11 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C11 / PROTEASOME COMPONENT C11 / PROTEINASE YSCE SUBUNIT 11


Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P22141, proteasome endopeptidase complex
#11: Protein PROTEASOME SUBUNIT BETA TYPE-5 / PSMB5 / MACROPAIN SUBUNIT PRE2 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PRE2 / PROTEASOME COMPONENT ...MACROPAIN SUBUNIT PRE2 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PRE2 / PROTEASOME COMPONENT PRE2 / PROTEINASE YSCE SUBUNIT PRE2


Mass: 23325.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P30656, proteasome endopeptidase complex
#12: Protein PROTEASOME SUBUNIT BETA TYPE-6 / / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C5 / PROTEASOME COMPONENT C5


Mass: 24883.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P23724, proteasome endopeptidase complex
#13: Protein PROTEASOME SUBUNIT BETA TYPE-7 / / MACROPAIN SUBUNIT PRE4 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PRE4 / PROTEASOME COMPONENT ...MACROPAIN SUBUNIT PRE4 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PRE4 / PROTEASOME COMPONENT PRE4 / PROTEINASE YSCE SUBUNIT PRE4


Mass: 25945.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P30657, proteasome endopeptidase complex

-
Non-polymers , 5 types, 352 molecules

#15: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#16: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#17: Chemical
ChemComp-7IM / N-[(2S)-3-{[(1S)-1-carboxy-2-phenylethyl]amino}-2-methyl-3-oxopropanoyl]-L-threonyl-N-[(3S,4S)-1,3-dihydroxy-6-methylheptan-4-yl]-L-allothreoninamide / Macyranone-A


Mass: 610.696 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C29H46N4O10
#18: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#19: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.67 Å3/Da / Density % sol: 66.48 % / Description: NONE
Crystal growpH: 6.8 / Details: 100 MM MES, PH 7.0 12% MPD 20 MM MGAC2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2014
RadiationMonochromator: LN2 COOLED FIXED-EXIT. SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 250454 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.7 / % possible all: 97

