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- PDB-5l61: Yeast 20S proteasome with human beta5c (1-138) and human beta6 (9... -

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Basic information

Entry
Database: PDB / ID: 5l61
TitleYeast 20S proteasome with human beta5c (1-138) and human beta6 (99-132) in complex with epoxyketone inhibitor 14
Components
  • (Proteasome subunit alpha type- ...) x 6
  • (Proteasome subunit beta type- ...) x 7
  • Probable proteasome subunit alpha type-7
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex / Proteasome / Mutant / Inhibitor / Binding Analysis
Function / homology
Function and homology information


Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / 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 ...Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / 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 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Degradation of DVL / proteasomal protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Degradation of AXIN / Defective CFTR causes cystic fibrosis / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Negative regulation of NOTCH4 signaling / G2/M Checkpoints / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / ABC-family proteins mediated transport / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / UCH proteinases / The role of GTSE1 in G2/M progression after G2 checkpoint / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / peptidase activity / ER-Phagosome pathway / proteasome-mediated ubiquitin-dependent protein catabolic process / secretory granule lumen / endopeptidase activity / response to oxidative stress / ficolin-1-rich granule lumen / Ub-specific processing proteases / mRNA binding / centrosome / Neutrophil degranulation / endoplasmic reticulum membrane / mitochondrion / proteolysis / extracellular exosome / extracellular region / nucleoplasm / 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-6N5 / Proteasome subunit beta type-1 / 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 ...Chem-6N5 / Proteasome subunit beta type-1 / 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-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 speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGroll, M. / Huber, E.M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationGR1861/10-1 Germany
CitationJournal: EMBO J. / Year: 2016
Title: A humanized yeast proteasome identifies unique binding modes of inhibitors for the immunosubunit beta 5i.
Authors: Huber, E.M. / Heinemeyer, W. / de Bruin, G. / Overkleeft, H.S. / Groll, M.
History
DepositionMay 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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,Proteasome subunit beta type-5
L: Proteasome subunit beta type-6,Proteasome subunit beta type-1,Proteasome subunit beta type-6,Proteasome subunit beta type-1,Proteasome subunit beta type-6
M: Proteasome subunit beta type-7
N: Proteasome subunit beta type-1
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,Proteasome subunit beta type-5
Z: Proteasome subunit beta type-6,Proteasome subunit beta type-1,Proteasome subunit beta type-6,Proteasome subunit beta type-1,Proteasome subunit beta type-6
a: Proteasome subunit beta type-7
b: Proteasome subunit beta type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)733,29247
Polymers730,94528
Non-polymers2,34719
Water4,846269
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.670, 300.680, 145.680
Angle α, β, γ (deg.)90.00, 112.84, 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(-0.999641, -0.000673, 0.026776), (-0.003925, -0.985217, -0.171268), (0.026496, -0.171312, 0.984861)67.75457, -289.40842, -26.0757

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Components

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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 (strain ATCC 204508 / S288c) (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 (strain ATCC 204508 / S288c) (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 (strain ATCC 204508 / S288c) (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 (strain ATCC 204508 / S288c) (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 (strain ATCC 204508 / S288c) (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 (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P21243, proteasome endopeptidase complex

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Protein , 1 types, 2 molecules FT

#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 (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P21242, proteasome endopeptidase complex

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Proteasome subunit beta type- ... , 7 types, 14 molecules HVIWJXKYLZMaNb

#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 (strain ATCC 204508 / S288c) (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 (strain ATCC 204508 / S288c) (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 (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P22141, proteasome endopeptidase complex
#11: Protein Proteasome subunit beta type-5,Proteasome subunit beta type-5 / / Macropain epsilon chain / Multicatalytic endopeptidase complex epsilon chain / Proteasome chain 6 / ...Macropain epsilon chain / Multicatalytic endopeptidase complex epsilon chain / Proteasome chain 6 / Proteasome epsilon chain / Proteasome subunit MB1 / Proteasome subunit X / Macropain subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2 / Proteasome component PRE2 / Proteinase YSCE subunit PRE2


