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- PDB-4hkj: Structure of Cowpox CPXV203 in complex with MHCI (H-2Kb) -

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Basic information

Entry
Database: PDB / ID: 4hkj
TitleStructure of Cowpox CPXV203 in complex with MHCI (H-2Kb)
Components
  • Beta-2-microglobulin
  • CPXV203 protein
  • H-2 class I histocompatibility antigen, K-B alpha chain
  • Ovalbumin
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / viral immune evasion proteins / antigen presentation / structural genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / inhibitor / intracellular / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


intracellular amino acid homeostasis / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / phagolysosome / monoatomic ion homeostasis / MHC class Ib protein complex / natural killer cell lectin-like receptor binding / TAP2 binding / TAP1 binding / cis-Golgi network membrane / embryo development ending in birth or egg hatching ...intracellular amino acid homeostasis / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / phagolysosome / monoatomic ion homeostasis / MHC class Ib protein complex / natural killer cell lectin-like receptor binding / TAP2 binding / TAP1 binding / cis-Golgi network membrane / embryo development ending in birth or egg hatching / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to steroid hormone / ER-Phagosome pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / response to corticosterone / inner ear development / CD8 receptor binding / beta-2-microglobulin binding / endoplasmic reticulum exit site / intracellular membrane-bounded organelle / TAP binding / MHC class I protein binding / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / T cell receptor binding / phagocytic vesicle / Neutrophil degranulation / response to progesterone / monoatomic ion transport / 14-3-3 protein binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / Neutrophil degranulation / DAP12 interactions / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / response to estrogen / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Modulation by Mtb of host immune system / sensory perception of smell / tertiary granule lumen / positive regulation of cellular senescence / MHC class II protein complex binding / T cell differentiation in thymus / DAP12 signaling / late endosome membrane / negative regulation of neuron projection development / protein refolding / protein-folding chaperone binding / ER-Phagosome pathway / protease binding / early endosome membrane / vesicle / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / early endosome / defense response to bacterium
Similarity search - Function
Viral Chemokine Inhibitor; Chain A - #30 / Poxvirus T4 protein, C-terminal / Poxvirus T4 protein, N-terminal / Apoptosis regulator, M-T4, endoplasmic reticulum / Apoptosis regulator, M-T4 superfamily / Poxvirus T4 protein, C terminus / Poxvirus T4 protein, N terminus / Viral Chemokine Inhibitor; Chain A / Serpin, conserved site / Serpins signature. ...Viral Chemokine Inhibitor; Chain A - #30 / Poxvirus T4 protein, C-terminal / Poxvirus T4 protein, N-terminal / Apoptosis regulator, M-T4, endoplasmic reticulum / Apoptosis regulator, M-T4 superfamily / Poxvirus T4 protein, C terminus / Poxvirus T4 protein, N terminus / Viral Chemokine Inhibitor; Chain A / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ovalbumin / H-2 class I histocompatibility antigen, K-B alpha chain / Beta-2-microglobulin / CPXV203 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
Cowpox virus
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, MOLECULAR REPLACEMENT / SAD / molecular replacement / Resolution: 3 Å
AuthorsMcCoy IV, W.H. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Plos Biol. / Year: 2012
Title: Structural Mechanism of ER Retrieval of MHC Class I by Cowpox.
Authors: McCoy, W.H. / Wang, X. / Yokoyama, W.M. / Hansen, T.H. / Fremont, D.H.
History
DepositionOct 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
C: Ovalbumin
D: CPXV203 protein
E: H-2 class I histocompatibility antigen, K-B alpha chain
F: Beta-2-microglobulin
G: Ovalbumin
H: CPXV203 protein
I: H-2 class I histocompatibility antigen, K-B alpha chain
J: Beta-2-microglobulin
K: Ovalbumin
L: CPXV203 protein
M: H-2 class I histocompatibility antigen, K-B alpha chain
N: Beta-2-microglobulin
O: Ovalbumin
P: CPXV203 protein


Theoretical massNumber of molelcules
Total (without water)275,98716
Polymers275,98716
Non-polymers00
Water1,29772
1
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
C: Ovalbumin
D: CPXV203 protein


Theoretical massNumber of molelcules
Total (without water)68,9974
Polymers68,9974
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-28 kcal/mol
Surface area27310 Å2
MethodPISA
2
E: H-2 class I histocompatibility antigen, K-B alpha chain
F: Beta-2-microglobulin
G: Ovalbumin
H: CPXV203 protein