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENRTY 1RYP

1ryp


Resolution: 2.8→15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 32.325 / SU ML: 0.26 / Cross valid method: THROUGHOUT / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21894 12523 5 %RANDOM
Rwork0.19407 ---
obs0.19531 237931 97.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.811 Å2
Baniso -1Baniso -2Baniso -3
1-5.33 Å20 Å2-3.16 Å2
2---8.05 Å20 Å2
3---3 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49303 0 293 333 49929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01950495
X-RAY DIFFRACTIONr_bond_other_d0.0030.0248250
X-RAY DIFFRACTIONr_angle_refined_deg0.9551.96968332
X-RAY DIFFRACTIONr_angle_other_deg0.7623.002111108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.07456306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05224.4082246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.734158736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.33115284
X-RAY DIFFRACTIONr_chiral_restr0.0550.27716
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0257198
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0211310
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3234.62725313
X-RAY DIFFRACTIONr_mcbond_other2.3234.62625312
X-RAY DIFFRACTIONr_mcangle_it2.9886.92631588
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2095.02825182
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr0.859398745
X-RAY DIFFRACTIONr_sphericity_free36.7925237
X-RAY DIFFRACTIONr_sphericity_bonded6.254597942
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3099tight positional00.05
11A3283tight positional0.070.05
11A3439tight positional0.010.05
11A3618tight positional0.010.05
11A3031tight positional0.010.05
12O3099tight positional00.05
12O3283tight positional0.070.05
12O3439tight positional0.010.05
12O3618tight positional0.010.05
12O3031tight positional0.010.05
11A3795tight thermal4.660.5
12O3795tight thermal4.660.5
21B3756tight thermal4.50.5
22P3756tight thermal4.50.5
31C3729tight thermal12.530.5
32Q3729tight thermal12.530.5
41D3578tight thermal6.380.5
42R3578tight thermal6.380.5
51E3509tight thermal8.620.5
52S3509tight thermal8.620.5
61F3749tight thermal6.130.5
62T3749tight thermal6.130.5
71G3769tight thermal3.130.5
72U3769tight thermal3.130.5
81H3418tight thermal2.780.5
82V3418tight thermal2.780.5
91I3119tight thermal3.130.5
92W3119tight thermal3.130.5
101J3099tight thermal3.110.5
102X3099tight thermal3.110.5
111K3283tight thermal3.370.5
112Y3283tight thermal3.370.5
121L3439tight thermal3.040.5
122Z3439tight thermal3.040.5
131M3618tight thermal2.750.5
132a3618tight thermal2.750.5
141N3031tight thermal2.340.5
142b3031tight thermal2.340.5
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 889 -
Rwork0.343 16890 -
obs--97.15 %
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)
10.1127-0.08650.04130.2165-0.12250.0821-0.06430.1007-0.050.14420.0168-0.1247-0.1093-0.03630.04750.2799-0.05910.01880.2608-0.05360.338466.687-92.144146.0279
20.1612-0.06680.03340.160.10520.2389-0.1374-0.0443-0.0972-0.1098-0.00630.0626-0.16990.09150.14370.3939-0.0770.1080.29140.08810.28859.2358-87.90716.444
30.22830.18090.02360.15050.01430.0141-0.0758-0.02030.0594-0.10410.01460.03050.02430.02520.06120.3875-0.00190.01250.23910.07820.231432.0298-87.5821.0784
40.2376-0.10370.03950.1408-0.05560.086-0.0331-0.095-0.0675-0.08080.00340.1841-0.02160.08730.02970.29820.0735-0.15980.20930.09550.42922.8159-90.336213.6361
50.0160.0321-0.00710.1538-0.11410.2121-0.0173-0.02260.00710.0066-0.01120.1492-0.07030.05290.02840.1680.09210.10180.23750.01260.527-3.5113-94.728845.6134
60.14880.0570.06270.03150.01530.0805-0.0342-0.02180.00750.0343-0.01650.0407-0.0453-0.01340.05070.43590.04380.25330.2708-0.09370.251214.9434-95.387269.8352
70.04580.00430.01570.05380.07310.21690.00660.081-0.01010.1091-0.012-0.031-0.0121-0.02210.00540.5192-0.031-0.03080.1746-0.06870.174247.4043-93.565371.1591
80.0355-0.0196-0.03660.20030.00820.03860.02690.09980.01250.1511-0.0354-0.2056-0.0273-0.10.00850.2116-0.0185-0.06390.3298-0.04980.340867.2376-130.19148.0799
