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- PDB-6vep: Human insulin in complex with the human insulin microreceptor in ... -

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Basic information

Entry
Database: PDB / ID: 6vep
TitleHuman insulin in complex with the human insulin microreceptor in turn in complex with Fv 83-7
Components
  • (Insulin receptor subunit ...) x 2
  • Fv 83-7 heavy chain
  • Fv 83-7 light chain
  • Insulin B chain
  • Insulin chain A
KeywordsHORMONE RECEPTOR/HORMONE/IMMUNE SYSTEM / HORMONE / HORMONE RECEPTOR-HORMONE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


regulation of female gonad development / positive regulation of meiotic cell cycle / insulin-like growth factor II binding / positive regulation of developmental growth / male sex determination / insulin receptor complex / insulin-like growth factor I binding / positive regulation of protein-containing complex disassembly / insulin receptor activity / exocrine pancreas development ...regulation of female gonad development / positive regulation of meiotic cell cycle / insulin-like growth factor II binding / positive regulation of developmental growth / male sex determination / insulin receptor complex / insulin-like growth factor I binding / positive regulation of protein-containing complex disassembly / insulin receptor activity / exocrine pancreas development / dendritic spine maintenance / cargo receptor activity / insulin binding / adrenal gland development / neuronal cell body membrane / PTB domain binding / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / amyloid-beta clearance / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / positive regulation of receptor internalization / regulation of embryonic development / insulin receptor substrate binding / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of respiratory burst involved in inflammatory response / protein kinase activator activity / epidermis development / activation of protein kinase B activity / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of lipid catabolic process / positive regulation of lipid biosynthetic process / heart morphogenesis / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / transport across blood-brain barrier / regulation of protein localization to plasma membrane / phosphatidylinositol 3-kinase binding / nitric oxide-cGMP-mediated signaling / transport vesicle / COPI-mediated anterograde transport / positive regulation of nitric-oxide synthase activity / Insulin receptor recycling / negative regulation of reactive oxygen species biosynthetic process / insulin-like growth factor receptor binding / positive regulation of brown fat cell differentiation / NPAS4 regulates expression of target genes / dendrite membrane / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / receptor-mediated endocytosis / Insulin receptor signalling cascade / positive regulation of glycolytic process / positive regulation of cytokine production / endosome lumen / positive regulation of long-term synaptic potentiation / acute-phase response / positive regulation of D-glucose import / positive regulation of protein secretion / learning / insulin receptor binding / positive regulation of cell differentiation / Regulation of insulin secretion / wound healing / positive regulation of neuron projection development / receptor protein-tyrosine kinase / hormone activity / negative regulation of protein catabolic process / regulation of synaptic plasticity / caveola / cellular response to growth factor stimulus / receptor internalization / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / cognition / memory / male gonad development / glucose metabolic process / cellular response to insulin stimulus / positive regulation of nitric oxide biosynthetic process / insulin receptor signaling pathway / late endosome / cell-cell signaling
Similarity search - Function
Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / Insulin receptor, trans-membrane domain / Insulin receptor trans-membrane segment / Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Alpha-Beta Horseshoe ...Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / Insulin receptor, trans-membrane domain / Insulin receptor trans-membrane segment / Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Alpha-Beta Horseshoe / Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Fibronectin type III domain / Growth factor receptor cysteine-rich domain superfamily / : / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Ribbon / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Insulin / Insulin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLawrence, M.C. / Menting, J.G.T.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1058233 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1143546 Australia
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2020
Title: A structurally minimized yet fully active insulin based on cone-snail venom insulin principles.
Authors: Xiong, X. / Menting, J.G. / Disotuar, M.M. / Smith, N.A. / Delaine, C.A. / Ghabash, G. / Agrawal, R. / Wang, X. / He, X. / Fisher, S.J. / MacRaild, C.A. / Norton, R.S. / Gajewiak, J. / ...Authors: Xiong, X. / Menting, J.G. / Disotuar, M.M. / Smith, N.A. / Delaine, C.A. / Ghabash, G. / Agrawal, R. / Wang, X. / He, X. / Fisher, S.J. / MacRaild, C.A. / Norton, R.S. / Gajewiak, J. / Forbes, B.E. / Smith, B.J. / Safavi-Hemami, H. / Olivera, B. / Lawrence, M.C. / Chou, D.H.
History
DepositionJan 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / 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.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _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.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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: Insulin chain A
B: Insulin B chain
C: Fv 83-7 heavy chain
D: Fv 83-7 light chain
E: Insulin receptor subunit alpha
F: Insulin receptor subunit beta
G: Insulin chain A
H: Insulin B chain
I: Fv 83-7 heavy chain
J: Fv 83-7 light chain
K: Insulin receptor subunit alpha
L: Insulin receptor subunit beta
M: Insulin chain A
N: Insulin B chain
O: Fv 83-7 heavy chain
P: Fv 83-7 light chain
Q: Insulin receptor subunit alpha
R: Insulin receptor subunit beta
S: Insulin chain A
T: Insulin B chain
U: Fv 83-7 heavy chain
V: Fv 83-7 light chain
W: Insulin receptor subunit alpha
X: Insulin receptor subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,39244
Polymers289,59324
Non-polymers9,79920
Water32418
1
A: Insulin chain A
B: Insulin B chain
C: Fv 83-7 heavy chain
D: Fv 83-7 light chain
E: Insulin receptor subunit alpha
F: Insulin receptor subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,87711
Polymers72,3986
Non-polymers2,4785
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Insulin chain A
H: Insulin B chain
I: Fv 83-7 heavy chain
J: Fv 83-7 light chain
K: Insulin receptor subunit alpha
L: Insulin receptor subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,73011
Polymers72,3986
Non-polymers2,3325
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
M: Insulin chain A
N: Insulin B chain
O: Fv 83-7 heavy chain
P: Fv 83-7 light chain
Q: Insulin receptor subunit alpha
R: Insulin receptor subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,38111
Polymers72,3986
Non-polymers1,9835
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
S: Insulin chain A
T: Insulin B chain
U: Fv 83-7 heavy chain
V: Fv 83-7 light chain
W: Insulin receptor subunit alpha
X: Insulin receptor subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,40411
Polymers72,3986
Non-polymers3,0065
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.030, 130.120, 148.180
Angle α, β, γ (deg.)90.00, 90.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide , 2 types, 8 molecules AGMSBHNT