Theoretical massNumber of molelcules
Total (without water)68,9974
Polymers68,9974
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7710 Å2
ΔGint-27 kcal/mol
Surface area27360 Å2
MethodPISA
3
I: H-2 class I histocompatibility antigen, K-B alpha chain
J: Beta-2-microglobulin
K: Ovalbumin
L: CPXV203 protein


Theoretical massNumber of molelcules
Total (without water)68,9974
Polymers68,9974
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint-28 kcal/mol
Surface area27340 Å2
MethodPISA
4
M: H-2 class I histocompatibility antigen, K-B alpha chain
N: Beta-2-microglobulin
O: Ovalbumin
P: CPXV203 protein


Theoretical massNumber of molelcules
Total (without water)68,9974
Polymers68,9974
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-28 kcal/mol
Surface area27300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.31, 88.25, 106.42
Angle α, β, γ (deg.)76.18, 69.29, 66.69
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11chain A and (resseq 1:277 )
21chain E and (resseq 1:277 )
31chain I and (resseq 1:277 )
41chain M and (resseq 1:277 )
12chain D and (resseq 5:190 )
22chain H and (resseq 5:190 )
32chain L and (resseq 5:190 )
42chain P and (resseq 5:190 )
13chain B and (resseq 0:99 )
23chain F and (resseq 0:99 )
33chain J and (resseq 0:99 )
43chain N and (resseq 0:99 )
14chain C and (resseq 1:8 )
24chain G and (resseq 1:8 )
34chain K and (resseq 1:8 )
44chain O and (resseq 1:8 )

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPROPROchain 'A' and (resseq 1:277 )AA1 - 2771 - 277
21GLYGLYPROPROchain 'E' and (resseq 1:277 )EE1 - 2771 - 277
31GLYGLYPROPROchain 'I' and (resseq 1:277 )II1 - 2771 - 277
41GLYGLYPROPROchain 'M' and (resseq 1:277 )MM1 - 2771 - 277
12ARGARGARGARGchain 'D' and (resseq 5:190 )DD5 - 1906 - 191
22ARGARGARGARGchain 'H' and (resseq 5:190 )HH5 - 1906 - 191
32ARGARGARGARGchain 'L' and (resseq 5:190 )LL5 - 1906 - 191
42ARGARGARGARGchain 'P' and (resseq 5:190 )PP5 - 1906 - 191
13METMETMETMETchain 'B' and (resseq 0:99 )BB0 - 991 - 100
23METMETMETMETchain 'F' and (resseq 0:99 )FF0 - 991 - 100
33METMETMETMETchain 'J' and (resseq 0:99 )JJ0 - 991 - 100
43METMETMETMETchain 'N' and (resseq 0:99 )NN0 - 991 - 100
14SERSERLEULEUchain 'C' and (resseq 1:8 )CC1 - 81 - 8
24SERSERLEULEUchain 'G' and (resseq 1:8 )GG1 - 81 - 8
34SERSERLEULEUchain 'K' and (resseq 1:8 )KK1 - 81 - 8
44SERSERLEULEUchain 'O' and (resseq 1:8 )OO1 - 81 - 8

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(-0.999943, -0.010689, -0.000431), (0.010654, -0.998721, 0.04942), (-0.000959, 0.049413, 0.998778)-1.98889, 6.00673, -0.261628
2given(-0.402409, -0.915458, -0.001919), (-0.914311, 0.402008, -0.049237), (0.045846, -0.018059, -0.998785)-36.596901, -9.47167, -56.515999
3given(0.398668, 0.91701, 0.012516), (0.917093, -0.398661, -0.003213), (0.002043, 0.012759, -0.999917)34.633598, 12.8478, -56.3442
4given(-0.999977, -0.006619, -0.001104), (0.006564, -0.998994, 0.044359), (-0.001396, 0.044351, 0.999015)-1.89813, 5.65823, -0.273655
5given(-0.399154, -0.916882, -0.001687), (-0.916071, 0.398877, -0.041366), (0.038601, -0.014966, -0.999143)-36.512501, -9.76068, -56.596001
6given(0.398647, 0.917095, 0.004267), (0.917088, -0.398607, -0.007873), (-0.005519, 0.007052, -0.99996)34.635201, 12.9628, -56.530499
7given(-0.999898, -0.011552, -0.008399), (0.01122, -0.999195, 0.038506), (-0.008837, 0.038408, 0.999223)-2.40128, 5.38897, -0.493067
8given(-0.403126, -0.915138, 0.00347), (-0.914245, 0.402559, -0.045843), (0.040556, -0.021653, -0.998943)-36.584099, -9.45763, -56.889599
9given(0.394744, 0.918733, 0.010334), (0.918789, -0.394694, -0.006582), (-0.001968, 0.012093, -0.999925)34.598598, 12.8839, -56.445202
10given(-0.999933, -0.010359, -0.00508), (0.010099, -0.998758, 0.048796), (-0.005579, 0.048742, 0.998796)-2.3336, 5.96404, -0.346973
11given(-0.417026, -0.908866, -0.007223), (-0.907765, 0.41689, -0.046529), (0.0453, -0.012846, -0.998891)-36.596901, -8.45064, -56.154099
12given(0.382956, 0.923717, 0.009563), (0.923725, -0.383016, 0.005493), (0.008737, 0.00673, -0.999939)34.037201, 13.1624, -56.1264

