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- PDB-3l95: Crystal structure of the human Notch1 Negative Regulatory Region ... -

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Basic information

Entry
Database: PDB / ID: 3l95
TitleCrystal structure of the human Notch1 Negative Regulatory Region (NRR) bound to the fab fragment of an antagonist antibody
Components
  • (anti-NRR1 fab fragment ...) x 2
  • Neurogenic locus notch homolog protein 1
KeywordsIMMUNE SYSTEM / NRR / fab fragment / antibody / ALPHA-BETA-SANDWICH / SEA DOMAIN / LNR / LIN12 NOTCH CYSTEINE-RICH / HD DOMAIN / CELL CYCLE / SIGNALING PROTEIN / Activator / ANK repeat / Cell membrane / Developmental protein / Differentiation / EGF-like domain / Glycoprotein / Membrane / Metal-binding / Notch signaling pathway
Function / homology
Function and homology information


Defective LFNG causes SCDO3 / coronary sinus valve morphogenesis / cardiac right atrium morphogenesis / cardiac right ventricle formation / growth involved in heart morphogenesis / Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation / cell differentiation in spinal cord / retinal cone cell differentiation / venous endothelial cell differentiation / arterial endothelial cell differentiation ...Defective LFNG causes SCDO3 / coronary sinus valve morphogenesis / cardiac right atrium morphogenesis / cardiac right ventricle formation / growth involved in heart morphogenesis / Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation / cell differentiation in spinal cord / retinal cone cell differentiation / venous endothelial cell differentiation / arterial endothelial cell differentiation / cardiac chamber formation / epithelial cell fate commitment / negative regulation of pro-B cell differentiation / Pre-NOTCH Processing in the Endoplasmic Reticulum / negative regulation of inner ear auditory receptor cell differentiation / mitral valve formation / cell migration involved in endocardial cushion formation / glomerular mesangial cell development / negative regulation of photoreceptor cell differentiation / negative regulation of cell proliferation involved in heart valve morphogenesis / regulation of somitogenesis / inhibition of neuroepithelial cell differentiation / endocardium morphogenesis / atrioventricular node development / foregut morphogenesis / regulation of cell adhesion involved in heart morphogenesis / distal tubule development / MAML1-RBP-Jkappa- ICN1 complex / regulation of epithelial cell proliferation involved in prostate gland development / auditory receptor cell fate commitment / positive regulation of aorta morphogenesis / negative regulation of endothelial cell chemotaxis / neuroendocrine cell differentiation / collecting duct development / negative regulation of extracellular matrix constituent secretion / positive regulation of transcription of Notch receptor target / cellular response to tumor cell / positive regulation of apoptotic process involved in morphogenesis / compartment pattern specification / vasculogenesis involved in coronary vascular morphogenesis / T-helper 17 type immune response / regulation of extracellular matrix assembly / endocardial cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / cardiac ventricle morphogenesis / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / positive regulation of smooth muscle cell differentiation / cardiac left ventricle morphogenesis / mesenchymal cell development / epidermal cell fate specification / coronary vein morphogenesis / negative regulation of collagen biosynthetic process / cardiac vascular smooth muscle cell development / negative regulation of myotube differentiation / somatic stem cell division / left/right axis specification / negative regulation of cardiac muscle hypertrophy / negative regulation of cell adhesion molecule production / interleukin-17-mediated signaling pathway / positive regulation of endothelial cell differentiation / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / apoptotic process involved in embryonic digit morphogenesis / endocardium development / positive regulation of cardiac epithelial to mesenchymal transition / Pre-NOTCH Processing in Golgi / cardiac epithelial to mesenchymal transition / cellular response to follicle-stimulating hormone stimulus / negative regulation of calcium ion-dependent exocytosis / pericardium morphogenesis / cardiac atrium morphogenesis / cardiac muscle cell myoblast differentiation / negative regulation of catalytic activity / neuronal stem cell population maintenance / tissue regeneration / regulation of stem cell proliferation / negative regulation of oligodendrocyte differentiation / positive regulation of astrocyte differentiation / calcium-ion regulated exocytosis / pulmonary valve morphogenesis / heart trabecula morphogenesis / negative regulation of biomineral tissue development / endoderm development / coronary artery morphogenesis / negative regulation of cell-cell adhesion mediated by cadherin / prostate gland epithelium morphogenesis / luteolysis / cardiac muscle tissue morphogenesis / ventricular trabecula myocardium morphogenesis / negative regulation of myoblast differentiation / tube formation / negative regulation of cell migration involved in sprouting angiogenesis / transcription regulator activator activity / negative regulation of stem cell differentiation / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of BMP signaling pathway / positive regulation of keratinocyte differentiation / astrocyte differentiation / inflammatory response to antigenic stimulus / negative regulation of ossification / positive regulation of Ras protein signal transduction
Similarity search - Function
GMP Synthetase; Chain A, domain 3 - #320 / Alpha-Beta Plaits - #3310 / Neurogenic locus notch homolog protein 1 / Notch, C-terminal / Domain of unknown function / Notch / Notch, NOD domain / Notch, NODP domain / NOTCH protein / NOTCH protein ...GMP Synthetase; Chain A, domain 3 - #320 / Alpha-Beta Plaits - #3310 / Neurogenic locus notch homolog protein 1 / Notch, C-terminal / Domain of unknown function / Notch / Notch, NOD domain / Notch, NODP domain / NOTCH protein / NOTCH protein / NOD / NODP / Notch-like domain superfamily / LNR (Lin-12/Notch) repeat profile. / LNR domain / Notch domain / Domain found in Notch and Lin-12 / EGF-like, conserved site / Human growth factor-like EGF / : / Calcium-binding EGF domain / Ankyrin repeats (many copies) / GMP Synthetase; Chain A, domain 3 / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / Ankyrin repeat / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Alpha-Beta Plaits / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Neurogenic locus notch homolog protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsHymowitz, S.G. / de Leon, G.P.
CitationJournal: Nature / Year: 2010
Title: Therapeutic antibody targeting of individual Notch receptors.
Authors: Wu, Y. / Cain-Hom, C. / Choy, L. / Hagenbeek, T.J. / de Leon, G.P. / Chen, Y. / Finkle, D. / Venook, R. / Wu, X. / Ridgway, J. / Schahin-Reed, D. / Dow, G.J. / Shelton, A. / Stawicki, S. / ...Authors: Wu, Y. / Cain-Hom, C. / Choy, L. / Hagenbeek, T.J. / de Leon, G.P. / Chen, Y. / Finkle, D. / Venook, R. / Wu, X. / Ridgway, J. / Schahin-Reed, D. / Dow, G.J. / Shelton, A. / Stawicki, S. / Watts, R.J. / Zhang, J. / Choy, R. / Howard, P. / Kadyk, L. / Yan, M. / Zha, J. / Callahan, C.A. / Hymowitz, S.G. / Siebel, C.W.
History
DepositionJan 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 25, 2013Group: Source and taxonomy
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_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 / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: anti-NRR1 fab fragment light chain
B: anti-NRR1 fab fragment heavy chain
X: Neurogenic locus notch homolog protein 1
L: anti-NRR1 fab fragment light chain
H: anti-NRR1 fab fragment heavy chain
Y: Neurogenic locus notch homolog protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,12114
Polymers149,3606
Non-polymers7618
Water1,45981
1
A: anti-NRR1 fab fragment light chain
B: anti-NRR1 fab fragment heavy chain
X: Neurogenic locus notch homolog protein 1
H: anti-NRR1 fab fragment heavy chain
Y: Neurogenic locus notch homolog protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,78313
Polymers126,0225
Non-polymers7618
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-55 kcal/mol
Surface area28910 Å2
MethodPISA
2
X: Neurogenic locus notch homolog protein 1
L: anti-NRR1 fab fragment light chain
H: anti-NRR1 fab fragment heavy chain
Y: Neurogenic locus notch homolog protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,44611
Polymers101,7814
Non-polymers6657
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-44 kcal/mol
Surface area27960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.254, 163.934, 179.620
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-IDDetails
11A
21L
12B
22H
13A
23L
14B
24H
15X
25Y

