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- PDB-2q7n: Crystal structure of Leukemia inhibitory factor in complex with L... -

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Basic information

Entry
Database: PDB / ID: 2q7n
TitleCrystal structure of Leukemia inhibitory factor in complex with LIF receptor (domains 1-5)
Components(Leukemia inhibitory ...) x 2
KeywordsCYTOKINE receptor/CYTOKINE / CYTOKINE CELL SURFACE RECEPTOR COMPLEX LIFR LIF / CYTOKINE receptor-CYTOKINE COMPLEX
Function / homology
Function and homology information


leukemia inhibitory factor receptor binding / spongiotrophoblast differentiation / meiotic nuclear division / oncostatin-M receptor activity / positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / IL-6-type cytokine receptor ligand interactions / leukemia inhibitory factor receptor activity / negative regulation of meiotic nuclear division / muscle organ morphogenesis / cell surface receptor signaling pathway via STAT ...leukemia inhibitory factor receptor binding / spongiotrophoblast differentiation / meiotic nuclear division / oncostatin-M receptor activity / positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / IL-6-type cytokine receptor ligand interactions / leukemia inhibitory factor receptor activity / negative regulation of meiotic nuclear division / muscle organ morphogenesis / cell surface receptor signaling pathway via STAT / oncostatin-M-mediated signaling pathway / ciliary neurotrophic factor receptor binding / leukemia inhibitory factor signaling pathway / lung vasculature development / ciliary neurotrophic factor-mediated signaling pathway / regulation of metanephric nephron tubule epithelial cell differentiation / negative regulation of hormone secretion / trophoblast giant cell differentiation / positive regulation of peptidyl-serine phosphorylation of STAT protein / lung lobe morphogenesis / negative regulation of muscle cell apoptotic process / positive regulation of macrophage differentiation / positive regulation of astrocyte differentiation / IL-6-type cytokine receptor ligand interactions / cytokine receptor activity / positive regulation of cell adhesion mediated by integrin / lung alveolus development / cytokine binding / regulation of cell differentiation / growth factor binding / Interleukin-10 signaling / somatic stem cell population maintenance / macrophage differentiation / decidualization / neuron development / blood vessel remodeling / animal organ regeneration / positive regulation of tyrosine phosphorylation of STAT protein / embryo implantation / neuron projection morphogenesis / cytokine activity / response to cytokine / stem cell differentiation / growth factor activity / cell morphogenesis / negative regulation of ERK1 and ERK2 cascade / cytokine-mediated signaling pathway / positive regulation of fibroblast proliferation / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of peptidyl-serine phosphorylation / gene expression / fibroblast proliferation / Interleukin-4 and Interleukin-13 signaling / positive regulation of MAPK cascade / membrane => GO:0016020 / response to hypoxia / receptor complex / immune response / negative regulation of cell population proliferation / external side of plasma membrane / signaling receptor binding / positive regulation of cell population proliferation / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / cytosol
Similarity search - Function
Leukemia inhibitory factor / Leukemia inhibitory factor receptor, D2 domain / Leukemia inhibitory factor receptor, N-terminal / Leukemia inhibitory factor receptor D2 domain / Leukemia inhibitory factor receptor N-terminal domain / Leukemia inhibitory factor /oncostatin / Leukemia inhibitory factor /oncostatin, conserved site / LIF / OSM family / LIF / OSM family signature. / leukemia inhibitory factor ...Leukemia inhibitory factor / Leukemia inhibitory factor receptor, D2 domain / Leukemia inhibitory factor receptor, N-terminal / Leukemia inhibitory factor receptor D2 domain / Leukemia inhibitory factor receptor N-terminal domain / Leukemia inhibitory factor /oncostatin / Leukemia inhibitory factor /oncostatin, conserved site / LIF / OSM family / LIF / OSM family signature. / leukemia inhibitory factor / Long hematopoietin receptor, Gp130 family 2, conserved site / Long hematopoietin receptor, gp130 family signature. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Leukemia inhibitory factor / Leukemia inhibitory factor receptor
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsHuyton, T. / Zhang, J.G. / Nicola, N.A. / Garrett, T.P.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: An unusual cytokine:Ig-domain interaction revealed in the crystal structure of leukemia inhibitory factor (LIF) in complex with the LIF receptor.
Authors: Huyton, T. / Zhang, J.G. / Luo, C.S. / Lou, M.Z. / Hilton, D.J. / Nicola, N.A. / Garrett, T.P.
History
DepositionJun 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 2.0May 13, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.type / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly_prop.biol_id / _pdbx_struct_assembly_prop.value / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_asym.entity_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leukemia inhibitory factor receptor
B: Leukemia inhibitory factor
C: Leukemia inhibitory factor receptor
D: Leukemia inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,37922
Polymers149,5164
Non-polymers8,86318
Water0
1
A: Leukemia inhibitory factor receptor
B: Leukemia inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,44511
Polymers74,7582
Non-polymers4,6879
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint65 kcal/mol
Surface area36210 Å2
MethodPISA
2
C: Leukemia inhibitory factor receptor
D: Leukemia inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,93411
Polymers74,7582
Non-polymers4,1769
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint50 kcal/mol
Surface area36320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.476, 240.131, 202.631
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22C
13A
23C
14A
24C
15A
25C
16B
26D

