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- PDB-5ffo: Integrin alpha V beta 6 in complex with pro-TGF-beta -

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Basic information

Entry
Database: PDB / ID: 5ffo
TitleIntegrin alpha V beta 6 in complex with pro-TGF-beta
Components
  • Integrin alpha-V
  • Integrin beta-6
  • Transforming growth factor beta-1
KeywordsCELL ADHESION / Integrin / TGF-beta
Function / homology
Function and homology information


cellular response to acetaldehyde / frontal suture morphogenesis / Influenza Virus Induced Apoptosis / adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains / positive regulation of microglia differentiation / regulation of interleukin-23 production / branch elongation involved in mammary gland duct branching / positive regulation of primary miRNA processing / columnar/cuboidal epithelial cell maturation / negative regulation of skeletal muscle tissue development ...cellular response to acetaldehyde / frontal suture morphogenesis / Influenza Virus Induced Apoptosis / adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains / positive regulation of microglia differentiation / regulation of interleukin-23 production / branch elongation involved in mammary gland duct branching / positive regulation of primary miRNA processing / columnar/cuboidal epithelial cell maturation / negative regulation of skeletal muscle tissue development / macrophage derived foam cell differentiation / response to laminar fluid shear stress / embryonic liver development / regulation of enamel mineralization / regulation of branching involved in mammary gland duct morphogenesis / regulation of cartilage development / TGFBR2 MSI Frameshift Mutants in Cancer / regulation of striated muscle tissue development / regulation of blood vessel remodeling / regulation of protein import into nucleus / regulatory T cell differentiation / tolerance induction to self antigen / extracellular matrix assembly / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of hyaluronan biosynthetic process / type III transforming growth factor beta receptor binding / myofibroblast differentiation / positive regulation of cardiac muscle cell differentiation / positive regulation of odontogenesis / connective tissue replacement involved in inflammatory response wound healing / Langerhans cell differentiation / TGFBR2 Kinase Domain Mutants in Cancer / positive regulation of smooth muscle cell differentiation / positive regulation of exit from mitosis / negative regulation of macrophage cytokine production / integrin alphav-beta8 complex / odontoblast differentiation / integrin alphav-beta6 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / opsonin binding / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / positive regulation of isotype switching to IgA isotypes / positive regulation of mesenchymal stem cell proliferation / enamel mineralization / positive regulation of receptor signaling pathway via STAT / membrane protein intracellular domain proteolysis / positive regulation of extracellular matrix assembly / retina vasculature development in camera-type eye / heart valve morphogenesis / bronchiole development / mammary gland branching involved in thelarche / hyaluronan catabolic process / integrin alphav-beta1 complex / Cross-presentation of particulate exogenous antigens (phagosomes) / extracellular matrix protein binding / TGFBR3 regulates TGF-beta signaling / positive regulation of vasculature development / lens fiber cell differentiation / ATP biosynthetic process / negative regulation of extracellular matrix disassembly / type II transforming growth factor beta receptor binding / receptor catabolic process / positive regulation of branching involved in ureteric bud morphogenesis / Laminin interactions / TGFBR1 LBD Mutants in Cancer / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / positive regulation of chemotaxis / type I transforming growth factor beta receptor binding / entry into host cell by a symbiont-containing vacuole / response to salt / germ cell migration / positive regulation of mononuclear cell migration / alphav-beta3 integrin-PKCalpha complex / endoderm development / negative regulation of biomineral tissue development / phospholipid homeostasis / negative regulation of cell-cell adhesion mediated by cadherin / negative regulation of myoblast differentiation / positive regulation of vascular permeability / alphav-beta3 integrin-HMGB1 complex / negative regulation of lipid transport / hard palate development / regulation of phagocytosis / response to cholesterol / oligodendrocyte development / Elastic fibre formation / cell-cell junction organization / negative regulation of interleukin-17 production / phosphate-containing compound metabolic process / surfactant homeostasis / alphav-beta3 integrin-IGF-1-IGF1R complex / transforming growth factor beta binding / positive regulation of small GTPase mediated signal transduction / deubiquitinase activator activity / sprouting angiogenesis / negative regulation of release of sequestered calcium ion into cytosol
Similarity search - Function
Jelly Rolls - #970 / Transforming growth factor beta-1 proprotein / Integrin domains. Chain A, domain 2 / Transforming growth factor-beta / Integrin alpha, N-terminal / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related ...Jelly Rolls - #970 / Transforming growth factor beta-1 proprotein / Integrin domains. Chain A, domain 2 / Transforming growth factor-beta / Integrin alpha, N-terminal / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta tail domain / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain, extracellular / EGF-like domain / Integrin alpha cytoplasmic region / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / Cystine-knot cytokine / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Jelly Rolls / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Transforming growth factor beta-1 proprotein / Integrin alpha-V / Integrin beta-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.49 Å
AuthorsDong, X. / Zhao, B. / Springer, T.A.
CitationJournal: Nature / Year: 2017
Title: Force interacts with macromolecular structure in activation of TGF-beta.
Authors: Dong, X. / Zhao, B. / Iacob, R.E. / Zhu, J. / Koksal, A.C. / Lu, C. / Engen, J.R. / Springer, T.A.
History
DepositionDec 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Feb 15, 2017Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_struct_conn_angle / 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.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 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 / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin alpha-V
B: Integrin beta-6
C: Transforming growth factor beta-1
D: Transforming growth factor beta-1
E: Integrin alpha-V
F: Integrin beta-6
G: Transforming growth factor beta-1
H: Transforming growth factor beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)368,61640
Polymers355,6278
Non-polymers12,98932
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34200 Å2
ΔGint75 kcal/mol
Surface area138500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.440, 91.440, 131.030
Angle α, β, γ (deg.)89.98, 86.25, 89.85
Int Tables number1
Space group name H-MP1

