[English] 日本語
Yorodumi
- PDB-4p02: Structure of Bacterial Cellulose Synthase with cyclic-di-GMP bound. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4p02
TitleStructure of Bacterial Cellulose Synthase with cyclic-di-GMP bound.
Components
  • (Cellulose Synthase subunit ...) x 2
  • unidentified peptide
KeywordsTRANSFERASE / membrane protein / allosteric activator / biofilm formation / cellulose biosynthesis
Function / homology
Function and homology information


cellulose synthase (UDP-forming) / cellulose synthase (UDP-forming) activity / cellulose biosynthetic process / UDP-alpha-D-glucose metabolic process / cyclic-di-GMP binding / endomembrane system / 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 / 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 / Cellulose synthase / predicted glycosyltransferase like domains / Glycosyltransferase like family 2 / PilZ domain / PilZ domain / Chitobiase; domain 2 / Glycosyl transferase family 2 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Galactose-binding domain-like / 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
1,2-Distearoyl-sn-glycerophosphoethanolamine / 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 / Resolution: 2.65 Å
AuthorsMorgan, J.L.W. / McNamara, J.T. / Zimmer, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM101001 United States
National Science Foundation (NSF, United States)DGE-1315231. United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Mechanism of activation of bacterial cellulose synthase by cyclic di-GMP.
Authors: Morgan, J.L. / McNamara, J.T. / Zimmer, J.
History
DepositionFeb 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Jul 16, 2014Group: Database references
Revision 1.3Dec 24, 2014Group: Database references
Revision 2.0Sep 27, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations / Other / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site_gen
Item: _atom_site.label_asym_id / _entity.formula_weight ..._atom_site.label_asym_id / _entity.formula_weight / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site_gen.label_asym_id
Revision 2.1Nov 27, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / refine_hist / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_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.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 3.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / struct_conn
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Revision 3.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cellulose Synthase subunit A
B: Cellulose Synthase subunit B
D: unidentified peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,85512
Polymers167,4363
Non-polymers7,4199
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16090 Å2
ΔGint-2 kcal/mol
Surface area57810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.640, 214.660, 220.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Cellulose Synthase subunit ... , 2 types, 2 molecules AB

#1: Protein Cellulose Synthase subunit A


Mass: 90014.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.1 / Gene: RSP_0333 / Production host: Escherichia coli (E. coli)
References: UniProt: Q3J125, cellulose synthase (UDP-forming)
#2: Protein Cellulose Synthase subunit B


Mass: 76636.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.1 / Gene: RSP_0332 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3J126

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

#3: Protein/peptide unidentified peptide


Mass: 783.958 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.1 / Production host: Escherichia coli (E. coli)
#4: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...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-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 2774.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,17,16/[a2122h-1b_1-5]/1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1/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
[][D-1-deoxy-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-Glcp]{}}}}}}}}}}}}}}}}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 8 molecules

#5: 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


Mass: 690.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#6: Chemical
ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM
#7: Chemical ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.78 Å3/Da / Density % sol: 74.28 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop
Details: The well solution contained: 1.65-1.9 M Sodium Acetate, 100 mM Sodium Citrate (pH 3-3.5)
PH range: 3-3.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→34.75 Å / Num. obs: 86345 / % possible obs: 92.3 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 7.8
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.114 / Mean I/σ(I) obs: 1.3 / % possible all: 94.3

