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- PDB-4p00: Bacterial Cellulose Synthase in complex with cyclic-di-GMP and UDP -

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Basic information

Entry
Database: PDB / ID: 4p00
TitleBacterial Cellulose Synthase in complex with cyclic-di-GMP and UDP
Components
  • (Cellulose Synthase ...) x 2
  • unidentified peptide
KeywordsTRANSFERASE / membrane protein / cellulose biosynthesis / biofilm / cyclic-di-GMP
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 / integral component of membrane / plasma membrane / metal ion binding
Cellulose synthase / Galactose-binding-like domain superfamily / PilZ domain / Cellulose synthase / Bacterial cellulose synthase subunit / Glycosyl transferase family 2 / Nucleotide-diphospho-sugar transferases / Cellulose synthase BcsB, bacterial / Glycosyltransferase 2-like / Cellulose synthase, subunit A / PilZ domain
Cellulose synthase catalytic subunit [UDP-forming] / Cyclic di-GMP-binding protein
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 SciencesR01GM101001 United States
National Science Foundation (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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionFeb 19, 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_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_description / _entity.pdbx_number_of_molecules / _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 2.1Mar 21, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)173,67826
Polymers167,4363
Non-polymers6,24323
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15650 Å2
ΔGint-14 kcal/mol
Surface area56830 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)67.490, 216.790, 219.620
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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Cellulose Synthase ... , 2 types, 2 molecules AB

#1: Protein/peptide Cellulose Synthase A subunit


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/peptide Cellulose Synthase B subunit


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

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Protein/peptide , 1 types, 1 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)

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Non-polymers , 6 types, 23 molecules

#4: Chemical
ChemComp-BGC / BETA-D-GLUCOSE


Mass: 180.156 Da / Num. of mol.: 17
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Glucose
#5: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Uridine diphosphate / Comment: UDP *YM
#6: 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 / Cyclic di-GMP
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Magnesium
#8: Chemical ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H65NO8P
#9: Chemical ChemComp-3PE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / 3-SN-PHOSPHATIDYLETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 1 / 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: 4.8 Å3/Da / Density % sol: 74.38 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop
Details: 1.65-1.9 M Sodium Acetate, 100 mM Sodium Citrate (pH 3-3.5)
PH range: 3-3.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 16, 2013
RadiationMonochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.2→49.62 Å / Num. obs: 53311 / % possible obs: 98.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.168 / Net I/σ(I): 8.7
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.085 / Mean I/σ(I) obs: 2.1 / % possible all: 99.5

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→48.98 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 23.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 2714 5.1 %
Rwork0.208 --
Obs0.21 53242 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.00211365
f_angle_d0.67315562
f_dihedral_angle_d13.8124281
f_chiral_restr0.0251818
f_plane_restr0.0031974
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2-3.25820.3221480.2982260899
3.2582-3.32090.32191360.2838265499
3.3209-3.38860.3191400.2744268199
3.3886-3.46230.28261540.2657259499
3.4623-3.54280.30351470.2559268599
3.5428-3.63140.29771330.2394264199
3.6314-3.72950.28411210.221266299
3.7295-3.83920.23561320.2225262999
3.8392-3.96310.26961590.2091267899
3.9631-4.10470.25171420.2023262899
4.1047-4.26890.22331420.1935266498
4.2689-4.46310.22241470.1847263498
4.4631-4.69820.21391400.1743264198
4.6982-4.99230.19761390.172266698
4.9923-5.37730.23531590.1842263998
5.3773-5.91760.22341540.2024266297
5.9176-6.7720.21011520.1975269297
6.772-8.52470.19921250.1805270997
8.5247-48.98570.19611440.2043276194
Refinement TLS params.

