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- PDB-2x1w: Crystal Structure of VEGF-C in Complex with Domains 2 and 3 of VEGFR2 -

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Basic information

Entry
Database: PDB / ID: 2x1w
TitleCrystal Structure of VEGF-C in Complex with Domains 2 and 3 of VEGFR2
Components(VASCULAR ENDOTHELIAL GROWTH FACTOR ...) x 2
KeywordsHORMONE/SIGNALING PROTEIN / HORMONE-SIGNALING PROTEIN COMPLEX / ANGIOGENESIS / GLYCOPROTEIN / HOST-VIRUS INTERACTION / MEMBRANE / RECEPTOR / LYMPHANGIOGENESIS / IMMUNOGLOBULIN DOMAIN / DEVELOPMENTAL PROTEIN / TRANSMEMBRANE / PHOSPHOPROTEIN / DISULFIDE BOND / MITOGEN
Function / homology
Function and homology information


vascular endothelial growth factor receptor 3 binding / substrate-dependent cell migration / positive regulation of nitric oxide-cGMP mediated signal transduction / positive regulation of lymphangiogenesis / blood vessel endothelial cell differentiation / VEGF ligand-receptor interactions / cellular response to hydrogen sulfide / positive regulation of mast cell chemotaxis / regulation of bone development / morphogenesis of embryonic epithelium ...vascular endothelial growth factor receptor 3 binding / substrate-dependent cell migration / positive regulation of nitric oxide-cGMP mediated signal transduction / positive regulation of lymphangiogenesis / blood vessel endothelial cell differentiation / VEGF ligand-receptor interactions / cellular response to hydrogen sulfide / positive regulation of mast cell chemotaxis / regulation of bone development / morphogenesis of embryonic epithelium / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / regulation of vascular endothelial growth factor receptor signaling pathway / Neurophilin interactions with VEGF and VEGFR / vascular endothelial growth factor binding / positive regulation of mesenchymal stem cell proliferation / vascular endothelial growth factor receptor-2 signaling pathway / endothelium development / VEGF binds to VEGFR leading to receptor dimerization / endocardium development / vascular wound healing / regulation of hematopoietic progenitor cell differentiation / post-embryonic camera-type eye morphogenesis / lymph vessel development / mesenchymal cell proliferation / positive regulation of vasculogenesis / endothelial cell differentiation / induction of positive chemotaxis / positive regulation of BMP signaling pathway / surfactant homeostasis / cell migration involved in sprouting angiogenesis / epithelial cell maturation / positive regulation of positive chemotaxis / sprouting angiogenesis / positive regulation of endothelial cell chemotaxis / anchoring junction / embryonic hemopoiesis / vascular endothelial growth factor signaling pathway / positive regulation of mesenchymal cell proliferation / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of mitochondrial fission / branching involved in blood vessel morphogenesis / positive regulation of neuroblast proliferation / lung alveolus development / positive regulation of stem cell proliferation / positive regulation of mitochondrial depolarization / growth factor binding / chemoattractant activity / sorting endosome / regulation of MAPK cascade / semaphorin-plexin signaling pathway / positive regulation of macroautophagy / positive regulation of cell division / cellular response to vascular endothelial growth factor stimulus / positive regulation of focal adhesion assembly / cell fate commitment / positive regulation of blood vessel endothelial cell migration / negative regulation of osteoblast differentiation / Integrin cell surface interactions / vascular endothelial growth factor receptor signaling pathway / glial cell proliferation / negative regulation of endothelial cell apoptotic process / vasculogenesis / peptidyl-tyrosine autophosphorylation / calcium ion homeostasis / coreceptor activity / ovarian follicle development / positive regulation of glial cell proliferation / negative regulation of blood pressure / positive regulation of endothelial cell proliferation / transmembrane receptor protein tyrosine kinase activity / positive regulation of endothelial cell migration / cellular response to leukemia inhibitory factor / cell surface receptor protein tyrosine kinase signaling pathway / platelet alpha granule lumen / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / epithelial cell proliferation / animal organ morphogenesis / stem cell proliferation / positive regulation of protein secretion / growth factor activity / Hsp90 protein binding / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation
