[English] 日本語
Yorodumi
- PDB-5eiy: Bacterial cellulose synthase bound to a substrate analogue -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5eiy
TitleBacterial cellulose synthase bound to a substrate analogue
Components
  • (Putative cellulose ...) x 2
  • poly(unk)
KeywordsMEMBRANE PROTEIN / cellulose biosynthesis / METAL BINDING PROTEIN
Function / homology
Function and homology information


cellulose synthase (UDP-forming) / cellulose synthase (UDP-forming) activity / cellulose biosynthetic process / UDP-glucose metabolic process / cyclic-di-GMP binding / metal ion binding / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4520 / Chitobiase; domain 2 - #20 / Chitobiase; domain 2 - #30 / : / Cellulose Synthase Subunit B, alpha-beta domain / Cellulose synthase, subunit A / Cellulose synthase BcsB, bacterial / Bacterial cellulose synthase subunit / Glycosyltransferase like family 2 / Cellulose synthase ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4520 / Chitobiase; domain 2 - #20 / Chitobiase; domain 2 - #30 / : / Cellulose Synthase Subunit B, alpha-beta domain / Cellulose synthase, subunit A / Cellulose synthase BcsB, bacterial / Bacterial cellulose synthase subunit / Glycosyltransferase like family 2 / Cellulose synthase / predicted glycosyltransferase like domains / PilZ domain / PilZ domain / Glycosyl transferase family 2 / Chitobiase; domain 2 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Galactose-binding domain-like / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Thrombin, subunit H / Jelly Rolls / Alpha-Beta Complex / Up-down Bundle / Beta Barrel / Sandwich / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-43Y / Chem-660 / Chem-C2E / DIUNDECYL PHOSPHATIDYL CHOLINE / Cellulose synthase catalytic subunit [UDP-forming] / Cyclic di-GMP-binding protein
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å
AuthorsMcNamara, J.T. / Zimmer, J.
CitationJournal: Nature / Year: 2016
Title: Observing cellulose biosynthesis and membrane translocation in crystallo.
Authors: Morgan, J.L. / McNamara, J.T. / Fischer, M. / Rich, J. / Chen, H.M. / Withers, S.G. / Zimmer, J.
History
DepositionOct 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Mar 30, 2016Group: Database references
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 / citation / 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_oper_list / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_conn_type / 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.pdbx_synonyms / _chem_comp.type / _citation.journal_id_CSD / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_oper_list.symmetry_operation / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative cellulose synthase
B: Putative cellulose synthase
D: poly(unk)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,03213
Polymers167,8123
Non-polymers6,22010
Water19811
1
A: Putative cellulose synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,21110
Polymers90,0151
Non-polymers6,1969
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative cellulose synthase
D: poly(unk)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8223
Polymers77,7972
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.475, 216.654, 221.335
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Putative cellulose ... , 2 types, 2 molecules AB

#1: Protein Putative cellulose synthase /


Mass: 90014.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158) (bacteria)
Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: RSP_0333 / Production host: Escherichia coli (E. coli)
References: UniProt: Q3J125, cellulose synthase (UDP-forming)
#2: Protein Putative cellulose synthase /


Mass: 77013.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: RSP_0332 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3J126

-
Protein/peptide / Sugars , 2 types, 2 molecules D

#3: Protein/peptide poly(unk)


Mass: 783.958 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Production host: Escherichia coli (E. coli)
#4: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-galactopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 2774.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,17,16/[a2122h-1b_1-5][a2112h-1b_1-5]/1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g4-h1_h4-i1_i4-j1_j4-k1_k4-l1_l4-m1_m4-n1_n4-o1_o4-p1_p4-q1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Galp]{}}}}}}}}}}}}}}}}}LINUCSPDB-CARE

-
Non-polymers , 7 types, 20 molecules

#5: Chemical ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM
#6: Chemical ChemComp-43Y / [(2R)-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-2-propanoyloxy-propyl] propanoate / 1,2-dipropionyl-sn-glycero-3-phosphocholine


Mass: 370.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H29NO8P
#7: Chemical ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate / Cyclic di-GMP


Mass: 690.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#8: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#10: Chemical ChemComp-660 / [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-[[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]methyl]phosphinic acid / UDP-glucose phosphonate


Mass: 564.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26N2O16P2
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 5.36 Å3/Da / Density % sol: 77.04 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: sodium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Oct 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→35 Å / Num. obs: 133706 / % possible obs: 99.3 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.28 / Net I/σ(I): 5.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P00