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Components

#1: Protein
H-2 class I histocompatibility antigen, K-B alpha chain / MHC class I H-2KB heavy chain / H-2K(B)


Mass: 32256.959 Da / Num. of mol.: 4 / Fragment: extracellular domain (UNP residues 22-301)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H-2KB, H2-K, H2-K1 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P01901
#2: Protein
Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 4 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, BETA-2 MICROGLOBULIN, CDABP0092, HDCMA22P / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P61769
#3: Protein/peptide
Ovalbumin / Allergen Gal d II / Egg albumin / Plakalbumin


Mass: 964.137 Da / Num. of mol.: 4 / Fragment: UNP residues 258-265 / Source method: obtained synthetically / Source: (synth.) Gallus gallus (chicken) / References: UniProt: P01012
#4: Protein
CPXV203 protein


Mass: 23896.361 Da / Num. of mol.: 4 / Fragment: UNP residues 17-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cowpox virus / Strain: Brighton Red / Gene: CPXV203, CPXV203 CDS / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q8QMP2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 52.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.55
Details: 10% PEG6000, 4% glucose, 2% ethylene glycol, 0.1 M tri-potassium citrate, 0.01% azide, pH 5.55, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97909 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Sep 10, 2010
RadiationMonochromator: Rosenbaum-Rock monochromator 1: high-resolution double crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97909 Å / Relative weight: 1
ReflectionRedundancy: 4.1 % / Av σ(I) over netI: 7.25 / Number: 198533 / Rmerge(I) obs: 0.164 / Χ2: 1.04 / D res high: 3 Å / D res low: 50 Å / Num. obs: 47950 / % possible obs: 87.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.455099.710.1071.0384.3
4.335.4592.410.1351.054
3.784.3383.610.1870.9974.1
3.433.7883.110.2771.0084.1
3.193.4383.810.3691.0644.2
33.1984.910.6221.064.2
ReflectionResolution: 3→50 Å / Num. all: 47950 / Num. obs: 47882 / % possible obs: 87.9 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 70.46 Å2 / Rmerge(I) obs: 0.164 / Χ2: 1.036 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
3-3.194.20.6222.5577141.0684.9
3.19-3.434.20.369476291.06483.8
3.43-3.784.10.2774.1975481.00883.1
3.78-4.334.10.1875.9375840.99783.6
4.33-5.4540.1358.4784011.0592.4
5.45-504.30.10710.890741.03899.7

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Phasing

Phasing
Method
SAD
molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.95 Å71.74 Å
Translation2.95 Å71.74 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
SOLVEphasing
RESOLVEphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
Blu-IceICEdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD, MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CLZ

