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- PDB-5ej1: Pre-translocation state of bacterial cellulose synthase -

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Basic information

Entry
Database: PDB / ID: 5ej1
TitlePre-translocation state of bacterial cellulose synthase
Components
  • (Putative cellulose ...) x 2
  • poly(unk)
KeywordsMETAL BINDING PROTEIN / cellulose biosynthesis / glycosyltransferase / membrane transport
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
1,2-Distearoyl-sn-glycerophosphoethanolamine / Chem-C2E / Chem-XP5 / Cellulose synthase catalytic subunit [UDP-forming] / Cyclic di-GMP-binding protein
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.4 Å
AuthorsMoragn, J.L.W. / 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 30, 2016Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / 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 / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_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_oper_list.symmetry_operation / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)159,69410
Polymers152,9153
Non-polymers6,7797
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14730 Å2
ΔGint-0 kcal/mol
Surface area59370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.355, 218.230, 220.765
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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

#1: Protein Putative cellulose synthase /


Mass: 81392.109 Da / Num. of mol.: 1 / Fragment: unp residues 13-740
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: 70909.273 Da / Num. of mol.: 1 / Fragment: unp residues 52-720
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_0332 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3J126

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

#3: Protein/peptide poly(unk)


Mass: 613.749 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-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-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 2936.550 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,18,17/[a2122h-1b_1-5]/1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1/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-q1_q4-r1WURCSPDB2Glycan 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-Glcp]{[(4+1)][b-D-Glcp]{}}}}}}}}}}}}}}}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 6 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 / Cyclic di-GMP


Mass: 690.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#6: Chemical ChemComp-XP5 / (4S,7R)-7-(heptanoyloxy)-4-hydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphahexadecan-1-aminium 4-oxide


Mass: 482.568 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H45NO8P
#7: Chemical ChemComp-3PE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / 3-SN-PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 748.065 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM

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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: 5.31 Å3/Da / Density % sol: 76.82 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / Details: sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Mar 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→29.5 Å / Num. obs: 86075 / % possible obs: 99.8 % / Redundancy: 6.6 % / Net I/σ(I): 9.6

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementResolution: 3.4→24.864 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 33.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2769 4367 5.07 %
Rwork0.2332 --
obs0.2354 86075 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→24.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10618 0 360 0 10978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411266
X-RAY DIFFRACTIONf_angle_d0.92215422
X-RAY DIFFRACTIONf_dihedral_angle_d13.4434059
X-RAY DIFFRACTIONf_chiral_restr0.0331808
X-RAY DIFFRACTIONf_plane_restr0.0041955
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4001-3.43860.45951600.3852615X-RAY DIFFRACTION100
3.4386-3.47890.38611180.39252767X-RAY DIFFRACTION100
3.4789-3.52120.39461720.38052773X-RAY DIFFRACTION100
3.5212-3.56570.38441670.34442729X-RAY DIFFRACTION100
3.5657-3.61250.33291390.33372657X-RAY DIFFRACTION100
3.6125-3.66180.34561540.33752704X-RAY DIFFRACTION100
3.6618-3.7140.33221300.34092757X-RAY DIFFRACTION100
3.714-3.76920.37591400.30822765X-RAY DIFFRACTION100
3.7692-3.82790.36461060.29882749X-RAY DIFFRACTION100
3.8279-3.89040.41651530.29662707X-RAY DIFFRACTION100
3.8904-3.95730.35921600.28882764X-RAY DIFFRACTION100
3.9573-4.02890.34481700.2672663X-RAY DIFFRACTION100
4.0289-4.10610.36841190.28482729X-RAY DIFFRACTION100
4.1061-4.18950.42921430.26952777X-RAY DIFFRACTION100
4.1895-4.28020.27931500.25682701X-RAY DIFFRACTION100
4.2802-4.37920.34661640.25122682X-RAY DIFFRACTION100
4.3792-4.48810.22691600.22152758X-RAY DIFFRACTION100
4.4881-4.60870.31291340.22132697X-RAY DIFFRACTION100
4.6087-4.74340.20391360.20892766X-RAY DIFFRACTION100
4.7434-4.89540.22281200.20922744X-RAY DIFFRACTION100
4.8954-5.06890.20821590.19872706X-RAY DIFFRACTION100
5.0689-5.27010.25781260.21872767X-RAY DIFFRACTION100
5.2701-5.50740.28351390.2272716X-RAY DIFFRACTION100
5.5074-5.79430.30771410.23042706X-RAY DIFFRACTION100
5.7943-6.15220.28841400.24392777X-RAY DIFFRACTION100
6.1522-6.61890.27141630.22812720X-RAY DIFFRACTION100
6.6189-7.26980.25411770.23232642X-RAY DIFFRACTION100
7.2698-8.28750.26891370.19042758X-RAY DIFFRACTION100
8.2875-10.31580.19881190.14882733X-RAY DIFFRACTION100
10.3158-24.86440.221710.20122679X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -6.7985 Å / Origin y: 10.5402 Å / Origin z: -58.7582 Å
111213212223313233
T1.3474 Å20.0531 Å2-0.0654 Å2-1.1533 Å2-0.1939 Å2--0.8759 Å2
L0.0496 °2-0.2078 °2-0.2518 °2-2.6931 °22.0319 °2--3.4503 °2
S0.1473 Å °0.1289 Å °-0.0499 Å °-0.3354 Å °-0.032 Å °-0.0873 Å °-0.2946 Å °0.1123 Å °-0.1076 Å °
Refinement TLS groupSelection details: all

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