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- PDB-5jwe: Crystal structure of H-2Db in complex with the LCMV-derived GP92-... -

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Basic information

Entry
Database: PDB / ID: 5jwe
TitleCrystal structure of H-2Db in complex with the LCMV-derived GP92-101 peptide
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • Pre-glycoprotein polyprotein GP complex
KeywordsIMMUNE SYSTEM / Immunology / antigen presentation / MHC class I
Function / homology
Function and homology information


TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction ...TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / cis-Golgi network membrane / positive regulation of natural killer cell activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / negative regulation of natural killer cell mediated cytotoxicity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / regulation of membrane depolarization / host cell Golgi membrane / positive regulation of natural killer cell proliferation / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / positive regulation of immunoglobulin production / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / MHC class I protein binding / cellular defense response / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / Neutrophil degranulation / T cell receptor binding / 14-3-3 protein binding / lumenal side of endoplasmic reticulum membrane / peptide binding / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / positive regulation of tumor necrosis factor production / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation
Similarity search - Function
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin ...Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain / Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesMus musculus (house mouse)
Lymphocytic choriomeningitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBuratto, J. / Badia-Martinez, D. / Norstrom, M. / Sandalova, T. / Achour, A.
CitationJournal: PLoS ONE / Year: 2017
Title: Crystal structures of H-2Db in complex with the LCMV-derived peptides GP92 and GP392 explain pleiotropic effects of glycosylation on antigen presentation and immunogenicity.
Authors: Hafstrand, I. / Badia-Martinez, D. / Josey, B.J. / Norstrom, M. / Buratto, J. / Pellegrino, S. / Duru, A.D. / Sandalova, T. / Achour, A.
History
DepositionMay 12, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
E: H-2 class I histocompatibility antigen, D-B alpha chain
F: Beta-2-microglobulin
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
P: Pre-glycoprotein polyprotein GP complex
Q: Pre-glycoprotein polyprotein GP complex
R: Pre-glycoprotein polyprotein GP complex
S: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,38740
Polymers179,75712
Non-polymers2,63028
Water4,918273
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
P: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,59610
Polymers44,9393
Non-polymers6577
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-41 kcal/mol
Surface area18770 Å2
MethodPISA
2
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
Q: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,59210
Polymers44,9393
Non-polymers6537
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-42 kcal/mol
Surface area18900 Å2
MethodPISA
3
E: H-2 class I histocompatibility antigen, D-B alpha chain
F: Beta-2-microglobulin
R: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4128
