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- PDB-5i0d: Cycloalternan-forming enzyme from Listeria monocytogenes in compl... -

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Basic information

Entry
Database: PDB / ID: 5i0d
TitleCycloalternan-forming enzyme from Listeria monocytogenes in complex with cycloalternan
ComponentsLmo2446 protein
KeywordsSUGAR BINDING PROTEIN / Complex / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process / metal ion binding
Similarity search - Function
: / Carbohydrate binding module (family 35) / glycosyl hydrolase (family 31) / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / CBM6 (carbohydrate binding type-6) domain profile. ...: / Carbohydrate binding module (family 35) / glycosyl hydrolase (family 31) / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Galactose mutarotase-like domain superfamily / Galactose-binding domain-like / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-D-glucopyranose / Lmo2446 protein
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsLight, S.H. / Minasov, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Structure / Year: 2017
Title: Transferase Versus Hydrolase: The Role of Conformational Flexibility in Reaction Specificity.
Authors: Light, S.H. / Cahoon, L.A. / Mahasenan, K.V. / Lee, M. / Boggess, B. / Halavaty, A.S. / Mobashery, S. / Freitag, N.E. / Anderson, W.F.
History
DepositionFeb 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Feb 22, 2017Group: Database references
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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 2.1Sep 27, 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 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lmo2446 protein
B: Lmo2446 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,76032
Polymers240,0032
Non-polymers6,75630
Water50,6762813
1
A: Lmo2446 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,93715
Polymers120,0021
Non-polymers2,93514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lmo2446 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,82317
Polymers120,0021
Non-polymers3,82116
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.753, 101.233, 166.391
Angle α, β, γ (deg.)90.00, 101.02, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-1479-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lmo2446 protein


Mass: 120001.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: lmo2446 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y4J2

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Sugars , 5 types, 13 molecules

#2: Polysaccharide
alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a6-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Polysaccharide
Cyclic alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-3)-alpha-D- ...Cyclic alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/1,4,4/[a2122h-1a_1-5]/1-1-1-1/a1-d6_a3-b1_b6-c1_c3-d1WURCSPDB2Glycan 1.1.0
#4: Polysaccharide alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-3DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a6-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(3+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#5: Polysaccharide Cyclic alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-6)-alpha-D- ...Cyclic alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,4,4/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2-2/a1-d6_a3-b1_b6-c1_c3-d1WURCSPDB2Glycan 1.1.0
#9: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 2830 molecules

#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2813 / 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: 2.61 Å3/Da / Density % sol: 52.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein: 0.5 NaCl, 10 mM Tris pH 8.3, 5 mM BME Condition: 200 mM magnesium formate and 25% PEG 3350 Soak in mother liquor supplemented with 100 mM cycloalternan

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.77→30 Å / Num. obs: 233478 / % possible obs: 98.6 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 14
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 2.1 / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KWU