2clz


Resolution: 3→49.36 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.47 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.96 / σ(I): 1.96 / Phase error: 28.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2394 5 %RANDOM
Rwork0.2295 ---
obs0.2307 47882 87.16 %-
all-47950 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.295 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso max: 243.52 Å2 / Biso mean: 83.3211 Å2 / Biso min: 14.43 Å2
Baniso -1Baniso -2Baniso -3
1--3.3931 Å21.0886 Å24.4702 Å2
2---3.7601 Å24.2764 Å2
3---7.1532 Å2
Refinement stepCycle: LAST / Resolution: 3→49.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18588 0 0 72 18660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00219096
X-RAY DIFFRACTIONf_angle_d0.53825840
X-RAY DIFFRACTIONf_chiral_restr0.0412720
X-RAY DIFFRACTIONf_plane_restr0.0023360
X-RAY DIFFRACTIONf_dihedral_angle_d9.6627060
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2255X-RAY DIFFRACTIONPOSITIONAL0.003
12E2255X-RAY DIFFRACTIONPOSITIONAL0.003
13I2255X-RAY DIFFRACTIONPOSITIONAL0.003
14M2255X-RAY DIFFRACTIONPOSITIONAL0.003
21D1489X-RAY DIFFRACTIONPOSITIONAL0.003
22H1489X-RAY DIFFRACTIONPOSITIONAL0.003
23L1489X-RAY DIFFRACTIONPOSITIONAL0.003
24P1489X-RAY DIFFRACTIONPOSITIONAL0.003
31B837X-RAY DIFFRACTIONPOSITIONAL0.003
32F837X-RAY DIFFRACTIONPOSITIONAL0.003
33J837X-RAY DIFFRACTIONPOSITIONAL0.003
34N837X-RAY DIFFRACTIONPOSITIONAL0.003
41C68X-RAY DIFFRACTIONPOSITIONAL0.003
42G68X-RAY DIFFRACTIONPOSITIONAL0.003
43K68X-RAY DIFFRACTIONPOSITIONAL0.003
44O68X-RAY DIFFRACTIONPOSITIONAL0.003
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
3-3.06130.38871220.350622442366224473
3.0613-3.12790.32551390.319826132752261385
3.1279-3.20060.37031380.289526312769263185
3.2006-3.28060.32071360.281726072743260784
3.2806-3.36930.28841340.268125312665253184
3.3693-3.46850.34781330.287725522685255283
3.4685-3.58040.281360.272525682704256883
3.5804-3.70830.27981340.296325402674254083
3.7083-3.85670.29011310.249725262657252683
3.8567-4.03220.27611340.257325182652251882
4.0322-4.24460.25061370.213925862723258684
4.2446-4.51040.21891350.198226382773263886
4.5104-4.85840.19281490.1928102959281091
4.8584-5.34680.22361540.194429553109295597
5.3468-6.11920.24171610.209530493210304999
6.1192-7.70490.25191610.2111305432153054100
7.7049-49.36690.20511600.1968306632263066100
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)
15.45820.1157-2.70522.87150.20665.8875-0.0495-0.9183-0.42540.4820.2432-0.21410.31730.7403-0.23430.46180.1025-0.17020.47780.01010.55421.5182-9.6231-48.3829
23.266-2.36750.13045.9635-0.50725.6540.1237-0.53730.91780.4171-0.1003-0.3021-0.83160.0578-0.03520.5952-0.0863-0.02590.661-0.37410.90878.167625.7786-46.2656
30.97610.66481.46914.36130.85282.9767-0.1301-0.8051.2640.40910.0634-0.6904-0.59770.55570.05120.5607-0.1927-0.05110.904-0.48011.211929.72217.6421-47.6419
42.0105-4.90782.00842.05482.30832.0106-0.3523-1.6548-1.2499-0.1110.41090.30241.55171.87830.02110.59010.17070.10740.6306-0.02670.930823.5674-16.3791-50.0576
54.55580.373-0.56964.0369-0.48123.40770.14740.29630.4628-0.3307-0.0278-0.1865-0.12930.1525-0.10510.3502-0.00390.05210.50020.00540.456415.657311.1008-72.32
64.9244-0.26011.66742.280.18626.3603-0.021-0.84330.20080.31870.2010.1308-0.3848-0.4483-0.19480.49260.02050.07990.41530.00760.3554-23.62612.9808-48.845