Similarity search - Function
CXCXC repeat / CXCXC repeat / Vascular endothelial growth factor receptor 2 (VEGFR2) / VEGFR-2, transmembrane domain / : / : / : / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-like domain / VEGFR1-3, N-terminal Ig-like domain ...CXCXC repeat / CXCXC repeat / Vascular endothelial growth factor receptor 2 (VEGFR2) / VEGFR-2, transmembrane domain / : / : / : / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-like domain / VEGFR1-3, N-terminal Ig-like domain / VEGFR-1-like, immunoglobulin-like domain / PDGF/VEGF domain / Platelet-derived growth factor, conserved site / PDGF/VEGF domain / Platelet-derived growth factor (PDGF) family signature. / Platelet-derived growth factor (PDGF) family profile. / Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Immunoglobulin domain / Cystine-knot cytokine / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Ribbon / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Vascular endothelial growth factor receptor 2 / Vascular endothelial growth factor C
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.7 Å
AuthorsLeppanen, V.M. / Prota, A.E. / Jeltsch, M. / Anisimov, A. / Kalkkinen, N. / Strandin, T. / Lankinen, H. / Goldman, A. / Ballmer-Hofer, K. / Alitalo, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural Determinants of Growth Factor Binding and Specificity by Vegf Receptor 2.
Authors: Leppanen, V.M. / Prota, A.E. / Jeltsch, M. / Anisimov, A. / Kalkkinen, N. / Strandin, T. / Lankinen, H. / Goldman, A. / Ballmer-Hofer, K. / Alitalo, K.
History
DepositionJan 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VASCULAR ENDOTHELIAL GROWTH FACTOR C
B: VASCULAR ENDOTHELIAL GROWTH FACTOR C
C: VASCULAR ENDOTHELIAL GROWTH FACTOR C
D: VASCULAR ENDOTHELIAL GROWTH FACTOR C
L: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2
M: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2
N: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2
O: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,98930
Polymers145,1988
Non-polymers8,79122
Water3,189177
1
A: VASCULAR ENDOTHELIAL GROWTH FACTOR C
B: VASCULAR ENDOTHELIAL GROWTH FACTOR C
M: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2
N: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,95614
Polymers72,5994
Non-polymers4,35710
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11830 Å2
ΔGint-33.7 kcal/mol
Surface area31640 Å2
MethodPISA
2
C: VASCULAR ENDOTHELIAL GROWTH FACTOR C
D: VASCULAR ENDOTHELIAL GROWTH FACTOR C
L: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2
O: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,03316
Polymers72,5994
Non-polymers4,43412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11970 Å2
ΔGint-19.8 kcal/mol
Surface area31930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.750, 123.830, 211.831
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 120:142 OR RESSEQ 151:169 OR RESSEQ 172:188 OR RESSEQ 196:213 )
211CHAIN B AND (RESSEQ 120:142 OR RESSEQ 151:169 OR RESSEQ 172:188 OR RESSEQ 196:213 )
112CHAIN C AND (RESSEQ 120:139 OR RESSEQ 141:146 OR RESSEQ...
212CHAIN D AND (RESSEQ 120:139 OR RESSEQ 141:146 OR RESSEQ...
113CHAIN M AND (RESSEQ 134:137 OR RESSEQ 144:201 OR RESSEQ 211:217)
213CHAIN N AND (RESSEQ 134:137 OR RESSEQ 144:201 OR RESSEQ 211:217)
114CHAIN M AND (RESSEQ 221:239 OR RESSEQ 241:264 OR RESSEQ...
214CHAIN N AND (RESSEQ 221:239 OR RESSEQ 241:264 OR RESSEQ...
115CHAIN L AND (RESSEQ 134:137 OR RESSEQ 145:201 OR RESSEQ 209:218)
215CHAIN O AND (RESSEQ 134:137 OR RESSEQ 145:201 OR RESSEQ 209:218)
116CHAIN L AND (RESSEQ 221:261 OR RESSEQ 285:325)
216CHAIN O AND (RESSEQ 221:261 OR RESSEQ 285:325)