#1: Protein/peptide
Insulin chain A


Mass: 2383.698 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Saccharomyces pastorianus CBS 1513 (yeast) / References: UniProt: P01308
#2: Protein/peptide
Insulin B chain


Mass: 3433.953 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Saccharomyces pastorianus CBS 1513 (yeast) / References: UniProt: P01308

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Insulin receptor subunit ... , 2 types, 8 molecules EKQWFLRX

#5: Protein
Insulin receptor subunit alpha / IR


Mass: 36231.762 Da / Num. of mol.: 4 / Fragment: residues 28-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INSR / Plasmid: pEE14 / Organ (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / Variant (production host): LEC 8 MUTANT
References: UniProt: P06213, receptor protein-tyrosine kinase
#6: Protein/peptide
Insulin receptor subunit beta / IR


Mass: 1922.143 Da / Num. of mol.: 4 / Fragment: residues 731-746 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: P06213, receptor protein-tyrosine kinase

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Antibody , 2 types, 8 molecules CIOUDJPV

#3: Antibody
Fv 83-7 heavy chain


Mass: 15058.748 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Igh / Production host: Brevibacillus brevis (bacteria)
#4: Antibody
Fv 83-7 light chain


Mass: 13367.913 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Brevibacillus brevis (bacteria)

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Sugars , 7 types, 20 molecules

#7: 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.: 2
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
#8: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-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.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_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
#9: 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.: 2
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
#10: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-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
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#11: 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.: 1
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
#12: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-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
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/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
#13: 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.: 8
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 , 1 types, 18 molecules

#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.33 Å3/Da / Density % sol: 63.01 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: Protein: 4.5 mg/ml in 10 mM HEPES pH 7.5 Well condition: 16% PEG 3350, 0.2 M sodium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 83231 / % possible obs: 99 % / Observed criterion σ(F): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 83.57 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.263 / Net I/σ(I): 5.7
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 3.6 % / Rmerge(I) obs: 3.64 / Mean I/σ(I) obs: 0.44 / Num. unique obs: 4086 / CC1/2: 0.112 / % possible all: 97.9