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 107
2114L1 - 107
1124B1 - 111
2124H1 - 111
1134A108 - 212
2134L108 - 212
1144B112 - 214
2144H112 - 214
1156X1461 - 1721
2156Y1461 - 1721

NCS ensembles :
ID
1
2
3
4
5

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Components

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Antibody , 2 types, 4 molecules ALBH

#1: Antibody anti-NRR1 fab fragment light chain


Mass: 23337.854 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic antibody generated with phage display / Source: (synth.) Homo sapiens (human)
#2: Antibody anti-NRR1 fab fragment heavy chain


Mass: 24241.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic antibody generated with phage display / Source: (synth.) Homo sapiens (human)

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Protein / Sugars , 2 types, 3 molecules XY

#3: Protein Neurogenic locus notch homolog protein 1 / Notch 1 / hN1 / Translocation-associated notch protein TAN-1 / Notch 1 extracellular truncation / ...Notch 1 / hN1 / Translocation-associated notch protein TAN-1 / Notch 1 extracellular truncation / Notch 1 intracellular domain


Mass: 27100.951 Da / Num. of mol.: 2 / Fragment: Negative regulatory region (NRR1)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Protein selected by phage display / Gene: human Notch 1, NOTCH1, TAN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P46531
#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.: 1
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