Mass: 23177.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: PSMB5, LMPX, MB1, X, PRE2, DOA3, PRG1, YPR103W, P8283.10
Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P28074, UniProt: P30656, proteasome endopeptidase complex
#12: Protein Proteasome subunit beta type-6,Proteasome subunit beta type-1,Proteasome subunit beta type-6,Proteasome subunit beta type-1,Proteasome subunit beta type-6 / / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Macropain subunit C5 / ...Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Proteasome gamma chain / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Proteasome gamma chain / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5


Mass: 24979.010 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Homo sapiens (human), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PRE7, PRS3, PTS1, YBL041W, YBL0407, PSMB1, PSC5
Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P23724, UniProt: P20618, 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: 27200.893 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P30657, proteasome endopeptidase complex
#14: Protein Proteasome subunit beta type-1 / PSMB1 / 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 (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P38624, proteasome endopeptidase complex

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Non-polymers , 5 types, 288 molecules

#15: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#16: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#17: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#18: Chemical ChemComp-6N5 / ~{N}-[(2~{S})-1-[[(2~{S})-3-(4-methoxyphenyl)-1-[[(2~{S},3~{S},4~{R})-4-methyl-3,5-bis(oxidanyl)-1-phenyl-pentan-2-yl]amino]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-propan-2-yl]-1-methyl-5~{H}-indene-2-carboxamide


Mass: 613.743 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H43N3O6
#19: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O

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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: 3.67 Å3/Da / Density % sol: 66.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 20 mM MgAC2, 13% MPD, 0.1 M MES / PH range: 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 29, 2015
RadiationMonochromator: LN2 COOLED FIXED-EXIT. SI(111) MONOCHROMATOR / 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: 256409 / % possible obs: 97.3 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 15.3
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 3.4 / % possible all: 96.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMAC5.7.0032refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CZ4