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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VASCULAR ENDOTHELIAL GROWTH FACTOR ... , 2 types, 8 molecules ABCDLMNO

#1: Protein
VASCULAR ENDOTHELIAL GROWTH FACTOR C / VEGF-C / VASCULAR ENDOTHELIAL GROWTH FACTOR-RELATED PROTEIN / VRP / FLT4 LIGAND / FLT4-L


Mass: 12390.194 Da / Num. of mol.: 4 / Fragment: VEGF HOMOLOGY DOMAIN, RESIDUES 112-215 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P49767
#2: Protein
VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2 / VEGF RECEPTOR 2 / VEGFR-2 / KINASE INSERT DOMAIN RECEPTOR / PROTEIN-TYROSINE KINASE RECEPTOR FLK-1 ...VEGF RECEPTOR 2 / VEGFR-2 / KINASE INSERT DOMAIN RECEPTOR / PROTEIN-TYROSINE KINASE RECEPTOR FLK-1 / CD309 / FLK-1


Mass: 23909.270 Da / Num. of mol.: 4 / Fragment: IG-LIKE DOMAINS 2 AND 3, RESIDUES 120-326
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P35968

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Sugars , 3 types, 20 molecules

#3: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}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.: 4
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
#6: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
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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Non-polymers , 2 types, 179 molecules

#5: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 137 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 137 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, CYS 137 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 137 TO ALA ENGINEERED RESIDUE IN CHAIN C, CYS 137 TO ALA ENGINEERED RESIDUE IN CHAIN D, CYS 137 TO ALA
Has protein modificationY
Nonpolymer detailsNAG, MAN: N-LINKED GLYCANS (NAG AND MAN) HAVE THE SAME CHAIN IDENTIFIER AS THE PROTEIN CHAIN THEY ...NAG, MAN: N-LINKED GLYCANS (NAG AND MAN) HAVE THE SAME CHAIN IDENTIFIER AS THE PROTEIN CHAIN THEY ARE ATTACHED TO.
Sequence detailsTHE PROTEIN STUDIED COVERS RESIDUES 112-215 WITH A C- TERMINAL 6HIS-TAG AND A C137A MUTATION. THE ...THE PROTEIN STUDIED COVERS RESIDUES 112-215 WITH A C- TERMINAL 6HIS-TAG AND A C137A MUTATION. THE PROTEIN STUDIED COVERS RESIDUES 120-326 WITH THE ARTIFICIAL RESIDUES DPIEGR AT THE C-TERMINUS.