74.9044-2.30240.39858.87040.69476.35320.461-0.0907-0.90130.3298-0.262-0.15730.75180.5031-0.19580.43940.0743-0.02110.67210.23410.8014-9.9012-22.1283-44.975
81.74121.2408-1.25565.2681-0.33762.94640.0574-0.6994-0.88230.4519-0.09821.00790.636-0.41620.06520.4902-0.0773-0.01680.6790.26681.05-31.5659-14.4252-46.9102
99.4934-2.23012.00512.01991.01991.99350.4843-0.39350.75190.26130.8828-1.2726-2.8198-0.586-1.06431.1978-0.14790.02080.6044-0.00770.5414-25.847619.6241-50.8726
103.922-0.08360.42944.1004-1.19964.19920.03650.4408-0.724-0.43250.06030.10480.19550.0985-0.05930.3994-0.0074-0.10920.4821-0.15750.5754-17.4188-8.7487-71.7534
112.68880.32090.08425.1767-1.76175.2074-0.18580.3905-0.1683-1.14920.5078-0.28610.606-0.089-0.31530.6286-0.0933-0.06260.5397-0.17170.5289-22.8747-53.4096-8.2273
127.1544-3.5765-1.01465.46340.41457.28150.17260.38860.175-0.38040.17480.6929-0.7116-0.3296-0.39350.8863-0.1852-0.26560.5350.17480.8328-49.7733-26.9944-12.0593
135.0565-0.7350.5441.22070.36083.0259-0.17960.6535-0.3264-0.7550.11631.274-0.0272-0.41660.02910.7993-0.259-0.45490.70840.21121.1453-51.1305-49.9702-10.2502
142.0354.6469-8.9941.98581.99331.99940.21550.60520.6462-0.70670.4288-0.95711.86891.5351-0.51930.684-0.0103-0.09810.8806-0.04810.5366-17.6167-58.065-6.1555
154.25840.2548-0.37775.0695-0.69414.44760.0964-0.27220.18630.25660.08130.5662-0.1359-0.0986-0.20070.4091-0.07810.02860.40640.07760.4902-40.5414-39.277114.7596
162.66720.44531.28065.48522.62095.1293-0.01650.26040.236-1.08780.3236-0.0591-0.7059-0.0994-0.31520.56480.01790.10530.43990.11210.519-25.8203-2.9672-8.0526
174.2494-3.2573-0.04616.3217-0.46074.0912-0.25650.1811-0.5109-0.44620.3927-1.12790.49920.5093-0.07370.93330.01030.37890.5537-0.28371.2351.3282-29.2959-10.4506
183.4992-1.0124-0.3981.6371-0.37482.6921-0.070.52160.0722-0.76730.0913-1.8629-0.11940.6979-0.12860.7766-0.20560.55480.7167-0.35371.6562.4295-6.2519-8.8844
198.31710.44172.21852.03521.9922.00220.45430.1283-0.2679-0.601-0.7840.4527-2.5267-1.3520.20110.74140.00060.11110.5474-0.04930.4431-31.24471.6846-6.3309
203.0393-0.0221-0.31664.1610.40653.850.0488-0.1388-0.26810.30820.1313-0.72670.10360.1201-0.17520.4795-0.0487-0.10580.4873-0.1840.7525-9.1859-16.773615.7226
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:180)A1 - 180
2X-RAY DIFFRACTION2chain 'A' and (resseq 181:277)A181 - 277
3X-RAY DIFFRACTION3chain 'B' and (resseq 0:99)B0 - 99
4X-RAY DIFFRACTION4chain 'C' and (resseq 1:8)C1 - 8
5X-RAY DIFFRACTION5chain 'D' and (resseq 5:190)D5 - 190
6X-RAY DIFFRACTION6chain 'E' and (resseq 1:180)E1 - 180
7X-RAY DIFFRACTION7chain 'E' and (resseq 181:277)E181 - 277
8X-RAY DIFFRACTION8chain 'F' and (resseq 0:99)F0 - 99
9X-RAY DIFFRACTION9chain 'G' and (resseq 1:8)G1 - 8
10X-RAY DIFFRACTION10chain 'H' and (resseq 5:190)H5 - 190
11X-RAY DIFFRACTION11chain 'I' and (resseq 1:180)I1 - 180
12X-RAY DIFFRACTION12chain 'I' and (resseq 181:277)I181 - 277
13X-RAY DIFFRACTION13chain 'J' and (resseq 0:99)J0 - 99
14X-RAY DIFFRACTION14chain 'K' and (resseq 1:8)K1 - 8
15X-RAY DIFFRACTION15chain 'L' and (resseq 5:190)L5 - 190
16X-RAY DIFFRACTION16chain 'M' and (resseq 1:180)M1 - 180
17X-RAY DIFFRACTION17chain 'M' and (resseq 181:277)M181 - 277
18X-RAY DIFFRACTION18chain 'N' and (resseq 0:99)N0 - 99
19X-RAY DIFFRACTION19chain 'O' and (resseq 1:8)O1 - 8
20X-RAY DIFFRACTION20chain 'P' and (resseq 5:190)P5 - 190

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