4p00


Resolution: 2.95→34.92 Å / FOM work R set: 0.7935 / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 28.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2481 6659 4.98 %
Rwork0.2215 127047 -
obs0.2229 133706 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 239.95 Å2 / Biso mean: 83.94 Å2 / Biso min: 38.99 Å2
Refinement stepCycle: final / Resolution: 2.95→34.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10689 0 408 11 11108
Biso mean--88.18 62.72 -
Num. residues----1395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311423
X-RAY DIFFRACTIONf_angle_d0.90515635
X-RAY DIFFRACTIONf_chiral_restr0.0321827
X-RAY DIFFRACTIONf_plane_restr0.0041980
X-RAY DIFFRACTIONf_dihedral_angle_d13.8034151
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-2.98350.39172070.357242984505100
2.9835-3.01860.32991840.340242664450100
3.0186-3.05540.3462200.334841834403100
3.0554-3.09410.36522520.326942684520100
3.0941-3.13480.35562440.329242394483100
3.1348-3.17770.38192070.336942194426100
3.1777-3.2230.38962040.316442404444100
3.223-3.27110.36252540.298242434497100
3.2711-3.32220.31442320.297841934425100
3.3222-3.37660.34442030.277342504453100
3.3766-3.43480.23552340.261642774511100
3.4348-3.49720.28182130.273441874400100
3.4972-3.56440.30942460.259542654511100
3.5644-3.63710.3092170.257742284445100
3.6371-3.71610.33272390.253842044443100
3.7161-3.80240.29912070.253442914498100
3.8024-3.89740.26442240.236141704394100
3.8974-4.00260.23542570.217742524509100
4.0026-4.12020.26511720.219142534425100
4.1202-4.2530.27082140.20142704484100
4.253-4.40470.20012330.199142034436100
4.4047-4.58070.22172030.190542944497100
4.5807-4.78870.19882520.181441574409100
4.7887-5.04050.17842400.177242314471100
5.0405-5.35520.24022450.178741964441100
5.3552-5.7670.20472020.192242624464100
5.767-6.34420.21451700.185743004470100
6.3442-7.25510.21191790.184142444423100
7.2551-9.11370.15462160.16164201441799
9.1137-34.92240.22762890.20164163445299
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)
10.8755-0.64080.99260.5421-0.621.53470.33480.2303-0.07130.7717-0.15850.77670.33960.7908-0.22571.0966-0.47450.23450.7391-0.34410.8894-23.5477-21.575576.1689
21.4789-0.17680.68981.94520.84473.40140.0328-0.13750.06650.4525-0.18450.08670.4724-0.2360.16290.6578-0.16410.050.5972-0.21410.5617-10.4367-12.852667.19
33.9479-4.3232-5.50879.05253.26849.5723-0.34510.2239-0.44510.0673-0.13170.22150.2337-0.65560.25460.8516-0.34020.03131.0745-0.32820.8103-23.02982.044592.7283
44.42030.5588-0.66544.57291.08043.87160.0787-0.6164-0.04031.11160.1233-0.45670.82280.4938-0.16321.18460.0008-0.05730.7256-0.18820.5655-3.280811.1685109.0788
54.40711.3626-1.26355.34893.25023.12860.1441-0.32690.3948-0.08930.0946-0.261-0.5301-0.36090.03850.6004-0.0713-00.7278-0.13090.6203-1.483614.950880.6888
60.6338-0.2687-0.76371.8841.86473.73080.0093-0.1107-0.1910.79490.1061-0.06570.69980.223-0.0990.86-0.0524-0.00350.6218-0.19650.6969-4.3082-3.640985.2362
78.7731.6527-5.3495.4798-5.01449.01020.4890.2043-0.6213-0.2566-0.8883-0.60480.59672.23980.40021.42330.5068-0.3951.1335-0.27831.014912.0814-9.343991.8221
83.51-1.51640.1014.1155-4.21075.1429-0.008-0.56910.64491.43010.7049-0.2737-0.65221.2041-0.76190.91490.0575-0.02791.2315-0.50171.04913.472513.891386.9406
91.6950.41410.22512.43280.26213.044-0.2350.488-0.1796-0.20580.7329-0.53120.01341.1626-0.46580.5443-0.12710.09180.9157-0.45360.818310.28570.262162.1181
103.327-0.6297-0.00685.30061.12222.6548-0.12250.48890.0759-0.2330.1005-0.1097-0.2147-0.010.04060.4941-0.10830.01370.5522-0.0950.4558-4.716139.238393.3835
117.33733.21986.88855.11345.14289.1975-0.13370.62710.2339-0.149-0.14170.59510.14670.23280.36240.58560.01240.10350.6839-0.06320.5536-10.655923.005394.2742
127.56632.30021.03122.9876-0.89683.4178-0.52290.50570.6385-0.50360.5403-0.6325-0.80120.7013-0.00420.8265-0.20340.24491.0254-0.49490.88428.68115.088469.524