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLYSLYSAA7 - 829 - 84
21ASPASPLYSLYSCC7 - 829 - 84
12ASPASPTHRTHRAA83 - 20285 - 204
22ASPASPTHRTHRCC83 - 20285 - 204
13GLUGLUCYSCYSAA203 - 293205 - 295
23GLUGLUCYSCYSCC203 - 293205 - 295
14GLUGLUTHRTHRAA294 - 380296 - 382
24GLUGLUTHRTHRCC294 - 380296 - 382
15GLUGLUTHRTHRAA381 - 486383 - 488
25GLUGLUTHRTHRCC381 - 486383 - 488
16SERSERPHEPHEBB1 - 1801 - 180
26SERSERPHEPHEDD1 - 1801 - 180

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Leukemia inhibitory ... , 2 types, 4 molecules ACBD

#1: Protein Leukemia inhibitory factor receptor / / LIF receptor / LIF-R / D-factor/LIF receptor / CD118 antigen


Mass: 55018.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lifr / Plasmid: pCHO1/mLIFR / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO-K1 / References: UniProt: P42703
#2: Protein Leukemia inhibitory factor / / LIF / Differentiation-stimulating factor / D factor / Melanoma-derived LPL inhibitor / MLPLI / Emfilermin


Mass: 19739.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIF, HILDA / Production host: Escherichia coli (E. coli) / References: UniProt: P15018

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Sugars , 6 types, 18 molecules

#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-2-3/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#8: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 7.866101 Å3/Da / Density % sol: 84.363281 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.5M sodium malonate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.968 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 30, 2005 / Details: mirrors
RadiationMonochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 4→20 Å / Num. all: 37104 / Num. obs: 37104 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.226 / Net I/σ(I): 6.3
Reflection shellResolution: 4→4.14 Å / Rmerge(I) obs: 0.857 / Mean I/σ(I) obs: 1 / % possible all: 72.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PVH CHAIN B