4kwu


Resolution: 1.77→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.039 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.094 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17086 11555 4.9 %RANDOM
Rwork0.14407 ---
obs0.1454 221914 98.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.203 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å2-0 Å20.56 Å2
2---0.06 Å2-0 Å2
3---0.63 Å2
Refinement stepCycle: 1 / Resolution: 1.77→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16686 0 431 2813 19930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0218119
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215580
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.9724799
X-RAY DIFFRACTIONr_angle_other_deg0.915336202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5015.0382250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24425.677909
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.299152518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4871550
X-RAY DIFFRACTIONr_chiral_restr0.0830.22727
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0221055
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024135
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4491.2338803
X-RAY DIFFRACTIONr_mcbond_other0.4491.2328802
X-RAY DIFFRACTIONr_mcangle_it0.7571.84711103
X-RAY DIFFRACTIONr_mcangle_other0.7571.84711104
X-RAY DIFFRACTIONr_scbond_it0.7691.3849316
X-RAY DIFFRACTIONr_scbond_other0.7691.3849316
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2072.04913697
X-RAY DIFFRACTIONr_long_range_B_refined6.51312.78123522
X-RAY DIFFRACTIONr_long_range_B_other6.51312.78123522
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.768→1.814 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 821 -
Rwork0.234 15376 -
obs--92.74 %
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)
11.2015-0.2736-0.02551.7763-0.33260.91720.0311-0.04310.03210.2728-0.01510.2521-0.0749-0.0473-0.0160.0546-0.01340.05540.0237-0.04210.115710.075258.3054222.9006
20.92060.1387-0.12261.0408-0.1290.53880.0190.10950.1663-0.08270.02170.1026-0.0886-0.0801-0.04070.04010.0187-0.02030.0360.02790.135724.98577.5087190.8577
30.3638-0.04610.0220.29540.02280.31270.0036-0.06640.0060.02620.01170.03340.03320.003-0.01530.0141-0.0049-0.00110.0225-0.00390.018345.837953.7059210.2004
40.5808-0.00140.12650.22170.0590.70290.02480.0707-0.0209-0.0280.01040.01490.05560.0872-0.03520.01820.0079-0.00990.0275-0.01090.008155.567946.1516185.6422
50.4306-0.020.0761.02370.9534.00630.0220.04120.0493-0.05640.0361-0.0806-0.26390.2486-0.0580.0263-0.03280.01480.0903-0.00560.030368.318759.663179.4937
61.46210.50830.270.6690.19981.20150.0099-0.0156-0.0392-0.08560.017-0.073-0.03010.2945-0.0270.03570.02610.01330.1533-0.01470.021772.612346.764173.5018
72.3812-0.6390.39452.1016-0.56531.7628-0.0328-0.0078-0.3238-0.03220.08550.08350.24220.0285-0.05270.09480.0486-0.02080.0503-0.02320.057358.708932.8886163.6843
82.4996-0.69260.71781.2225-0.19881.59980.050.2624-0.2436-0.0905-0.0359-0.02170.18790.2058-0.01420.08960.0573-0.01080.0894-0.04770.047660.150333.1618156.1941
91.17230.1441-0.28741.20620.12381.4341-0.07370.03380.0611-0.14420.0151-0.010.03340.16570.05860.03380.0085-0.00360.05850.05680.0822104.0513110.1974190.3445
100.9781-0.2109-0.22840.81840.24120.72580.0325-0.08080.14520.06160.0456-0.0833-0.07750.0489-0.07810.0301-0.0067-0.02050.01340.00590.130784.7119128.9091220.3504
112.7690.3270.87017.6814-2.32531.04490.0418-0.2538-0.0110.4756-0.00830.0942-0.1385-0.0865-0.03350.0604-0.0011-0.00470.0393-0.00140.062786.9012116.7152224.0847
120.45140.06-0.00550.29910.05720.36970.00680.14470.0359-0.04530.0177-0.03770.0051-0.0461-0.02450.0310.0017-0.0090.07230.04460.069368.3176107.0762196.8927
130.50210.1288-0.06170.7012-0.05450.6170.00050.0887-0.0619-0.01580.0069-0.03360.1143-0.0454-0.00740.0321-0.014-0.0210.04330.0130.044862.394791.826205.933
140.5478-0.0635-0.03170.406-0.11350.6919-0.00260.02150.03710.0460.02040.02230.0041-0.1378-0.01780.0294-0.0093-0.01740.0460.03020.044251.572899.4892223.0977
151.128-0.58650.2621.1815-0.39911.2382-0.02660.11310.07090.07850.06020.1046-0.0565-0.3306-0.03360.0237-0.01320.00820.16910.02360.048935.637696.4835231.6742
162.52841.2880.64141.66790.63250.81660.063-0.0655-0.18370.1869-0.0297-0.09830.0155-0.0001-0.03330.064-0.016-0.01060.03010.00530.014347.011982.922247.9129
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 144
2X-RAY DIFFRACTION2A145 - 275
3X-RAY DIFFRACTION3A276 - 712
4X-RAY DIFFRACTION4A713 - 864
5X-RAY DIFFRACTION5A865 - 900
6X-RAY DIFFRACTION6A901 - 979
7X-RAY DIFFRACTION7A980 - 1018
8X-RAY DIFFRACTION8A1019 - 1091
9X-RAY DIFFRACTION9B32 - 143
10X-RAY DIFFRACTION10B144 - 267
11X-RAY DIFFRACTION11B268 - 271
12X-RAY DIFFRACTION12B272 - 607
13X-RAY DIFFRACTION13B608 - 721
14X-RAY DIFFRACTION14B722 - 903
15X-RAY DIFFRACTION15B904 - 978
16X-RAY DIFFRACTION16B979 - 1091

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Yorodumi

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  • 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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