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Components

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Protein , 3 types, 8 molecules AEBFCDGH

#1: Protein Integrin alpha-V / Vitronectin receptor subunit alpha


Mass: 65982.922 Da / Num. of mol.: 2 / Fragment: UNP residues 31-627
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAV, MSK8, VNRA / Production host: Homo sapiens (human) / References: UniProt: P06756
#2: Protein Integrin beta-6


Mass: 28851.707 Da / Num. of mol.: 2 / Fragment: Unp residues 128-378
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB6 / Production host: Homo sapiens (human) / References: UniProt: P18564
#3: Protein
Transforming growth factor beta-1 / TGF-beta-1


Mass: 41489.371 Da / Num. of mol.: 4 / Fragment: UNP residues 34-390
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFB1, TGFB / Production host: Homo sapiens (human) / References: UniProt: P01137

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Sugars , 8 types, 18 molecules

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


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e6-f1WURCSPDB2Glycan 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-D-Manp]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 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-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#7: 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)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_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]{}}}}}LINUCSPDB-CARE
#8: 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
#9: 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)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/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
#10: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#12: 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.: 4
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 , 3 types, 19 molecules

#11: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#13: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 8% PEG8000 0.1M Immidazole / PH range: 7.5-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03318 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 3.49→50 Å / Num. obs: 45279 / % possible obs: 94.6 % / Redundancy: 1.8 % / CC1/2: 0.988 / Rmerge(I) obs: 0.168 / Net I/σ(I): 4.6
Reflection shellResolution: 3.5→3.64 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 0.4 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 3.49→45.72 Å / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 27.95 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2774 1116 2.46 %
Rwork0.2236 --
obs0.2257 45279 94.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.49→45.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22945 0 836 5 23786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00724469
X-RAY DIFFRACTIONf_angle_d0.79833145
X-RAY DIFFRACTIONf_dihedral_angle_d11.43514775
X-RAY DIFFRACTIONf_chiral_restr0.0453786
X-RAY DIFFRACTIONf_plane_restr0.0044184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4948-3.65350.30781390.28145647X-RAY DIFFRACTION95
3.6535-3.84560.29441290.28325610X-RAY DIFFRACTION94
3.8456-4.08590.29051350.28895609X-RAY DIFFRACTION94
4.0859-4.40020.35651470.28095430X-RAY DIFFRACTION92
4.4002-4.84080.30771200.25045551X-RAY DIFFRACTION93
4.8408-5.53640.26111380.22585496X-RAY DIFFRACTION93
5.5364-6.95680.31551240.21325485X-RAY DIFFRACTION92
6.9568-27.62760.23281260.16685273X-RAY DIFFRACTION89
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)