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→19.99 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 24.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.23 4307 5.01 %
Rwork0.199 --
obs0.2 85948 91.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10666 0 369 0 11035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311330
X-RAY DIFFRACTIONf_angle_d0.75415496
X-RAY DIFFRACTIONf_dihedral_angle_d14.7974276
X-RAY DIFFRACTIONf_chiral_restr0.0271810
X-RAY DIFFRACTIONf_plane_restr0.0041964
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.68010.36191350.32882718X-RAY DIFFRACTION92
2.6801-2.71150.32241610.30182772X-RAY DIFFRACTION93
2.7115-2.74450.33171430.27762680X-RAY DIFFRACTION93
2.7445-2.77910.30751620.28342716X-RAY DIFFRACTION93
2.7791-2.81560.31211520.26932785X-RAY DIFFRACTION93
2.8156-2.85410.29791220.24992715X-RAY DIFFRACTION93
2.8541-2.89470.28991280.25382724X-RAY DIFFRACTION93
2.8947-2.93780.28011250.25162804X-RAY DIFFRACTION93
2.9378-2.98360.31141310.24852707X-RAY DIFFRACTION93
2.9836-3.03230.24871450.23682725X-RAY DIFFRACTION93
3.0323-3.08440.28641150.23112806X-RAY DIFFRACTION92
3.0844-3.14030.28051410.22382667X-RAY DIFFRACTION93
3.1403-3.20050.24661560.23222745X-RAY DIFFRACTION92
3.2005-3.26550.26261400.21642690X-RAY DIFFRACTION92
3.2655-3.33620.26541460.21712731X-RAY DIFFRACTION92
3.3362-3.41340.2291380.20662730X-RAY DIFFRACTION92
3.4134-3.49840.27541450.20892724X-RAY DIFFRACTION92
3.4984-3.59240.22861560.2052712X-RAY DIFFRACTION92
3.5924-3.69750.25551480.19722700X-RAY DIFFRACTION91
3.6975-3.81610.23511480.19412713X-RAY DIFFRACTION92
3.8161-3.95140.19161640.18112702X-RAY DIFFRACTION91
3.9514-4.10830.23851450.18112702X-RAY DIFFRACTION91
4.1083-4.29360.23191450.17042711X-RAY DIFFRACTION91
4.2936-4.51750.19111410.17042732X-RAY DIFFRACTION91
4.5175-4.79680.17071260.16042718X-RAY DIFFRACTION90
4.7968-5.16130.18551370.16762699X-RAY DIFFRACTION90
5.1613-5.66990.231700.18762681X-RAY DIFFRACTION89
5.6699-6.46590.21181260.19742702X-RAY DIFFRACTION89
6.4659-8.05660.23131590.18872688X-RAY DIFFRACTION88
8.0566-19.98660.16991570.17462742X-RAY DIFFRACTION86
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)
11.14630.51030.30532.9611-0.94852.30030.08930.1421-0.1243-0.5093-0.1584-0.25920.5430.2260.12840.57180.14120.05650.54310.22390.516712.8742-15.2332-69.1505
22.00321.0079-0.79233.9298-3.34226.58510.07160.1843-0.3452-0.5902-0.2836-0.31280.58761.04780.43630.83160.33630.21150.81720.20740.629223.86472.4627-95.7718
31.5223-0.4271-0.07713.0283-0.72222.56860.05480.125-0.1955-1.03150.08360.38290.5998-0.4324-0.19231.10820.0262-0.07010.67450.14780.5612.528910.8773-109.7584
40.86080.0808-0.541.3775-1.47792.55160.02560.055-0.066-0.69090.09850.10040.5521-0.1554-0.11420.77420.0512-0.010.59020.17790.61484.3484-2.1114-85.2804
52.29480.27190.00231.45860.84643.12730.06590.28620.0679-0.8279-0.2261.4908-0.2883-0.6604-0.29860.8567-0.1024-0.25340.95420.11511.0088-13.0387-3.0043-91.1022
62.9491-0.36480.39612.73280.01163.78710.0229-0.09510.1523-0.54980.37540.89820.3364-0.8274-0.35770.50420.0168-0.0440.71990.39690.8925-16.22169.8894-77.9898
70.37790.30410.18752.6159-2.13051.43750.0129-0.1288-0.00870.12810.09240.2175-0.1104-0.0438-0.11910.50310.09850.07180.47410.08440.45312.18226.0651-85.3731
81.7527-0.54840.08283.0928-1.23731.9089-0.164-0.55910.40410.44230.3040.5237-0.5004-0.3006-0.3280.67020.0880.16110.67940.22520.6049-6.054614.4801-70.5826