Polymers44,9393
Non-polymers4725
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-57 kcal/mol
Surface area18520 Å2
MethodPISA
4
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
S: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,78812
Polymers44,9393
Non-polymers8499
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-71 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.500, 176.300, 85.600
Angle α, β, γ (deg.)90.000, 119.800, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 1:6 or (resid 7 and (name...
21(chain C and (resseq 1:6 or (resid 7 and (name...
31(chain E and (resseq 1:6 or (resid 7 and (name...
41(chain G and (resseq 1:6 or (resid 7 and (name...
12(chain B and (resseq 2 or (resid 3 and (name...
22(chain D and (resseq 2:18 or resseq 20:33 or resseq...
32(chain F and (resseq 2 or (resid 3 and (name...
42(chain H and (resseq 2 or (resid 3 and (name...
13(chain Q and (resseq 1:8 or (resid 9 and (name...
23(chain P and (resseq 1:8 or (resid 9 and (name...
33(chain R and (resseq 1:8 or (resid 9 and (name...
43(chain S and (resseq 1:8 or (resid 9 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 1:6 or (resid 7 and (name...A0
211(chain C and (resseq 1:6 or (resid 7 and (name...C1 - 6
221(chain C and (resseq 1:6 or (resid 7 and (name...C7
231(chain C and (resseq 1:6 or (resid 7 and (name...C1 - 276
241(chain C and (resseq 1:6 or (resid 7 and (name...C1 - 276
251(chain C and (resseq 1:6 or (resid 7 and (name...C1 - 276
261(chain C and (resseq 1:6 or (resid 7 and (name...C1 - 276
271(chain C and (resseq 1:6 or (resid 7 and (name...C1 - 276
281(chain C and (resseq 1:6 or (resid 7 and (name...C1 - 276
291(chain C and (resseq 1:6 or (resid 7 and (name...C1 - 276
311(chain E and (resseq 1:6 or (resid 7 and (name...E1 - 6
321(chain E and (resseq 1:6 or (resid 7 and (name...E7
331(chain E and (resseq 1:6 or (resid 7 and (name...E1 - 276
341(chain E and (resseq 1:6 or (resid 7 and (name...E1 - 276
351(chain E and (resseq 1:6 or (resid 7 and (name...E1 - 276
361(chain E and (resseq 1:6 or (resid 7 and (name...E1 - 276
371(chain E and (resseq 1:6 or (resid 7 and (name...E1 - 276
381(chain E and (resseq 1:6 or (resid 7 and (name...E1 - 276
391(chain E and (resseq 1:6 or (resid 7 and (name...E1 - 276
411(chain G and (resseq 1:6 or (resid 7 and (name...G1 - 6
421(chain G and (resseq 1:6 or (resid 7 and (name...G7
431(chain G and (resseq 1:6 or (resid 7 and (name...G1 - 276
441(chain G and (resseq 1:6 or (resid 7 and (name...G1 - 276
451(chain G and (resseq 1:6 or (resid 7 and (name...G1 - 276
461(chain G and (resseq 1:6 or (resid 7 and (name...G1 - 276
471(chain G and (resseq 1:6 or (resid 7 and (name...G1 - 276
481(chain G and (resseq 1:6 or (resid 7 and (name...G1 - 276
491(chain G and (resseq 1:6 or (resid 7 and (name...G1 - 276
112(chain B and (resseq 2 or (resid 3 and (name...B2
122(chain B and (resseq 2 or (resid 3 and (name...B3
132(chain B and (resseq 2 or (resid 3 and (name...B1 - 99
142(chain B and (resseq 2 or (resid 3 and (name...B1 - 99
152(chain B and (resseq 2 or (resid 3 and (name...B1 - 99
162(chain B and (resseq 2 or (resid 3 and (name...B1 - 99
172(chain B and (resseq 2 or (resid 3 and (name...B1 - 99
182(chain B and (resseq 2 or (resid 3 and (name...B1 - 99
212(chain D and (resseq 2:18 or resseq 20:33 or resseq...D2 - 18
222(chain D and (resseq 2:18 or resseq 20:33 or resseq...D20 - 33
232(chain D and (resseq 2:18 or resseq 20:33 or resseq...D35