1pvh


Resolution: 4→20 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.868 / SU B: 91.108 / SU ML: 0.596 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0.857 / ESU R Free: 0.663 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28696 1852 5 %RANDOM
Rwork0.23724 ---
all0.23978 35239 --
obs0.23978 35239 93.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 102.084 Å2
Baniso -1Baniso -2Baniso -3
1-10.49 Å20 Å20 Å2
2---2.61 Å20 Å2
3----7.88 Å2
Refinement stepCycle: LAST / Resolution: 4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10252 0 587 0 10839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02211166
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7392.00515341
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.33451316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.18824.375448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.328151650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2221548
X-RAY DIFFRACTIONr_chiral_restr0.1090.21871
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028128
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2790.24950
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3270.27249
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2390
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5271.56759
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.964210772
X-RAY DIFFRACTIONr_scbond_it1.0234963
X-RAY DIFFRACTIONr_scangle_it1.774.54569
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A304medium positional0.490.5
2A480medium positional0.460.5
3A364medium positional0.310.5
4A348medium positional0.230.5
5A424medium positional0.320.5
6B720medium positional0.280.5
1A280loose positional0.885
2A480loose positional0.925
3A313loose positional0.625
4A323loose positional0.475
5A424loose positional0.575
6B667loose positional0.615
1A304medium thermal0.662
2A480medium thermal0.392
3A364medium thermal0.362
4A348medium thermal0.432
5A424medium thermal0.352
6B720medium thermal0.322
1A280loose thermal1.4210
2A480loose thermal110
3A313loose thermal0.8910
4A323loose thermal1.0910
5A424loose thermal0.9210
6B667loose thermal1.1810
LS refinement shellResolution: 4→4.105 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 89 -
Rwork0.349 1703 -
obs-1792 63.86 %
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)
13.4473-4.24554.01717.0558-8.369720.1816-0.51480.4930.54590.9829-0.6225-0.8329-1.67291.45961.1374-0.39680.1728-0.38460.69120.25260.294561.74564.39179.579
25.3315-1.5137.72251.2522-4.256516.368-0.4774-0.79690.18980.8532-0.494-0.2892-0.8415-0.15180.9713-0.17560.2901-0.14590.28250.35020.282645.58974.95350.459
33.1242-2.1060.73120.01952.56562.75690.0798-0.1164-0.72840.5703-0.1537-0.3740.83580.91180.0739-0.53450.3959-0.0442-0.09950.1091-0.123134.04672.54920.676
42.1344-3.10741.592113.5076-3.72563.42210.2103-0.1401-0.04340.6743-0.31230.09590.20090.70880.1019-0.6619-0.1092-0.0381-0.07640.1176-0.445326.47108.80423.275
56.5207-1.42094.91658.9957-7.19610.39550.08530.060.5810.3328-0.14880.08910.0261-0.47120.0634-0.735-0.15550.1327-0.4761-0.1965-0.207612.94135.9036.651
617.05871.67781.40093.72-0.09143.43010.05550.0393-0.317-0.3244-0.13290.38190.9993-0.24080.0774-0.1961-0.05790.0567-0.5412-0.0791-0.42034.7175.0378.976
76.80939.96422.321320.47352.26172.54890.4468-0.1357-0.55320.2696-0.1908-0.14880.17940.1195-0.256-0.6087-0.30770.0802-0.06540.0636-0.0789-62.18926.4494.383
811.632510.13634.912413.91567.74634.4376-0.23160.2872-0.3598-0.66520.2463-0.4959-0.50980.4776-0.0148-0.5277-0.49570.05080.06840.2072-0.0635-43.11554.71710.576
91.74232.4467-1.71499.0121-7.199214.66430.2539-0.57570.3321.127-0.28361.13510.1452-1.14730.0297-0.5418-0.54330.20680.2727-0.2890.1943-29.61877.21228.471
102.79254.494-1.255610.0968-4.26084.8427-0.0286-0.0518-0.0858-0.5635-0.18890.41410.9155-0.17770.2176-0.2246-0.2182-0.1794-0.2278-0.15910.3249-22.11994.517-3.268
118.2033.13091.323715.2053-2.06787.53220.23430.1268-0.217-0.68870.06340.21280.35260.0474-0.2977-0.56040.2075-0.0784-0.1867-0.0663-0.2413-8.455123.288-16.927
1216.5218-0.78533.05783.80890.61314.2387-0.3511-0.296-0.11510.2642-0.17170.25730.4407-0.20.5229-0.4196-0.22260.134-0.4602-0.0379-0.4516-0.2787.98832.753
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA50 - 12552 - 127
2X-RAY DIFFRACTION2AA126 - 245128 - 247
3X-RAY DIFFRACTION3AA246 - 326248 - 328
4X-RAY DIFFRACTION4AA327 - 423329 - 425
5X-RAY DIFFRACTION5AA424 - 486426 - 488
6X-RAY DIFFRACTION6BB1 - 1801 - 180
7X-RAY DIFFRACTION7CC50 - 12552 - 127
8X-RAY DIFFRACTION8CC126 - 245128 - 247
9X-RAY DIFFRACTION9CC246 - 326248 - 328
10X-RAY DIFFRACTION10CC327 - 423329 - 425
11X-RAY DIFFRACTION11CC424 - 486426 - 488
12X-RAY DIFFRACTION12DD1 - 1801 - 180

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