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OGA

4oga


Resolution: 2.9→48.89 Å / Cor.coef. Fo:Fc: 0.9012 / Cor.coef. Fo:Fc free: 0.8787 / SU R Cruickshank DPI: 1.071 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.812 / SU Rfree Blow DPI: 0.305 / SU Rfree Cruickshank DPI: 0.316
RfactorNum. reflection% reflectionSelection details
Rfree0.2253 4126 5 %RANDOM
Rwork0.1932 ---
obs0.1949 82572 98.11 %-
Displacement parametersBiso mean: 101.68 Å2
Baniso -1Baniso -2Baniso -3
1-9.7275 Å20 Å20.9692 Å2
2---35.1361 Å20 Å2
3---25.4085 Å2
Refine analyzeLuzzati coordinate error obs: 0.552 Å
Refinement stepCycle: 1 / Resolution: 2.9→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18652 0 648 18 19318
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0119863HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2327060HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6869SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes464HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2817HARMONIC5
X-RAY DIFFRACTIONt_it19863HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.37
X-RAY DIFFRACTIONt_other_torsion19.72
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2693SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact21263SEMIHARMONIC4
LS refinement shellResolution: 2.9→2.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 270 5 %
Rwork0.2349 5134 -
all0.2357 5404 -
obs--98.11 %
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)
14.8409-4.1080.10815.0555-2.24435.97140.058-0.8692-0.10490.35-0.00650.18510.0813-0.3886-0.05150.2894-0.1092-0.06970.26020.0478-0.243-52.6534-12.462252.688
23.0510.63171.91660.70330.02844.9236-0.3410.00630.2453-0.0272-0.02630.0806-0.1578-0.65240.3674-0.0772-0.075-0.05010.2499-0.0883-0.0963-80.0251.0459-8.3619
39.84232.2417-3.39583.06280.9619.9403-0.17452.98381.40870.3758-0.3825-0.1839-2.12462.11240.557-0.1455-0.5342-0.2586-1.0860.2814-0.0574-61.042111.5983-10.3981
42.3992-0.92481.8421.0861-0.99635.40660.07880.1676-0.2751-0.0436-0.2371-0.0120.8120.07960.15840.0285-0.1401-0.0344-0.28520.002-0.2702-55.1158-12.582322.5226
5-0.00621.03622.26210.0216-1.179718.0651-0.0531-0.64230.275-0.02020.07440.3733-0.2097-0.201-0.02120.2799-0.1641-0.118-0.30850.0146-0.0875-52.338-8.059944.0958
63.7995-1.609-1.0972.66810.497712.8081-0.18240.7105-0.661-0.75060.24820.0821-0.5052-0.3246-0.06590.2048-0.1729-0.00330.1138-0.0537-0.1839-62.24168.7478-95.6336
73.5745-0.2539-2.05881.11330.51137.3005-0.1799-0.1883-0.1961-0.3135-0.19370.18560.405-0.54320.3737-0.0588-0.18140.0050.1963-0.0606-0.1516-80.1886-7.6023-31.8426
83.8237-0.93431.05742.54310.217611.4056-0.2121-0.6448-0.45650.021-0.1597-0.21511.06242.03450.3717-0.24470.06540.10470.41610.1182-0.2287-59.2427-12.6095-31.7419
91.69321.0985-0.77352.1724-1.45444.02840.0037-0.23530.2253-0.1325-0.2845-0.1321-0.0323-0.09750.2808-0.030.03930.0683-0.1645-0.0475-0.2306-63.20699.6403-65.4256