5cz4


Resolution: 2.8→15 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 24.721 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R Free: 0.267 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20537 12821 5 %RANDOM
Rwork0.17877 ---
obs0.18011 243587 97.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 63.357 Å2
Baniso -1Baniso -2Baniso -3
1-3.87 Å20 Å2-1.14 Å2
2---5.48 Å2-0 Å2
3---1.54 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49366 0 151 269 49786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01950410
X-RAY DIFFRACTIONr_bond_other_d0.0020.0248184
X-RAY DIFFRACTIONr_angle_refined_deg0.921.96768200
X-RAY DIFFRACTIONr_angle_other_deg0.7563.001110942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7956312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9324.3692252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.215158754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.64715290
X-RAY DIFFRACTIONr_chiral_restr0.050.27670
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0257188
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0211310
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_it2.3075.4325338
X-RAY DIFFRACTIONr_mcbond_other2.3075.4325337
X-RAY DIFFRACTIONr_mcangle_it3.0678.1331620
X-RAY DIFFRACTIONr_mcangle_other3.0678.1331621
X-RAY DIFFRACTIONr_scbond_it2.3045.89625072
X-RAY DIFFRACTIONr_scbond_other2.3045.89625072
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8128.66836581
X-RAY DIFFRACTIONr_long_range_B_refined3.50542.62354105
X-RAY DIFFRACTIONr_long_range_B_other3.49342.62254076
X-RAY DIFFRACTIONr_rigid_bond_restr1.312398594
X-RAY DIFFRACTIONr_sphericity_free37.2245187
X-RAY DIFFRACTIONr_sphericity_bonded14.923597783
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3099TIGHT POSITIONAL00.05
1A3271TIGHT POSITIONAL0.020.05
1A3449TIGHT POSITIONAL00.05
1A3618TIGHT POSITIONAL00.05
1A2949TIGHT POSITIONAL00.05
1A3795TIGHT THERMAL3.940.5
2B3756TIGHT THERMAL3.450.5
3C3729TIGHT THERMAL7.70.5
4D3578TIGHT THERMAL7.620.5
5E3509TIGHT THERMAL4.770.5
6F3749TIGHT THERMAL5.80.5
7G3770TIGHT THERMAL4.110.5
8H3403TIGHT THERMAL3.020.5
9I3119TIGHT THERMAL2.750.5
10J3099TIGHT THERMAL2.570.5
11K3271TIGHT THERMAL3.10.5
12L3449TIGHT THERMAL30.5
13M3618TIGHT THERMAL2.860.5
14N2949TIGHT THERMAL2.270.5
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 904 -
Rwork0.304 17173 -
obs--96.35 %
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)
10.00220.00020.00030.0028-0.00150.0029-0.00610.0069-0.00440.00240.0043-0.0155-0.0056-0.01130.00180.1018-0.0072-0.00340.0783-0.00470.108267.1621-92.199346.2333
20.01510.01240.00870.01050.00770.0085-0.0196-0.0060.0092-0.020.00040.0094-0.00940.00980.01920.0722-0.00740.02550.07910.00980.093159.8693-88.059116.5191
30.00410.0063-0.0090.0112-0.01790.03670.0093-0.0024-0.00240.01160.00570.00310.0077-0.0076-0.0150.10350.0057-0.0030.07910.00540.10132.4408-87.68211.2154
40.0215-0.01020.00940.0112-0.0030.0074-0.0016-0.0145-0.0035-0.01090.0020.0228-0.012-0.001-0.00040.07440.0182-0.00050.05880.01280.10423.2025-90.041913.8513
50.0034-0.00350.01250.014-0.01920.0634-0.00410.00580.00010.00590.00240.0307-0.0042-0.00050.00170.04840.01610.02040.07210.00010.1206-3.0315-94.349945.8714
60.0037-0.0009-0.00010.00210.00110.0021-0.00130.0047-0.00830.0117-0.00850.00880.0080.00260.00990.11240.00140.02940.0677-0.01330.095415.4481-94.949970.0709
70.0150.0004-0.01670.00740.00530.02480.01570.0195-0.00290.0231-0.0133-0.012-0.0014-0.0305-0.00240.1198-0.0077-0.00160.0407-0.01080.093947.9469-93.466171.323
80.00370.00190.0050.02710.01290.03610.00910.0036-0.00060.0289-0.002-0.0408-0.0027-0.0287-0.00710.0886-0.0021-0.00590.0519-0.01170.101167.944-129.631747.8062
90.0286-0.0737-0.01850.19540.04830.01210.00540.00060.00090.0003-0.0031-0.0162-0.0028-0.0011-0.00230.0787-0.00040.030.0740.00310.09268.5847-127.672721.1746