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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: 2.9 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growpH: 5.2
Details: 100 MM MES BUFFER, PH 5.0-5.6, 50 MM CSCL AND 28-32 % (W/V) JEFFAMINE 600.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→53 Å / Num. obs: 53953 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.1
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.8 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
SHELXCDE IMPLEMENTED IN HKL2MAPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.7→52.958 Å / SU ML: 0.44 / σ(F): 2 / Phase error: 28.61 / Stereochemistry target values: ML
Details: RESIDUES A112-A115, B112-B116, B215, C112-C118, D112-D116, M120-M133, M203-M209, M265- -M268, M280- M282, N120-N123, N127-N131, N266-N269, L120- -L122, L129-L132, L205-L207, O120-O122, O128- ...Details: RESIDUES A112-A115, B112-B116, B215, C112-C118, D112-D116, M120-M133, M203-M209, M265- -M268, M280- M282, N120-N123, N127-N131, N266-N269, L120- -L122, L129-L132, L205-L207, O120-O122, O128-O131, O266- -O268 AND O281 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2798 2746 5.09 %
Rwork0.2269 --
obs0.2297 53953 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.118 Å2 / ksol: 0.313 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.4363 Å20 Å20 Å2
2--5.1571 Å20 Å2
3----6.5934 Å2
Refinement stepCycle: LAST / Resolution: 2.7→52.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8980 0 563 177 9720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059778
X-RAY DIFFRACTIONf_angle_d1.00413229
X-RAY DIFFRACTIONf_dihedral_angle_d25.3173725
X-RAY DIFFRACTIONf_chiral_restr0.0621612
X-RAY DIFFRACTIONf_plane_restr0.0031579
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A600X-RAY DIFFRACTIONPOSITIONAL
12B600X-RAY DIFFRACTIONPOSITIONAL0.035
21C631X-RAY DIFFRACTIONPOSITIONAL
22D631X-RAY DIFFRACTIONPOSITIONAL0.046
31M539X-RAY DIFFRACTIONPOSITIONAL
32N539X-RAY DIFFRACTIONPOSITIONAL0.024
41M720X-RAY DIFFRACTIONPOSITIONAL
42N720X-RAY DIFFRACTIONPOSITIONAL0.041
51L558X-RAY DIFFRACTIONPOSITIONAL
52O558X-RAY DIFFRACTIONPOSITIONAL0.03
61L639X-RAY DIFFRACTIONPOSITIONAL
62O639X-RAY DIFFRACTIONPOSITIONAL0.037
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.74660.37791550.30652500X-RAY DIFFRACTION99
2.7466-2.79650.33191480.28012483X-RAY DIFFRACTION100
2.7965-2.85030.33321130.27322565X-RAY DIFFRACTION100
2.8503-2.90850.30761310.26412521X-RAY DIFFRACTION99
2.9085-2.97170.31231270.26942540X-RAY DIFFRACTION100
2.9717-3.04080.35021490.27172506X-RAY DIFFRACTION100
3.0408-3.11690.34761400.27052544X-RAY DIFFRACTION100
3.1169-3.20110.31571480.26012549X-RAY DIFFRACTION100
3.2011-3.29530.32821340.252506X-RAY DIFFRACTION100
3.2953-3.40170.31011270.2382565X-RAY DIFFRACTION100
3.4017-3.52320.29651580.23042540X-RAY DIFFRACTION100
3.5232-3.66420.24981270.21742544X-RAY DIFFRACTION100
3.6642-3.8310.28111040.21042577X-RAY DIFFRACTION100
3.831-4.03290.25521600.20182544X-RAY DIFFRACTION100
4.0329-4.28540.2531390.18232555X-RAY DIFFRACTION100
4.2854-4.61610.23351460.17072588X-RAY DIFFRACTION100
4.6161-5.08040.1971190.16512587X-RAY DIFFRACTION100
5.0804-5.81470.23871400.18522607X-RAY DIFFRACTION100
5.8147-7.32280.24771430.20952640X-RAY DIFFRACTION99
7.3228-52.96790.28871380.25882746X-RAY DIFFRACTION99
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)
10.8401-0.01131.08451.9836-1.55663.59920.0041-0.2489-0.08710.0777-0.3019-0.2526-0.6301-0.28170.26630.5038-0.02940.00650.32790.13250.3587-6.6294-9.465910.8369
26.2004-5.37420.87795.4063-1.23462.08380.05611.00680.40260.0106-0.6136-0.136-0.0292-0.17150.46010.41510.00390.0480.3713-0.00720.3839-27.44361.8417-3.3131
33.8177-5.18741.12058.1226-0.73871.4587-0.32590.3878-1.44890.39110.22652.13080.0729-0.57680.06790.11610.08090.02120.3603-0.04820.4499-34.5321.3699-2.2784
