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- PDB-3b2u: Crystal structure of isolated domain III of the extracellular reg... -

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Basic information

Entry
Database: PDB / ID: 3b2u
TitleCrystal structure of isolated domain III of the extracellular region of the epidermal growth factor receptor in complex with the Fab fragment of IMC-11F8
Components
  • (IMC-11F8 Fab ...) x 2
  • Epidermal growth factor receptor
KeywordsIMMUNE SYSTEM/TRANSFERASE / CELL SURFACE RECEPTOR / GLYCOPROTEIN / ANTIGEN:ANTIBODY COMPLEX / FAB FRAGMENT / ANTITUMOR / DRUG / Anti-oncogene / ATP-binding / Cell cycle / Disease mutation / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Secreted / Transferase / Transmembrane / Tyrosine-protein kinase / IMMUNE SYSTEM-TRANSFERASE COMPLEX
Function / homology
Function and homology information


response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of protein kinase C activity / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / diterpenoid metabolic process / Shc-EGFR complex / ovulation cycle / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity ...response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of protein kinase C activity / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / diterpenoid metabolic process / Shc-EGFR complex / ovulation cycle / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / positive regulation of mucus secretion / epidermal growth factor binding / response to UV-A / tongue development / PLCG1 events in ERBB2 signaling / midgut development / hydrogen peroxide metabolic process / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / ERBB2-EGFR signaling pathway / PTK6 promotes HIF1A stabilization / digestive tract morphogenesis / morphogenesis of an epithelial fold / ERBB2 Activates PTK6 Signaling / intracellular vesicle / Signaling by EGFR / transmembrane receptor protein tyrosine kinase activator activity / negative regulation of epidermal growth factor receptor signaling pathway / response to cobalamin / Signaling by ERBB4 / protein tyrosine kinase activator activity / eyelid development in camera-type eye / protein insertion into membrane / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / immunoglobulin complex / regulation of JNK cascade / Respiratory syncytial virus (RSV) attachment and entry / PI3K events in ERBB2 signaling / positive regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of mitotic cell cycle / MAP kinase kinase kinase activity / hair follicle development / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / embryonic placenta development / positive regulation of bone resorption / GAB1 signalosome / positive regulation of G1/S transition of mitotic cell cycle / salivary gland morphogenesis / peptidyl-tyrosine autophosphorylation / positive regulation of phosphorylation / regulation of peptidyl-tyrosine phosphorylation / positive regulation of glial cell proliferation / Signaling by ERBB2 / positive regulation of vasoconstriction / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / cellular response to epidermal growth factor stimulus / cellular response to cadmium ion / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / GRB2 events in ERBB2 signaling / transmembrane receptor protein tyrosine kinase activity / positive regulation of DNA repair / SHC1 events in ERBB2 signaling / cellular response to dexamethasone stimulus / ossification / regulation of ERK1 and ERK2 cascade / positive regulation of synaptic transmission, glutamatergic / basal plasma membrane / neuron projection morphogenesis / neurogenesis / positive regulation of epithelial cell proliferation / positive regulation of superoxide anion generation / positive regulation of DNA replication / epithelial cell proliferation / Signal transduction by L1 / cellular response to estradiol stimulus / astrocyte activation / NOTCH3 Activation and Transmission of Signal to the Nucleus / liver regeneration / positive regulation of protein localization to plasma membrane / Signaling by ERBB2 TMD/JMD mutants / cellular response to amino acid stimulus / positive regulation of smooth muscle cell proliferation / EGFR downregulation / lung development / positive regulation of MAP kinase activity / Constitutive Signaling by EGFRvIII / clathrin-coated endocytic vesicle membrane / Signaling by ERBB2 ECD mutants / epidermal growth factor receptor signaling pathway / Signaling by ERBB2 KD Mutants / negative regulation of protein catabolic process / receptor protein-tyrosine kinase / kinase binding / positive regulation of miRNA transcription / Downregulation of ERBB2 signaling / cell-cell adhesion / ruffle membrane
Similarity search - Function
24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Alpha-Beta Horseshoe / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain ...24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Alpha-Beta Horseshoe / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / 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 / : / Growth factor receptor cysteine-rich domain superfamily / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Tyrosine-protein kinase, active site / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / 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 / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Epidermal growth factor receptor / IGH@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.58 Å
AuthorsFerguson, K.M. / Li, S. / Kussie, P.
CitationJournal: Structure / Year: 2008
Title: Structural basis for EGF receptor inhibition by the therapeutic antibody IMC-11F8.
Authors: Li, S. / Kussie, P. / Ferguson, K.M.
History
DepositionOct 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_validate_close_contact / software
Item: _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 ..._pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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_ref_seq_dif / 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 / _chem_comp.type / _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_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IMC-11F8 Fab Light chain
H: IMC-11F8 Fab Heavy chain
A: Epidermal growth factor receptor
D: IMC-11F8 Fab Light chain
C: IMC-11F8 Fab Heavy chain
B: Epidermal growth factor receptor
G: IMC-11F8 Fab Light chain
F: IMC-11F8 Fab Heavy chain
E: Epidermal growth factor receptor
K: IMC-11F8 Fab Light chain
J: IMC-11F8 Fab Heavy chain
I: Epidermal growth factor receptor
O: IMC-11F8 Fab Light chain
N: IMC-11F8 Fab Heavy chain
M: Epidermal growth factor receptor
R: IMC-11F8 Fab Light chain
Q: IMC-11F8 Fab Heavy chain
P: Epidermal growth factor receptor
U: IMC-11F8 Fab Light chain
T: IMC-11F8 Fab Heavy chain
S: Epidermal growth factor receptor
X: IMC-11F8 Fab Light chain
W: IMC-11F8 Fab Heavy chain
V: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)577,65164
Polymers563,55224
Non-polymers14,09940
Water18,6641036
1
L: IMC-11F8 Fab Light chain
H: IMC-11F8 Fab Heavy chain
A: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1568
Polymers70,4443
Non-polymers1,7125
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
MethodPISA
2
D: IMC-11F8 Fab Light chain
C: IMC-11F8 Fab Heavy chain
B: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8977
Polymers70,4443
Non-polymers1,4534
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
MethodPISA
3
G: IMC-11F8 Fab Light chain
F: IMC-11F8 Fab Heavy chain
E: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2529
Polymers70,4443
Non-polymers1,8086
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
MethodPISA
4
K: IMC-11F8 Fab Light chain
J: IMC-11F8 Fab Heavy chain
I: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5218
Polymers70,4443
Non-polymers2,0775
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
MethodPISA
5
O: IMC-11F8 Fab Light chain
N: IMC-11F8 Fab Heavy chain
M: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8458
Polymers70,4443
Non-polymers2,4015
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
MethodPISA
6
R: IMC-11F8 Fab Light chain
Q: IMC-11F8 Fab Heavy chain
P: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8977
Polymers70,4443
Non-polymers1,4534
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
MethodPISA
7
U: IMC-11F8 Fab Light chain
T: IMC-11F8 Fab Heavy chain
S: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9938
Polymers70,4443
Non-polymers1,5495
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
MethodPISA
8
X: IMC-11F8 Fab Light chain
W: IMC-11F8 Fab Heavy chain
V: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0909
Polymers70,4443
Non-polymers1,6456
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.373, 139.122, 175.325
Angle α, β, γ (deg.)90.000, 90.020, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABEIMPSV

