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- PDB-5ejz: Bacterial Cellulose Synthase Product-Bound State -

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Basic information

Entry
Database: PDB / ID: 5ejz
TitleBacterial Cellulose Synthase Product-Bound State
Components
  • (Putative cellulose ...) x 2
  • poly(unk)
KeywordsMETAL BINDING PROTEIN / cellulose synthase / translocation / biopolymer
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 / URIDINE-5'-DIPHOSPHATE / UNDECANE / 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: 2.94 Å
AuthorsMorgan, 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
DepositionNov 2, 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 / pdbx_validate_close_contact / 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 / _atom_site.label_entity_id / _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 / _pdbx_validate_close_contact.auth_asym_id_2 / _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 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 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / 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 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)174,98114
Polymers167,4363
Non-polymers7,54511
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16940 Å2
ΔGint-24 kcal/mol
Surface area57330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.269, 216.838, 221.117
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: 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: 76636.938 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_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: 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 2-deoxy-2-fluoro-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)- ...2-deoxy-2-fluoro-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: 2938.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,18,17/[a2122h-1b_1-5][a2122h-1b_1-5_2*F]/1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-2/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-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-Glcp2fluoro]{}}}}}}}}}}}}}}}}}}LINUCSPDB-CARE

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Non-polymers , 6 types, 10 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-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM
#9: 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
#10: Chemical ChemComp-UND / UNDECANE / LIPID FRAGMENT


Mass: 156.308 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.87 Å3/Da / Density % sol: 74.73 %
Crystal growTemperature: 304 K / Method: vapor diffusion, sitting drop / Details: 1.9M NaOAc, Na Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.03 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.94→39.4 Å / Num. obs: 68897 / % possible obs: 98.6 % / Redundancy: 5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.3
Reflection shellResolution: 2.94→3.01 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.959 / Num. unique all: 3800 / % possible all: 82.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4p02

4p02


Resolution: 2.94→34.351 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 25.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2331 3429 4.99 %
Rwork0.2061 --
obs0.2074 68775 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.94→34.351 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10668 0 407 0 11075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111369
X-RAY DIFFRACTIONf_angle_d1.24715558
X-RAY DIFFRACTIONf_dihedral_angle_d17.9824126
X-RAY DIFFRACTIONf_chiral_restr0.0471820
X-RAY DIFFRACTIONf_plane_restr0.0041969
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9401-2.98210.3826850.34291922X-RAY DIFFRACTION71
2.9821-3.02660.341320.30872754X-RAY DIFFRACTION100
3.0266-3.07380.33131530.30222686X-RAY DIFFRACTION98
3.0738-3.12420.35461230.30082691X-RAY DIFFRACTION100
3.1242-3.1780.29141120.29222775X-RAY DIFFRACTION100
3.178-3.23580.30511420.2782710X-RAY DIFFRACTION99
3.2358-3.2980.2691360.25312732X-RAY DIFFRACTION100
3.298-3.36520.31211400.25082775X-RAY DIFFRACTION99
3.3652-3.43830.30931330.24042698X-RAY DIFFRACTION100
3.4383-3.51820.27061610.23562746X-RAY DIFFRACTION100
3.5182-3.60610.24521510.22082693X-RAY DIFFRACTION100
3.6061-3.70350.24561650.2122735X-RAY DIFFRACTION100
3.7035-3.81240.23211310.20672738X-RAY DIFFRACTION100
3.8124-3.93530.23381730.20652732X-RAY DIFFRACTION100
3.9353-4.07570.23311250.19412733X-RAY DIFFRACTION100
4.0757-4.23860.2011330.19042793X-RAY DIFFRACTION100
4.2386-4.43110.22861510.17962760X-RAY DIFFRACTION100
4.4311-4.66420.2011370.16612739X-RAY DIFFRACTION100
4.6642-4.95560.18491550.16882765X-RAY DIFFRACTION100
4.9556-5.3370.24471660.18012770X-RAY DIFFRACTION100
5.337-5.87160.24311650.19642786X-RAY DIFFRACTION100
5.8716-6.71580.21341480.19772836X-RAY DIFFRACTION100
6.7158-8.44040.19021790.18422818X-RAY DIFFRACTION100
8.4404-34.35330.18791330.18772959X-RAY DIFFRACTION98
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)
11.496-0.32821.02962.86870.08981.86830.10150.2149-0.2574-0.7042-0.2127-0.34620.57030.1645-0.00650.64490.15290.05370.74930.28290.639613.1622-14.1231-68.9254
21.27950.1188-0.62473.599-0.8113.51390.07520.4101-0.17-1.18780.12180.51310.5491-0.4531-01.26990.0213-0.10180.83210.18650.70462.668411.1097-108.9037
31.42860.93040.5111.2072-0.32380.9374-0.0882-0.2340.0054-0.59420.124-0.02580.37130.34240.0030.92610.20090.08490.65690.21330.654210.135211.0115-93.2829
40.8970.3352-0.79091.662-1.39292.26750.0250.1939-0.0644-1.01280.07720.09720.7291-0.111300.9320.08-0.02790.73040.22120.73853.6196-3.3161-84.6627
51.94620.0346-0.25542.00990.11910.26760.00280.0953-0.4693-0.76460.74050.70640.0269-1.0757-0.03040.58620.0672-0.0210.90550.38160.9932-13.5464.6499-75.77
6-0.00920.00320.51611.2877-1.23341.0535-0.0672-0.16070.12610.1560.12940.1737-0.3525-0.00070.00030.72090.15960.12790.63690.12380.70882.193831.1016-86.0988
70.07970.2643-0.01792.3538-1.33661.1184-0.0624-0.2030.03270.11340.21740.2287-0.278-0.20520.00070.64440.15240.06890.83750.20150.68160.676819.6039-81.3243
81.3903-0.33420.00661.2391.34511.459-0.15320.10770.2775-0.38930.0016-0.0879-0.1105-0.4551-00.721-0.1041-0.01260.74090.08660.62882.5176-36.5862-10.372
92.543-1.08570.06091.83630.16772.4669-0.0067-0.19280.03920.22420.01930.11130.1628-0.157200.7539-0.13880.01370.52570.05740.63827.4145-40.808-8.9862
100.535-0.31130.18561.0805-0.72921.65810.13330.13210.0922-0.0555-0.1444-0.08710.27720.17170.00140.4965-0.0295-0.0020.66110.18810.637112.8051-28.0058-35.5882
110.003-0.00630.00690.0131-0.01890.0213-0.164-0.3810.46910.2376-0.14790.058-0.2676-0.0379-00.7460.12860.01090.8256-0.13591.193141.9493-22.9979-25.2958
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 120 )
2X-RAY DIFFRACTION2chain 'A' and (resid 121 through 244 )
3X-RAY DIFFRACTION3chain 'A' and (resid 245 through 296 )
4X-RAY DIFFRACTION4chain 'A' and (resid 297 through 496 )
5X-RAY DIFFRACTION5chain 'A' and (resid 497 through 545 )
6X-RAY DIFFRACTION6chain 'A' and (resid 546 through 673 )
7X-RAY DIFFRACTION7chain 'A' and (resid 674 through 740 )
8X-RAY DIFFRACTION8chain 'B' and (resid 54 through 102 )
9X-RAY DIFFRACTION9chain 'B' and (resid 103 through 272 )
10X-RAY DIFFRACTION10chain 'B' and (resid 273 through 720 )
11X-RAY DIFFRACTION11chain 'D' and (resid 169 through 177 )

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