41.20750.0247-0.09520.0114-0.31132.0097-0.0044-0.55870.0750.3759-0.34350.05490.80950.01070.16910.626-0.0021-0.01590.2732-0.02920.5446-33.621712.44187.9237
5-0.0712-0.1094-0.14850.27420.39121.6568-0.09380.15860.1891-0.4352-0.0535-0.2-0.58270.1253-0.23050.4016-0.0580.04820.1280.15790.3242-11.28961.1811-1.5343
60.5777-0.28460.63581.9089-0.46171.0022-0.12780.5170.57850.2174-0.209-1.0172-0.09190.48510.26950.37-0.12120.01190.49440.13280.5916-4.63842.26310.4008
75.00890.53730.52518.2117-5.30743.5247-0.3505-1.2747-0.05221.3401-0.43530.214-0.87590.37620.47440.4393-0.08370.0880.32760.03650.1738-30.1003-17.668763.3013
80.9781.6669-1.21183.9043-2.49361.5445-0.36940.06270.0841-0.6908-0.0018-0.110.32520.03140.34270.1804-0.0398-0.02610.266-0.09280.2926-25.26345.164154.071
92.24820.60640.93621.311-0.32510.5445-0.0003-0.19510.4041-0.03960.00330.43630.0308-0.04150.0170.1228-0.01170.01610.1856-0.10160.2486-27.994810.710556.0724
102.4317-0.29790.82451.49450.85761.4615-0.2695-1.31260.06830.7347-0.2613-0.1233-0.2223-0.53730.03640.27650.0359-0.20780.5484-0.08870.2371-15.849211.148866.273
110.61830.18-0.23341.4649-0.1120.2028-0.15390.0755-0.1659-0.2979-0.0282-0.1080.0962-0.18040.12810.251-0.05250.01680.3389-0.1090.2421-22.0036-10.442652.0047
122.6148-0.30140.44190.85290.17123.25510.27050.1777-1.1310.33310.0562-0.59940.89540.1198-0.31780.31630.07630.00160.2499-0.15970.5809-18.9689-16.382952.2172
130.3340.5564-0.62580.8416-0.74471.15670.3603-0.0151-0.20040.5235-0.2364-0.111-0.13260.0179-0.07440.5259-0.15740.1060.3368-0.11650.4096-48.0187-23.259763.2995
141.3507-0.7668-0.92111.57741.57945.05460.1839-0.0002-0.0172-0.3185-0.29690.0579-0.5624-0.52040.10630.3361-0.063-0.0210.1836-0.02980.1662-34.3956-22.581225.1451
152.1654-0.49450.94580.71720.7261.1363-0.7007-0.29210.42970.16620.46940.066-1.3642-0.16880.31341.18630.3022-0.29740.48510.04430.517-31.394731.63554.4263
161.4209-0.2725-0.19521.88150.50562.1871-0.32850.324-0.1109-0.18650.06480.3704-0.5011-0.37810.14710.16210.1665-0.05960.37730.02620.2448-37.317311.7693-30.1049
173.9703-1.20550.90881.5964-2.10622.79050.1186-0.2184-0.4079-0.0602-0.0498-0.04040.91070.1686-0.04140.62990.09250.13110.33310.15440.3508-8.5247-28.15399.7103
180.99940.55440.97171.9367-0.74541.7509-0.23220.31470.34160.24640.1989-0.1671-0.10890.25710.00540.11580.08940.05570.21580.06590.19451.6071-13.9217-28.2411
190.3625-0.2921-0.24821.3624-0.29442.6723-0.0312-0.39790.33440.1454-0.138-0.6524-0.23680.9372-0.00140.1257-0.1764-0.14240.52310.01260.53272.332214.446265.6796
200.8563-0.02130.69553.114-1.38024.4260.03980.22820.07-0.4512-0.2756-0.2168-0.26790.82620.17560.3810.01440.08990.30080.04570.3836-9.020622.100326.3328
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 116:130)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 131:170)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 171:213)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 117:130)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 131:170)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 171:214)
7X-RAY DIFFRACTION7(CHAIN C AND RESID 119:130)
8X-RAY DIFFRACTION8(CHAIN C AND RESID 131:170)
9X-RAY DIFFRACTION9(CHAIN C AND RESID 171:215)
10X-RAY DIFFRACTION10(CHAIN D AND RESID 117:130)
11X-RAY DIFFRACTION11(CHAIN D AND RESID 131:170)
12X-RAY DIFFRACTION12(CHAIN D AND RESID 171:215)
13X-RAY DIFFRACTION13(CHAIN L AND RESID 123:219)
14X-RAY DIFFRACTION14(CHAIN L AND RESID 220:326)
15X-RAY DIFFRACTION15(CHAIN M AND RESID 133:219)
16X-RAY DIFFRACTION16(CHAIN M AND RESID 220:326)
17X-RAY DIFFRACTION17(CHAIN N AND RESID 124:219)
18X-RAY DIFFRACTION18(CHAIN N AND RESID 220:326)
19X-RAY DIFFRACTION19(CHAIN O AND RESID 123:219)
20X-RAY DIFFRACTION20(CHAIN O AND RESID 220:325)

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