#3: Protein
Epidermal growth factor receptor / Receptor tyrosine-protein kinase ErbB-1


Mass: 23786.088 Da / Num. of mol.: 8 / Fragment: sequence database residues 335-538
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR, ERBB1 / Production host: Mus musculus (house mouse) / Strain (production host): NS0
References: UniProt: P00533, receptor protein-tyrosine kinase

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Antibody , 2 types, 16 molecules LDGKORUXHCFJNQTW

#1: Antibody
IMC-11F8 Fab Light chain


Mass: 23053.557 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
#2: Antibody
IMC-11F8 Fab Heavy chain


Mass: 23604.381 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse) / Strain (production host): NS0 / References: UniProt: Q6GMX6*PLUS

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Sugars , 5 types, 32 molecules

#4: 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
#5: 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
#6: 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.: 7
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
#7: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-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: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 14
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, 1044 molecules

#9: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1036 / 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: 3.34 Å3/Da / Density % sol: 63.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5
Details: 12 % PEG 3350, 0.25 M ammonium acetate, 50 mM sodium acetate, pH 5.0, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.57→50 Å / Num. all: 231454 / Num. obs: 231454 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 53 Å2 / Rmerge(I) obs: 0.097 / Χ2: 1.025 / Net I/σ(I): 9.7
Reflection shellResolution: 2.57→2.69 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 2.4 / Num. unique all: 22862 / Χ2: 0.991 / % possible all: 99

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
DMphasing
REFMACrefinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1yy9, 1ce1, and 1dn0

1yy9

1ce1

1dn0


Resolution: 2.58→43.07 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.843 / SU B: 23.221 / SU ML: 0.252 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.467 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.291 11664 5 %RANDOM
Rwork0.227 ---
all0.23 233995 --
obs0.23 231396 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.071 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å2-0.04 Å2
2--0.39 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.58→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37083 0 916 1036 39035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02238967
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.97953294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.70754952
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39924.5381428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.2155714
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.33415127
X-RAY DIFFRACTIONr_chiral_restr0.0930.26282
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0228878
X-RAY DIFFRACTIONr_nbd_refined0.2080.213579
X-RAY DIFFRACTIONr_nbtor_refined0.3030.225586
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.21357
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.25
X-RAY DIFFRACTIONr_mcbond_it0.4241.525370
X-RAY DIFFRACTIONr_mcangle_it0.757239910
X-RAY DIFFRACTIONr_scbond_it1.193315519
X-RAY DIFFRACTIONr_scangle_it1.9874.513384
LS refinement shellResolution: 2.58→2.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 773 -
Rwork0.32 13941 -
all-14714 -
obs-14714 85.95 %

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  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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