139.63224.01626.24875.1281.30054.5178-0.0821-0.59110.52370.09990.13250.2838-1.179-1.08740.32090.54760.05680.04790.5346-0.06740.6262-7.7718-37.941310.9622
144.55432.1294-0.28499.51510.76565.88420.08090.26990.1293-0.1394-0.2434-0.4882-0.71630.74580.12450.5108-0.0171-0.01210.6092-0.00870.49564.1295-35.194610.4548
156.05214.1640.97613.29312.42447.62591.3354-0.96720.74811.4516-0.23750.3073-1.76260.4998-0.92841.0276-0.25540.27640.8669-0.29040.984210.0871-18.556716.6685
167.45744.019-0.48932.7531-0.46842.4870.06020.32750.14120.10920.00410.10870.1999-0.245-0.00950.54650.06310.00110.3905-0.06050.4232-15.5241-44.85959.6402
173.49511.4834-2.36627.10042.24943.3881-0.89721.87540.5061-1.04391.4618-0.30621.74670.2497-0.68371.0873-0.14130.16891.0797-0.06980.8056-31.4646-48.01340.0313
187.2111-0.4468-1.78295.1943-0.59294.3447-0.11680.2012-1.3624-0.22240.09640.560.8776-0.32850.0690.7025-0.09-0.10350.5601-0.06790.6943-22.3462-56.88157.0486
193.20790.9095-0.26472.71990.69791.73620.1509-0.0095-0.07150.01650.0935-0.36460.18910.3371-0.25950.54750.0729-0.03670.7179-0.22110.54015.1114-27.680736.6521
202.12841.4130.86744.04112.05997.15640.1043-0.6395-0.25080.4238-0.38330.42390.424-0.70570.14650.5378-0.0820.11890.6635-0.12830.5471-24.7107-40.897929.4007
218.0994.5512-2.82742.8367-1.01452.54810.4699-0.64270.6317-0.0543-0.81091.6442-0.7656-1.79520.35970.80070.2748-0.06581.2-0.31920.9207-33.9521-23.507824.7041
220.40850.78710.81464.98892.29666.21210.1222-0.14020.5329-0.2221-0.31580.9709-0.398-1.18050.13660.73730.08210.01540.9785-0.26930.7028-15.7427-11.248842.5195
236.1434-1.91793.41826.1158-0.77774.2129-0.1588-0.12820.80160.1545-0.1974-0.2038-0.2667-0.18350.27210.5445-0.00320.03770.5362-0.18360.5453-22.3103-28.465926.694
242.3594-0.1298-1.00523.23270.0954.9260.1856-0.20140.06290.3649-0.34240.36781.0688-0.23880.22050.5685-0.3470.19310.7997-0.2940.5977-22.943-22.34863.0519
253.7798-3.1468-1.06726.18455.00725.18130.4762-0.4994-0.4037-0.0239-0.3411.314-0.70170.1639-0.17560.9614-0.18480.14150.96620.10991.1739-42.1282-19.603424.0463
263.23512.9304-2.76484.7564-3.14724.7156-0.94750.9851-0.4135-0.52190.3776-0.08370.251-0.2566-0.24751.1285-0.1521-0.51980.4682-0.37421.3736-44.3331-30.637629.2868
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 13:35)A13 - 35
2X-RAY DIFFRACTION2(CHAIN A AND RESID 36:117)A36 - 117
3X-RAY DIFFRACTION3(CHAIN A AND RESID 118:135)A118 - 135
4X-RAY DIFFRACTION4(CHAIN A AND RESID 136:277)A136 - 277
5X-RAY DIFFRACTION5(CHAIN A AND RESID 278:297)A278 - 297
6X-RAY DIFFRACTION6(CHAIN A AND RESID 298:488)A298 - 488
7X-RAY DIFFRACTION7(CHAIN A AND RESID 489:502)A489 - 502
8X-RAY DIFFRACTION8(CHAIN A AND RESID 503:522)A503 - 522
9X-RAY DIFFRACTION9(CHAIN A AND RESID 523:575)A523 - 575
10X-RAY DIFFRACTION10(CHAIN A AND RESID 576:674)A576 - 674
11X-RAY DIFFRACTION11(CHAIN A AND RESID 675:706)A675 - 706
12X-RAY DIFFRACTION12(CHAIN A AND RESID 707:740)A707 - 740
13X-RAY DIFFRACTION13(CHAIN B AND RESID 54:67)B54 - 67
14X-RAY DIFFRACTION14(CHAIN B AND RESID 68:153)B68 - 153
15X-RAY DIFFRACTION15(CHAIN B AND RESID 154:169)B154 - 169
16X-RAY DIFFRACTION16(CHAIN B AND RESID 170:242)B170 - 242
17X-RAY DIFFRACTION17(CHAIN B AND RESID 243:248)B243 - 248
18X-RAY DIFFRACTION18(CHAIN B AND RESID 249:303)B249 - 303
19X-RAY DIFFRACTION19(CHAIN B AND RESID 304:451)B304 - 451
20X-RAY DIFFRACTION20(CHAIN B AND RESID 452:504)B452 - 504
21X-RAY DIFFRACTION21(CHAIN B AND RESID 505:531)B505 - 531
22X-RAY DIFFRACTION22(CHAIN B AND RESID 544:599)B544 - 599
23X-RAY DIFFRACTION23(CHAIN B AND RESID 600:665)B600 - 665
24X-RAY DIFFRACTION24(CHAIN B AND RESID 666:720)B666 - 720
25X-RAY DIFFRACTION25(CHAIN D AND RESID 169:174)D169 - 174
26X-RAY DIFFRACTION26(CHAIN D AND RESID 175:177)D175 - 177

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • 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

-
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

Read more