13.20781.23070.63883.4324-1.14184.6346-0.0145-0.22480.5827-0.4781-0.3381-0.87170.45231.8850.32910.84140.8803-0.13772.4760.24412.60285.891-12.773428.0881
20.6045-0.14431.93010.534-0.16676.05720.0497-0.00960.73530.8469-0.3804-0.3132-0.12471.61320.43492.0681-0.0538-0.58933.0336-0.46822.346220.9843-13.421478.5475
32.5677-1.6587-0.52978.59371.51088.18641.79930.22.4533-2.4543-1.50294.3965-0.5156-0.9771-0.50620.8671-0.1914-0.58521.03410.41612.338-25.912-1.121723.2451
45.9439-3.39550.42335.1988-3.07223.59530.82110.8581-0.7611-2.0155-0.62250.33151.18670.3923-0.24892.29820.0296-0.1131.7862-0.42931.4506-21.6655-17.3987-46.163
51.78440.8997-2.88151.07070.30549.66690.17120.89890.7853-1.15740.39190.21330.3524-1.4933-0.50812.49770.5953-0.3392.1728-0.0941.929-44.76785.3811-48.5697
66.8323-0.5789-2.82683.21430.31485.6067-0.18460.7337-1.74870.2339-0.20440.03990.29780.93980.3871.73380.3236-0.56481.5444-0.20471.6575-29.3088-14.6847-11.8844
73.54552.8342-5.02547.7608-3.43338.26370.7824-0.24650.8045-0.4917-0.11170.37870.01780.8212-0.49421.95091.1581-0.47212.2985-0.39481.5946-40.819813.0102-19.7696
84.14121.0825-0.72980.55750.60417.1412-0.00540.42920.7251-0.132-0.48970.8695-0.9027-1.80920.38371.83950.7612-0.1441.5728-0.24721.7493-6.3688-58.3939-26.871
94.1476-1.23750.76172.8021-1.7182.621-0.29571.23760.2808-0.45110.29090.38820.5943-0.465-0.1132.10840.3535-0.34682.8865-0.12422.3933-21.4691-58.958-76.9923
109.8717-2.0624-2.18765.3751.28584.4994-1.07490.8798-0.6311-0.50521.08761.8643-0.8674-1.11270.16682.1365-0.0354-0.57441.52350.17072.557825.6069-46.8526-21.9897
117.48790.2011-0.02675.9341-0.41526.06150.1442-1.6511-1.45071.56610.35250.55340.876-0.5787-0.36081.99730.07130.23151.82320.44011.512721.3391-63.136747.3858
122.92483.2482-3.51963.8854-5.13219.14620.8315-1.1154-0.2951.5704-1.7243-0.7349-2.61680.82010.71942.64710.2881-0.30562.01240.02691.603944.0283-40.199549.8581
136.88792.49171.78283.1124-1.4032.3240.06510.8059-0.37750.10250.2079-0.09840.397-0.2333-0.28182.09720.29030.32021.4558-0.29161.250428.6073-60.797513.4684
144.76781.96190.54531.7955-2.25926.4019-1.02730.1765-1.15340.5810.01590.14320.54040.77281.14291.74120.6372-0.27670.6167-0.49272.45840.5503-32.415720.6862
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:438 )A1 - 438
2X-RAY DIFFRACTION2( CHAIN A AND RESID 439:594 )A439 - 594
3X-RAY DIFFRACTION3( CHAIN B AND ( RESID 113:354 OR RESID 2001:2004 ) )B113 - 354
4X-RAY DIFFRACTION3( CHAIN B AND ( RESID 113:354 OR RESID 2001:2004 ) )B2001 - 2004
5X-RAY DIFFRACTION4( CHAIN C AND RESID 42:240 )C42 - 240
6X-RAY DIFFRACTION5( CHAIN C AND ( RESID 8:41 OR RESID 250:361 ) )C8 - 41
7X-RAY DIFFRACTION5( CHAIN C AND ( RESID 8:41 OR RESID 250:361 ) )C250 - 361
8X-RAY DIFFRACTION6( CHAIN D AND RESID 42:240 )D42 - 240
9X-RAY DIFFRACTION7( CHAIN D AND ( RESID 7:41 OR RESID 256:361 ) )D7 - 41
10X-RAY DIFFRACTION7( CHAIN D AND ( RESID 7:41 OR RESID 256:361 ) )D256 - 361
11X-RAY DIFFRACTION8( CHAIN E AND RESID 1:438 )E1 - 438
12X-RAY DIFFRACTION9( CHAIN E AND RESID 439:591 )E439 - 591
13X-RAY DIFFRACTION10( CHAIN F AND ( RESID 113:354 OR RESID 2001:2004 ) )F113 - 354
14X-RAY DIFFRACTION10( CHAIN F AND ( RESID 113:354 OR RESID 2001:2004 ) )F2001 - 2004
15X-RAY DIFFRACTION11( CHAIN G AND RESID 42:240 )G42 - 240
16X-RAY DIFFRACTION12( CHAIN G AND ( RESID 10:41 OR RESID 250:361 ) )G10 - 41
17X-RAY DIFFRACTION12( CHAIN G AND ( RESID 10:41 OR RESID 250:361 ) )G250 - 361
18X-RAY DIFFRACTION13( CHAIN H AND RESID 42:240 )H42 - 240
19X-RAY DIFFRACTION14( CHAIN H AND ( RESID 5:41 OR RESID 259:361 ) )H5 - 41
20X-RAY DIFFRACTION14( CHAIN H AND ( RESID 5:41 OR RESID 259:361 ) )H259 - 361

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