93.3058-0.78350.25526.89280.3373.85480.141-0.15020.2487-0.2401-0.1263-0.1248-0.25660.01120.10480.5291-0.069-0.00590.4720.10660.45443.3022-36.7269-12.1589
103.3862-1.1439-0.35342.93990.03661.91660.0357-0.20640.30380.1686-0.03910.1964-0.1586-0.2196-0.04270.4216-0.02490.03010.44810.01230.5313-6.4438-31.6335-9.9294
113.3314-0.29720.782.4185-0.07112.59260.1537-0.1638-0.3829-0.03040.0398-0.0290.44840.3305-0.06930.64840.0009-0.07810.40790.0840.52921.1071-51.0811-7.2608
120.9319-0.98840.69841.853-1.79232.21940.33750.0335-0.3754-0.38980.21770.20280.910.0435-0.26750.7163-0.0411-0.08920.49670.00910.460912.4302-51.7877-24.4776
131.5906-0.5262-0.03671.5118-0.36061.52830.04260.11660.0468-0.0640.09290.27540.275-0.3363-0.18460.4005-0.09370.00240.58090.19690.4819-6.4743-26.9105-38.2816
142.3178-1.7052-0.00092.34960.47720.50230.23960.6695-0.09470.1129-0.09450.02560.05850.13130.06620.3306-0.0071-0.01350.55880.21650.47642.6666-27.0311-39.4189
150.96880.03730.14521.2693-0.44691.94250.20850.2831-0.0735-0.1465-0.16580.03070.33580.1034-0.05570.4157-0.0816-0.0050.37760.13460.39588.6312-33.9506-30.2282
163.03080.69770.13054.60480.22642.51930.3910.41270.4003-0.3828-0.6687-0.6089-0.26630.32620.19260.46180.03020.03170.81190.2230.549431.3776-29.8751-27.5561
170.9846-0.60861.12261.391-1.92382.9410.09290.24320.45380.2244-0.1027-0.0677-0.08970.01040.11490.5604-0.02750.03110.75060.19580.600210.2242-13.1322-40.4767
181.9244-0.12752.83050.373-0.36624.21670.31510.11210.70830.5099-0.247-0.7647-0.63761.13820.43410.7966-0.13640.09451.19960.33991.15828.2045-7.8366-43.4815
192.3432-0.07261.4692.641-1.00262.35110.1120.11430.39850.1622-0.15310.1097-0.14650.0054-0.03530.4772-0.03710.03660.50060.13660.461221.9565-28.2045-27.3425
200.25770.2638-0.87731.8973-1.10274.23820.04370.2083-0.0496-0.3271-0.2722-0.30810.72630.40660.17390.5040.21320.11240.92730.27580.556322.5074-22.798-63.5932
218.83012.2994-0.23912.1201-3.26316.8470.2239-0.0647-0.26920.41730.3610.39220.0453-0.3081-0.39380.51260.06020.00250.59290.15050.718541.876-23.4088-26.0321
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 13:117)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 118:138)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 139:269)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 270:487)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 488:511)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 512:529)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 530:702)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 703:740)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 54:92)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 93:187)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 188:286)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 287:317)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 318:401)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 402:420)
15X-RAY DIFFRACTION15(CHAIN B AND RESID 421:492)
16X-RAY DIFFRACTION16(CHAIN B AND RESID 493:528)
17X-RAY DIFFRACTION17(CHAIN B AND RESID 529:582)
18X-RAY DIFFRACTION18(CHAIN B AND RESID 583:597)
19X-RAY DIFFRACTION19(CHAIN B AND RESID 598:666)
20X-RAY DIFFRACTION20(CHAIN B AND RESID 667:720)
21X-RAY DIFFRACTION21(CHAIN D AND RESID 169:177)

+
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