100.01863.3896-2.01192.3636-1.635315.0081-0.0850.406-0.5474-0.17550.15460.29410.1931-0.0746-0.06970.0373-0.05570.04150.23420.0104-0.1309-60.78984.4925-87.4688
112.3921-0.25-3.428101.454413.83340.0481-1.0077-0.21120.4901-0.27210.1203-0.17680.11440.22390.2176-0.0116-0.080.0890.0068-0.1233-37.159111.991152.873
122.2595-0.4447-2.26091.3747-0.87576.4636-0.26390.3078-0.3710.0481-0.1719-0.2532-0.02060.55220.4357-0.3191-0.15040.05760.4713-0.1026-0.2493-9.49890.6087-8.604
134.45370.55060.0973.18481.70117.5025-0.43470.5886-0.6056-0.2130.11050.16870.8973-0.58660.3242-0.2459-0.29910.17540.3873-0.2197-0.1428-28.4995-10.1801-10.7203
142.1359-0.5543-1.18890.83571.34274.9669-0.02780.51620.19950.034-0.3272-0.0011-0.62830.00230.3551-0.0826-0.1161-0.0129-0.1449-0.0152-0.3431-34.172112.663223.0302
150.0464-0.9106-4.96280-0.746518.7321-0.1117-0.43-0.43980.4610.25150.00560.37760.1359-0.13970.2432-0.1044-0.0076-0.1873-0.0819-0.0545-37.2937.743544.3258
164.66230.441.1523.22611.15088.4006-0.0510.70290.325-0.4499-0.0207-0.41970.54590.79020.07170.23260.0110.0550.32920.0481-0.2417-26.18-9.17-95.6107
173.38341.01181.80510.0997-0.69689.0687-0.2468-0.15570.4171-0.2176-0.2694-0.1215-1.0120.75940.5162-0.1757-0.1854-0.04220.5125-0.0624-0.3127-9.28869.942-31.5258
183.4821.1249-0.80542.5340.325512.30720.1241-0.73590.5516-0.078-0.48090.6047-1.8162-1.95040.3568-0.33120.2937-0.16040.7511-0.2938-0.4193-30.392214.9447-31.233
192.26161.10261.97562.72151.15164.93390.0569-0.2501-0.1379-0.1608-0.27560.02880.30080.39110.2187-0.0290.0577-0.0451-0.05660.0052-0.2956-25.8627-7.8408-64.8376
202.99471.35924.058800.636414.4140.01590.47450.17390.03430.0695-0.2704-0.03730.3698-0.08540.16360.0694-0.11320.00270.0638-0.1437-27.7995-4.2927-87.3359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|21 B|1 - B|27 }A1 - 21
2X-RAY DIFFRACTION1{ A|1 - A|21 B|1 - B|27 }B1 - 27
3X-RAY DIFFRACTION2{ C|1 - C|121 }C1 - 121
4X-RAY DIFFRACTION3{ D|-1 - D|114 }D-1 - 114
5X-RAY DIFFRACTION4{ E|4 - E|309 }E4 - 309
6X-RAY DIFFRACTION5{ F|704 - F|719 }F704 - 719
7X-RAY DIFFRACTION6{ H|3 - H|27 G|1 - G|21 }H3 - 27
8X-RAY DIFFRACTION6{ H|3 - H|27 G|1 - G|21 }G1 - 21
9X-RAY DIFFRACTION7{ I|1 - I|117 }I1 - 117
10X-RAY DIFFRACTION8{ J|0 - J|112 }J0 - 112
11X-RAY DIFFRACTION9{ K|4 - K|309 }K4 - 309
12X-RAY DIFFRACTION10{ L|704 - L|719 }L704 - 719
13X-RAY DIFFRACTION11{ M|1 - M|21 N|2 - N|27 }M1 - 21
14X-RAY DIFFRACTION11{ M|1 - M|21 N|2 - N|27 }N2 - 27
15X-RAY DIFFRACTION12{ O|1 - O|122 }O1 - 122
16X-RAY DIFFRACTION13{ P|0 - P|112 }P0 - 112
17X-RAY DIFFRACTION14{ Q|5 - Q|310 }Q5 - 310
18X-RAY DIFFRACTION15{ R|704 - R|719 }R704 - 719
19X-RAY DIFFRACTION16{ S|1 - S|21 T|2 - T|27 }S1 - 21
20X-RAY DIFFRACTION16{ S|1 - S|21 T|2 - T|27 }T2 - 27
21X-RAY DIFFRACTION17{ U|1 - U|117 }U1 - 117
22X-RAY DIFFRACTION18{ V|-2 - V|111 }V-2 - 111
23X-RAY DIFFRACTION19{ W|4 - W|309 }W4 - 309
24X-RAY DIFFRACTION20{ X|704 - X|719 }X704 - 719

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