90.0091-0.01690.01150.6076-0.08070.02470.0195-0.0577-0.0016-0.1142-0.0109-0.1287-0.0092-0.0541-0.00860.1521-0.01370.23610.4021-0.00210.372368.2021-127.567420.7675
100.061-0.0562-0.00290.445-0.15810.0720.0676-0.10950.0326-0.2179-0.01190.0720.03140.0577-0.05560.3635-0.00730.15740.34450.01330.187144.5533-126.7086-0.6398
110.02490.04210.05040.35260.29090.32810.0206-0.0293-0.0204-0.15030.02250.123-0.0420.0982-0.04310.27760.0132-0.1390.28350.03840.3210.6886-131.1382.4845
120.0225-0.06310.00790.440.09960.1460.0003-0.0353-0.032-0.0620.01080.2371-0.05010.0797-0.01110.04650.02330.07870.36340.06090.5033-4.6614-134.622428.5924
130.09580.03290.08850.23480.03910.09340.04890.05810.02890.1481-0.02450.07130.0220.0186-0.02440.25230.00860.25160.37390.01240.29857.6476-138.275160.4226
140.1925-0.0121-0.11690.5153-0.01550.07870.06280.14160.0490.2517-0.0506-0.1244-0.0039-0.0859-0.01230.4456-0.0080.03340.3004-0.04010.093839.887-134.421870.5485
150.0536-0.0104-0.03290.3080.16960.12530.00680.07070.06540.08840.02210.05450.1064-0.0343-0.02880.2613-0.0793-0.09380.20720.07490.39091.8975-206.913336.5078
160.01610.0149-0.03350.06180.01540.1547-0.0275-0.0113-0.0063-0.09410.0115-0.02050.0296-0.03520.01590.3232-0.0431-0.18340.1723-0.06690.35358.3073-205.62226.4242
170.2820.07190.2410.10110.05380.30930.20470.0748-0.1062-0.0697-0.05790.11320.02280.1157-0.14680.52290.1163-0.18950.1371-0.20550.309135.442-203.3244-9.5044
180.1658-0.03610.110.15190.06560.140.1467-0.0950.0536-0.1973-0.0939-0.12410.0205-0.1008-0.05290.40520.10170.1990.2765-0.07060.323664.902-202.78682.9638
190.13760.23990.06570.45110.0790.14920.05380.0597-0.14350.08890.1334-0.290.0216-0.0713-0.18730.08710.089-0.08380.203-0.12490.704972.0375-204.022834.6274
200.17630.1106-0.08830.0807-0.01680.19460.16350.0065-0.20440.1109-0.0617-0.1646-0.0737-0.1378-0.10190.39470.0168-0.3530.12560.13260.501554.284-207.847958.9966
210.0354-0.0520.0260.2392-0.09850.0860.06170.0269-0.00960.11760.00550.0054-0.0081-0.0039-0.06720.4515-0.0401-0.12170.13690.10080.26621.8969-210.053360.8015
220.05420.07790.04450.2915-0.02840.09150.080.02320.0310.1013-0.03590.20160.04110.1054-0.04410.1286-0.01630.10830.38980.080.40561.4984-169.812145.3094
230.1187-0.06550.06790.2299-0.09360.0811-0.0059-0.05740.0214-0.14740.03830.15440.05170.0468-0.03240.151-0.0029-0.11370.31140.01070.398-0.2183-167.484817.9797
240.0941-0.22820.00280.5968-0.01050.00280.0328-0.033-0.0295-0.149-0.0070.0351-0.00510.0221-0.02570.3724-0.0016-0.07430.2563-0.04060.204122.8766-164.4602-3.8442
250.0278-0.11470.02590.4966-0.10610.03710.0323-0.02090.0081-0.1670.0145-0.03920.00270.0166-0.04670.26870.0230.23620.3811-0.06890.275556.8828-160.6364-0.7249
260.01930.0428-0.07890.2293-0.17730.34380.00390.01050.0146-0.00810.0024-0.18840.0276-0.0625-0.00630.0850.05130.09220.3623-0.05530.490172.8693-161.798625.1815
270.1125-0.00540.04830.27160.01360.06040.01460.1086-0.03940.2376-0.03-0.1369-0.0002-0.03110.01540.26470.0075-0.1360.2869-0.0070.317261.4145-163.930857.4093
280.15280.2140.08380.3980.14710.07510.11450.0823-0.03770.2838-0.0374-0.06960.0389-0.0297-0.07710.4242-0.0170.08360.31090.07210.140429.4583-169.613967.4935
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 250
2X-RAY DIFFRACTION2B1 - 244
3X-RAY DIFFRACTION3C1 - 240
4X-RAY DIFFRACTION4D1 - 242
5X-RAY DIFFRACTION5E3 - 233
6X-RAY DIFFRACTION6F2 - 244
7X-RAY DIFFRACTION7G2 - 242
8X-RAY DIFFRACTION8H1 - 222
9X-RAY DIFFRACTION9I1 - 204
10X-RAY DIFFRACTION10J1 - 195
11X-RAY DIFFRACTION11K1 - 212
12X-RAY DIFFRACTION12L1 - 222
13X-RAY DIFFRACTION13M1 - 233
14X-RAY DIFFRACTION14N1 - 196
15X-RAY DIFFRACTION15O1 - 250
16X-RAY DIFFRACTION16P1 - 244
17X-RAY DIFFRACTION17Q1 - 240
18X-RAY DIFFRACTION18R1 - 242
19X-RAY DIFFRACTION19S3 - 233
20X-RAY DIFFRACTION20T2 - 244
21X-RAY DIFFRACTION21U2 - 242
22X-RAY DIFFRACTION22V1 - 222
23X-RAY DIFFRACTION23W1 - 204
24X-RAY DIFFRACTION24X1 - 195
25X-RAY DIFFRACTION25Y1 - 212
26X-RAY DIFFRACTION26Z1 - 222
27X-RAY DIFFRACTION27a1 - 233
28X-RAY DIFFRACTION28b1 - 196

+
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