242(chain D and (resseq 2:18 or resseq 20:33 or resseq...D37 - 43
252(chain D and (resseq 2:18 or resseq 20:33 or resseq...D44
262(chain D and (resseq 2:18 or resseq 20:33 or resseq...D1 - 99
272(chain D and (resseq 2:18 or resseq 20:33 or resseq...D1 - 99
282(chain D and (resseq 2:18 or resseq 20:33 or resseq...D1 - 99
292(chain D and (resseq 2:18 or resseq 20:33 or resseq...D1 - 99
312(chain F and (resseq 2 or (resid 3 and (name...F2
322(chain F and (resseq 2 or (resid 3 and (name...F3
332(chain F and (resseq 2 or (resid 3 and (name...F1 - 99
342(chain F and (resseq 2 or (resid 3 and (name...F1 - 99
352(chain F and (resseq 2 or (resid 3 and (name...F1 - 99
362(chain F and (resseq 2 or (resid 3 and (name...F1 - 99
372(chain F and (resseq 2 or (resid 3 and (name...F1 - 99
382(chain F and (resseq 2 or (resid 3 and (name...F1 - 99
412(chain H and (resseq 2 or (resid 3 and (name...H2
422(chain H and (resseq 2 or (resid 3 and (name...H3
432(chain H and (resseq 2 or (resid 3 and (name...H1 - 99
442(chain H and (resseq 2 or (resid 3 and (name...H1 - 99
452(chain H and (resseq 2 or (resid 3 and (name...H1 - 99
462(chain H and (resseq 2 or (resid 3 and (name...H1 - 99
472(chain H and (resseq 2 or (resid 3 and (name...H1 - 99
482(chain H and (resseq 2 or (resid 3 and (name...H1 - 99
113(chain Q and (resseq 1:8 or (resid 9 and (name...Q1 - 8
123(chain Q and (resseq 1:8 or (resid 9 and (name...Q9
133(chain Q and (resseq 1:8 or (resid 9 and (name...Q1 - 10
143(chain Q and (resseq 1:8 or (resid 9 and (name...Q1 - 10
153(chain Q and (resseq 1:8 or (resid 9 and (name...Q1 - 10
163(chain Q and (resseq 1:8 or (resid 9 and (name...Q1 - 10
173(chain Q and (resseq 1:8 or (resid 9 and (name...Q1 - 10
183(chain Q and (resseq 1:8 or (resid 9 and (name...Q1 - 10
193(chain Q and (resseq 1:8 or (resid 9 and (name...Q1 - 10
213(chain P and (resseq 1:8 or (resid 9 and (name...P1 - 8
223(chain P and (resseq 1:8 or (resid 9 and (name...P9
233(chain P and (resseq 1:8 or (resid 9 and (name...P1 - 10
243(chain P and (resseq 1:8 or (resid 9 and (name...P1 - 10
253(chain P and (resseq 1:8 or (resid 9 and (name...P1 - 10
263(chain P and (resseq 1:8 or (resid 9 and (name...P1 - 10
273(chain P and (resseq 1:8 or (resid 9 and (name...P1 - 10
283(chain P and (resseq 1:8 or (resid 9 and (name...P1 - 10
293(chain P and (resseq 1:8 or (resid 9 and (name...P1 - 10
313(chain R and (resseq 1:8 or (resid 9 and (name...R1 - 8
323(chain R and (resseq 1:8 or (resid 9 and (name...R9
333(chain R and (resseq 1:8 or (resid 9 and (name...R1 - 10
343(chain R and (resseq 1:8 or (resid 9 and (name...R1 - 10
353(chain R and (resseq 1:8 or (resid 9 and (name...R1 - 10
363(chain R and (resseq 1:8 or (resid 9 and (name...R1 - 10
373(chain R and (resseq 1:8 or (resid 9 and (name...R1 - 10
383(chain R and (resseq 1:8 or (resid 9 and (name...R1 - 10
393(chain R and (resseq 1:8 or (resid 9 and (name...R1 - 10
413(chain S and (resseq 1:8 or (resid 9 and (name...S1 - 8
423(chain S and (resseq 1:8 or (resid 9 and (name...S9
433(chain S and (resseq 1:8 or (resid 9 and (name...S1 - 10
443(chain S and (resseq 1:8 or (resid 9 and (name...S1 - 10
453(chain S and (resseq 1:8 or (resid 9 and (name...S1 - 10
463(chain S and (resseq 1:8 or (resid 9 and (name...S1 - 10
473(chain S and (resseq 1:8 or (resid 9 and (name...S1 - 10
483(chain S and (resseq 1:8 or (resid 9 and (name...S1 - 10
493(chain S and (resseq 1:8 or (resid 9 and (name...S1 - 10