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Non-polymers , 3 types, 88 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7.5
Details: Equal volumes of protein and well solutions. Protein: 6 mg/mL in 150 mM NaCl, 20 mM Bis-Tris pH 6.5. Well solution: 300 mM di-Ammonium Sulfate, 20% PEG 5000 MME, 100 mM Tris pH 7.5, VAPOR ...Details: Equal volumes of protein and well solutions. Protein: 6 mg/mL in 150 mM NaCl, 20 mM Bis-Tris pH 6.5. Well solution: 300 mM di-Ammonium Sulfate, 20% PEG 5000 MME, 100 mM Tris pH 7.5, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→30 Å / Num. all: 71794 / Num. obs: 69923 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rsym value: 0.098 / Net I/σ(I): 14.9
Reflection shellResolution: 2.19→2.32 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 4.2 / Rsym value: 0.496 / % possible all: 88.5

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb 2OO4, fab fragment

2oo4


Resolution: 2.19→30 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.898 / SU B: 17.318 / SU ML: 0.209 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.341 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27076 6979 10 %RANDOM
Rwork0.22233 ---
obs0.22721 62930 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.279 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å20 Å20 Å2
2--0.4 Å20 Å2
3---1.51 Å2
Refinement stepCycle: LAST / Resolution: 2.19→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9986 0 39 81 10106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02210292
X-RAY DIFFRACTIONr_bond_other_d0.0010.026840
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.94114012
X-RAY DIFFRACTIONr_angle_other_deg0.8213.00616619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.87251302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23624.568451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.618151590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1491543
X-RAY DIFFRACTIONr_chiral_restr0.0660.21534
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211599
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022072
X-RAY DIFFRACTIONr_nbd_refined0.1880.22043
X-RAY DIFFRACTIONr_nbd_other0.1850.26794
X-RAY DIFFRACTIONr_nbtor_refined0.1740.24950
X-RAY DIFFRACTIONr_nbtor_other0.0820.25539
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2247
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.219
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.267
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.2140
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3972.56708
X-RAY DIFFRACTIONr_mcbond_other0.572.52654
X-RAY DIFFRACTIONr_mcangle_it3.579510463
X-RAY DIFFRACTIONr_scbond_it2.2022.54187
X-RAY DIFFRACTIONr_scangle_it3.19953548
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1373medium positional0.420.5
2B1542medium positional0.390.5
3A1366medium positional0.410.5
4B1224medium positional0.420.5
5X2697loose positional0.595
1A1373medium thermal0.562
2B1542medium thermal0.62
3A1366medium thermal0.32
4B1224medium thermal0.392
5X2697loose thermal3.2210
LS refinement shellResolution: 2.19→2.235 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.362 322 -
Rwork0.295 3061 -
obs--81.91 %
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)
11.4419-0.20740.22541.10340.34980.73210.0340.09430.101-0.0582-0.04980.0322-0.08160.00480.0158-0.1362-0.00230.0086-0.1808-0.014-0.0868-12.1002-25.43321.3977
23.71990.39450.33810.61120.03231.17230.0168-0.4188-0.02730.0456-0.0514-0.0075-0.0447-0.01270.0347-0.1511-0.00290.0028-0.1338-0.0159-0.2433-4.0428-30.979528.449
33.43991.7021-1.57261.6613-1.80685.4864-0.0091-0.00240.19960.21540.2959-0.0378-0.5495-0.6572-0.28680.01210.09590.0371-0.0027-0.018-0.1758-2.5366-30.885563.3461
41.7346-0.3479-0.23121.22110.25721.3379-0.0369-0.2490.0204-0.0798-0.01470.0208-0.0384-0.0030.0516-0.0593-0.0017-0.0276-0.1216-0.08080.0171-18.488320.112616.418
52.70950.66811.08913.2052-0.50495.2128-0.165-0.5337-0.34040.05240.0125-0.26460.6946-0.12820.15250.0690.11430.06220.2230.00020.0234-26.18489.276143.0114
64.56292.8562-1.82592.5132-2.32999.0204-0.11070.1923-0.197-0.2396-0.2474-0.20521.4866-0.31690.35810.62640.33220.03790.2958-0.06460.1061-28.6178-2.056674.9825
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X1447 - 1727
2X-RAY DIFFRACTION2A1 - 106
3X-RAY DIFFRACTION2B1 - 111
4X-RAY DIFFRACTION3A107 - 212
5X-RAY DIFFRACTION3B112 - 214
6X-RAY DIFFRACTION4Y1461 - 1726
7X-RAY DIFFRACTION5L1 - 106
8X-RAY DIFFRACTION5H1 - 111
9X-RAY DIFFRACTION6L107 - 212
10X-RAY DIFFRACTION6H112 - 213

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  • 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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