100.051-0.0446-0.01910.04560.01660.00880.0032-0.00960.013-0.0159-0.00050.00050.0098-0.0027-0.00270.105-0.00670.01180.07520.01320.079544.7946-126.7979-0.2569
110.01630.0312-0.00930.0675-0.01510.0076-0.0118-0.00780.022-0.03440.01390.05430.01940.0125-0.00210.07310.0136-0.01450.0670.01010.089310.8285-130.88573.2786
120.0323-0.01450.04010.017-0.020.05580.00050.0042-0.01040.01370.00020.0313-0.01830.0168-0.00070.07350.00740.00540.05490.02080.1022-4.499-134.368428.8607
130.0138-0.00790.00520.12030.00370.00280.01260.01830.02520.033-0.02360.01680.01240.00380.01110.0923-0.00640.02920.0644-0.00330.0937.8964-137.852660.6898
140.0734-0.016-0.02410.07920.00110.00860.02090.0152-0.00020.0275-0.0133-0.0058-0.0075-0.003-0.00770.1218-0.00610.00260.0668-0.00190.083939.9338-134.055571.1982
150.06990.0114-0.03790.0027-0.00460.0275-0.00980.01340.00010.00010.0030.00630.01320.01120.00680.1031-0.0108-0.00730.07110.00510.11291.7334-206.680837.4232
160.00060.0004-0.00080.0017-0.00020.0012-0.0051-0.00420.0005-0.0120.00580.00310.00590.0077-0.00070.1061-0.0033-0.02180.07-0.00580.10688.2496-205.78417.2251
170.01480.00920.01660.00660.01180.0223-0.0009-0.0154-0.0029-0.01160.0027-0.0061-0.0136-0.0055-0.00180.10820.0086-0.00060.0546-0.01360.07735.3847-203.7295-8.5253
180.00450.0027-0.00580.011-0.0210.0461-0.0117-0.01180.0065-0.0231-0.0096-0.02020.05070.0170.02140.0580.02610.01860.0313-0.02060.097664.8966-203.40343.6744
190.0011-0.0009-0.00030.00630.00160.00060.0028-0.00070.01060.01480.0021-0.01930.0016-0.003-0.00490.06150.0263-0.01450.0513-0.00410.120271.9623-204.442335.7675
200.03920.0247-0.00770.0181-0.00280.00520.0238-0.0014-0.02370.0208-0.0163-0.0269-0.0118-0.0111-0.00750.10720.0005-0.04190.03830.01010.093554.0391-207.907360.1129
210.0014-0.00050.00050.0032-0.0020.0013-0.00320.00890.00280.01820.00340.006-0.01210.0003-0.00010.1314-0.0047-0.0130.06550.00860.094321.641-209.85161.7851
220.0029-0.00040.00080.0117-0.00230.00410.01140.01130.00280.0093-0.00650.03140.01470.001-0.00490.099-0.00770.00640.06680.00110.1061.1407-170.087445.255
230.01440.04180.0160.16230.03240.02840.00740.0001-0.00140.0053-0.00820.020.0007-0.0080.00070.0892-0.00320.00020.0710.00580.1017-0.1637-167.581118.5907
240.0187-0.0310.01630.0542-0.02820.01650.0164-0.00260.002-0.0375-0.00950.0020.00890.0065-0.00690.10730.0044-0.01290.0793-00.09223.1122-164.806-3.2204
250.0009-0.00110.00020.00440.0010.00080.0006-0.00710.0035-0.01670.0052-0.0117-0.0058-0.0024-0.00590.08380.01230.03450.0576-0.02280.080557.1556-161.36990.154
260.0133-0.0270.00450.1228-0.00340.00220.0135-0.0046-0.00780.0244-0.0068-0.02220.0047-0.005-0.00670.07690.00910.0040.0642-0.00150.109973.1081-162.167625.6475
270.0232-0.0426-0.00260.12490.01150.00770.01510.0084-0.010.0313-0.0172-0.02010.0082-0.01950.00210.10090.0047-0.00880.0570.00150.100561.4991-164.02657.8788
280.0127-0.03290.01550.0986-0.0440.02130.0094-0.0008-0.00570.0088-0.0049-0.0001-0.0017-0.0075-0.00460.114-0.00520.00790.07030.00750.085729.7423-169.577168.3881
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999
5X-RAY DIFFRACTION5E-10 - 9999
6X-RAY DIFFRACTION6F-10 - 9999
7X-RAY DIFFRACTION7G-10 - 9999
8X-RAY DIFFRACTION8H-10 - 9999
9X-RAY DIFFRACTION9I-10 - 9999
10X-RAY DIFFRACTION10J-10 - 9999
11X-RAY DIFFRACTION11K-10 - 9999
12X-RAY DIFFRACTION12L-10 - 9999
13X-RAY DIFFRACTION13M-10 - 9999
14X-RAY DIFFRACTION14N-10 - 9999
15X-RAY DIFFRACTION15O-10 - 9999
16X-RAY DIFFRACTION16P-10 - 9999
17X-RAY DIFFRACTION17Q-10 - 9999
18X-RAY DIFFRACTION18R-10 - 9999
19X-RAY DIFFRACTION19S-10 - 9999
20X-RAY DIFFRACTION20T-10 - 9999
21X-RAY DIFFRACTION21U-10 - 9999
22X-RAY DIFFRACTION22V-10 - 9999
23X-RAY DIFFRACTION23W-10 - 9999
24X-RAY DIFFRACTION24X-10 - 9999
25X-RAY DIFFRACTION25Y-10 - 9999
26X-RAY DIFFRACTION26Z-10 - 9999
27X-RAY DIFFRACTION27a-10 - 9999
28X-RAY DIFFRACTION28b-10 - 9999

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