NCS ensembles :
ID
1
2
3

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
H-2 class I histocompatibility antigen, D-B alpha chain / H-2D(B)


Mass: 32087.703 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01899
#2: Protein
Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11704.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli (E. coli) / References: UniProt: P01887

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Protein/peptide , 1 types, 4 molecules PQRS

#3: Protein/peptide
Pre-glycoprotein polyprotein GP complex


Mass: 1147.222 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Lymphocytic choriomeningitis virus / References: UniProt: P09991

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Non-polymers , 3 types, 301 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 3.11 Å3/Da / Density % sol: 60.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Ammonium Sulfate, 100 mM Tris-HCl, 25% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.4→19.61 Å / Num. obs: 84550 / % possible obs: 94.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.7
Reflection shellResolution: 2.4→2.43 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.8 / % possible all: 91

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N5A

1n5a


Resolution: 2.4→19.45 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.81
RfactorNum. reflection% reflectionSelection details
Rfree0.2589 4220 4.99 %Random
Rwork0.1994 ---
obs0.2024 84550 98.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 205.33 Å2 / Biso mean: 67.8522 Å2 / Biso min: 29.04 Å2
Refinement stepCycle: final / Resolution: 2.4→19.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12264 0 155 273 12692
Biso mean--95.71 56.38 -
Num. residues----1529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112826
X-RAY DIFFRACTIONf_angle_d1.24117459
X-RAY DIFFRACTIONf_chiral_restr0.0641768
X-RAY DIFFRACTIONf_plane_restr0.0092260
X-RAY DIFFRACTIONf_dihedral_angle_d18.4737536
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4082X-RAY DIFFRACTION9.74TORSIONAL
12C4082X-RAY DIFFRACTION9.74TORSIONAL
13E4082X-RAY DIFFRACTION9.74TORSIONAL
14G4082X-RAY DIFFRACTION9.74TORSIONAL
21B1732X-RAY DIFFRACTION9.74TORSIONAL
22D1732X-RAY DIFFRACTION9.74TORSIONAL
23F1732X-RAY DIFFRACTION9.74TORSIONAL
24H1732X-RAY DIFFRACTION9.74TORSIONAL
31Q168X-RAY DIFFRACTION9.74TORSIONAL
32P168X-RAY DIFFRACTION9.74TORSIONAL
33R168X-RAY DIFFRACTION9.74TORSIONAL
34S168X-RAY DIFFRACTION9.74TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.42720.39971350.34762463259891
2.4272-2.45570.40351240.33632589271394
2.4557-2.48560.38221230.30342633275699
2.4856-2.5170.33141490.29127762925100
2.517-2.55010.35511420.299926232765100
2.5501-2.58490.35371580.283727172875100
2.5849-2.62180.36161300.293826532783100
2.6218-2.66080.33851350.283827462881100
2.6608-2.70230.35021450.272726872832100
2.7023-2.74650.3671200.272627132833100
2.7465-2.79370.35211550.271827092864100
2.7937-2.84440.32291530.265126992852100
2.8444-2.89890.32171410.244726542795100
2.8989-2.95790.28851520.24327492901100
2.9579-3.02190.32951290.245926862815100
3.0219-3.0920.31751430.242626912834100
3.092-3.1690.33131110.240127512862100
3.169-3.25430.33731180.230226972815100
3.2543-3.34960.28011660.224426942860100
3.3496-3.45710.30761520.21327072859100
3.4571-3.57990.23481330.198227162849100
3.5799-3.72230.23681310.183927672898100
3.7223-3.89040.2831660.180526622828100
3.8904-4.09380.23661510.172827062857100
4.0938-4.34760.19871330.149227022835100
4.3476-4.67890.20091580.137726642822100
4.6789-5.14190.18221430.131327342877100
5.1419-5.8680.18661620.154726832845100
5.868-7.32670.2481370.18727402877100
7.3267-19.45050.22071250.19062319244484
Refinement TLS params.Method: refined / Origin x: -1.7349 Å / Origin y: -13.288 Å / Origin z: 0.0355 Å
111213212223313233
T0.3911 Å20.0009 Å2-0.0017 Å2-0.3813 Å2-0.0423 Å2--0.2943 Å2
L0.5678 °2-0.0031 °2-0.0154 °2-0.3661 °2-0.172 °2---0.0368 °2
S0.0249 Å °0.0049 Å °-0.0028 Å °-0.0012 Å °-0.0202 Å °0.0033 Å °0.0061 Å °-0.0009 Å °-0.0042 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 276
2X-RAY DIFFRACTION1allB1 - 99
3X-RAY DIFFRACTION1allC1 - 276
4X-RAY DIFFRACTION1allD1 - 99
5X-RAY DIFFRACTION1allE1 - 276
6X-RAY DIFFRACTION1allF1 - 99
7X-RAY DIFFRACTION1allG1 - 276
8X-RAY DIFFRACTION1allH1 - 99
9X-RAY DIFFRACTION1allP1 - 10
10X-RAY DIFFRACTION1allQ1 - 10
11X-RAY DIFFRACTION1allR1 - 10
12X-RAY DIFFRACTION1allS1 - 10
13X-RAY DIFFRACTION1allI1 - 5
14X-RAY DIFFRACTION1allI6 - 15
15X-RAY DIFFRACTION1allI16
16X-RAY DIFFRACTION1allI17 - 19
17X-RAY DIFFRACTION1allX1 - 17
18X-RAY DIFFRACTION1allY1 - 299

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