Method: refined / Refinement-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.67820.745-0.1244.50220.70.42670.3554-0.16-0.03730.9439-0.2201-0.76280.1674-0.17220.52870.8229-0.5101-0.14090.84610.30860.8817-10.491121.3398-34.3259
20.52130.4752-0.44390.6233-0.14241.41560.0240.01270.21550.4969-0.1459-0.0366-0.53810.10070.09440.5385-0.0696-0.03370.56430.24060.5536-23.491812.5555-43.3231
33.37-1.58881.97043.9427-2.89626.72350.11270.35510.3419-0.1923-0.20360.07070.33770.95680.12510.8483-0.2219-0.02030.86280.24750.754-10.6147-2.3122-18.1214
42.18370.36790.18823.2187-0.77092.34390.0495-0.38430.03461.10850.09810.3467-0.7683-0.2927-0.11441.1454-0.05020.08130.66170.14990.5391-30.3569-11.3334-1.8417
52.40980.94661.62271.6613-1.595.5085-0.06970.3597-0.07810.26480.28980.42330.52430.0898-0.18710.6476-0.0413-0.04340.65120.09450.5631-32.1528-15.3619-30.2775
60.4478-0.22520.3321.4598-1.24182.32860.0307-0.1070.03890.83860.17770.0928-0.6057-0.1473-0.22630.851-0.07060.00280.56650.16410.6142-29.5373.1691-25.5885
71.6380.95151.94330.55591.05093.6495-0.4018-0.72880.34790.1203-0.71960.4013-0.4534-1.21070.13820.99880.32970.28320.86820.2090.7517-45.76118.7289-18.1523
82.60280.99693.06861.99512.02796.43780.4548-0.2445-0.02790.53440.53411.0650.6695-0.9997-0.59870.5741-0.08910.0370.84280.32450.7151-46.9604-14.2713-23.9435
90.3967-0.4860.12651.499-0.44380.8740.06830.28930.1832-0.03680.58930.40350.1051-0.9986-0.46430.3826-0.077-0.08030.73650.38370.7242-43.9828-0.6922-48.6792
101.6007-0.235-0.76192.649-0.57931.5218-0.11430.30820.0740.09720.07030.12160.2448-0.00680.05970.6305-0.1306-0.04640.49050.10490.5083-28.9662-39.5581-17.3907
111.80051.5219-1.63073.0322-2.6163.1465-0.20580.2197-0.41740.3186-0.2191-0.5999-0.21960.0440.18030.6897-0.0352-0.09790.62620.12250.5316-23.0665-23.2804-16.6535
123.58611.6317-0.87532.35310.02081.6648-0.3490.6993-0.6807-0.34950.34680.52520.7512-0.4172-0.0430.7161-0.2277-0.13390.85930.3180.7485-42.2386-15.4256-41.3623
132.32471.111-1.21522.1276-0.34025.6426-0.0703-0.4957-0.7641-0.01150.2058-0.25370.88120.648-0.06130.53490.0509-0.03070.56560.15790.5573-26.088737.9273-99.0972
141.95020.6904-0.48122.496-0.57882.1645-0.06120.26210.0097-0.4535-0.16530.15970.0796-0.33270.20080.50870.0485-0.0580.49120.0360.4893-38.081235.2537-99.5759
151.11332.3236-0.99235.4786-2.14631.04080.7022-1.0245-0.66731.0793-0.6489-0.58870.5113-0.3209-0.15290.9175-0.0652-0.11410.81590.20680.9719-43.937818.5767-93.6383
162.98250.94920.1251.4696-0.15271.9274-0.09510.18930.16180.01810.07260.0109-0.28110.2012-0.03370.62720.03390.00330.44850.07440.4173-18.468244.8848-100.2417
170.30340.7413-0.86542.353-2.75093.217-0.00751.4401-0.7288-0.79470.5546-0.0513-0.1294-0.2525-0.17930.9174-0.255-0.10771.0521-0.01090.8184-2.728147.9051-109.7356
183.1963-0.34580.72714.06370.78413.1669-0.07220.05240.8242-0.11340.159-0.5006-0.84090.3061-0.10310.7813-0.08250.10260.46080.00210.6623-11.759456.9315-102.9214
192.17170.69060.55821.784-0.09861.31950.1180.0223-0.03750.03160.00840.2847-0.2671-0.3033-0.09020.43260.10910.02910.60290.19990.5191-38.955827.5115-73.5723
200.60590.36320.43361.829-1.01422.20980.0853-0.23030.31830.1808-0.2125-0.2959-0.41580.34230.03720.4616-0.0816-0.02910.60660.16750.5745-9.382540.8192-80.6621
215.14281.44281.43945.12960.63035.2410.2176-0.3748-0.5961-0.1518-0.6088-1.28420.70710.28250.11210.49110.29930.04720.9410.31110.8536-0.435623.3539-85.7182
220.06630.03520.29982.0388-0.40461.5677-0.0265-0.5559-0.4996-0.4486-0.2376-0.47490.51380.79760.12270.54290.11770.0630.8830.37690.6843-18.135111.0772-67.8807
232.4655-1.0412-1.23292.6589-0.56742.5318-0.0243-0.0918-0.52-0.1304-0.2073-0.0329-0.21370.21230.20340.46160.0071-0.02640.52640.16750.5806-11.774128.4286-83.4912
240.9505-0.2246-0.34861.18510.80884.52090.4612-0.3223-0.05860.0239-0.396-0.2809-0.69110.5070.44160.4063-0.2808-0.1730.82470.30250.6015-11.029422.0222-47.304
259.5996-4.193-1.83957.0282-4.26795.3013-0.56290.4983-0.3626-0.4103-0.061-0.30410.42850.0923-0.01990.64210.0446-0.11690.5574-0.10761.29757.778119.6745-85.9036
262.3326-0.09850.1064.05531.63452.7703-0.17710.26550.3741-0.3731-0.1723-0.141-0.22290.264-0.23880.9236-0.35530.20380.62170.17421.09329.85630.8314-80.8676
Refinement TLS group

Refinement-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection details
11(CHAIN A AND RESID 13:35)
22(CHAIN A AND RESID 36:117)
33(CHAIN A AND RESID 118:135)
44(CHAIN A AND RESID 136:277)
55(CHAIN A AND RESID 278:297)
66(CHAIN A AND RESID 298:488)
77(CHAIN A AND RESID 489:502)
88(CHAIN A AND RESID 503:522)
99(CHAIN A AND RESID 523:575)
1010(CHAIN A AND RESID 576:674)
1111(CHAIN A AND RESID 675:706)
1212(CHAIN A AND RESID 707:740)
1313(CHAIN B AND RESID 54:67)
1414(CHAIN B AND RESID 68:153)
1515(CHAIN B AND RESID 154:169)
1616(CHAIN B AND RESID 170:242)
1717(CHAIN B AND RESID 243:248)
1818(CHAIN B AND RESID 249:303)
1919(CHAIN B AND RESID 304:451)
2020(CHAIN B AND RESID 452:504)
2121(CHAIN B AND RESID 505:531)
2222(CHAIN B AND RESID 544:599)
2323(CHAIN B AND RESID 600:665)
2424(CHAIN B AND RESID 666:720)
2525(CHAIN D AND RESID 169:174)
2626(CHAIN D AND RESID 175:177)

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