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- PDB-4p02: Structure of Bacterial Cellulose Synthase with cyclic-di-GMP bound. -

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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-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: 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 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 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)175,14328
Polymers167,4363
Non-polymers7,70725
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16090 Å2
ΔGint-2 kcal/mol
Surface area57810 Å2
MethodPISA
Unit cell
γ
α
β
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

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Components

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

#1: Protein/peptide 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/peptide 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

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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 , 5 types, 25 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-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
#6: Chemical
ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C32H65NO8P
#7: 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
#8: Chemical ChemComp-MG / MAGNESIUM ION


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

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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: 4.78 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

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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

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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
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.00311330
f_angle_d0.75415496
f_dihedral_angle_d14.7974276
f_chiral_restr0.0271810
f_plane_restr0.0041964
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.65-2.68010.36191350.3288271892
2.6801-2.71150.32241610.3018277293
2.7115-2.74450.33171430.2776268093
2.7445-2.77910.30751620.2834271693
2.7791-2.81560.31211520.2693278593
2.8156-2.85410.29791220.2499271593
2.8541-2.89470.28991280.2538272493
2.8947-2.93780.28011250.2516280493
2.9378-2.98360.31141310.2485270793
2.9836-3.03230.24871450.2368272593
3.0323-3.08440.28641150.2311280692
3.0844-3.14030.28051410.2238266793
3.1403-3.20050.24661560.2322274592
3.2005-3.26550.26261400.2164269092
3.2655-3.33620.26541460.2171273192
3.3362-3.41340.2291380.2066273092
3.4134-3.49840.27541450.2089272492
3.4984-3.59240.22861560.205271292
3.5924-3.69750.25551480.1972270091
3.6975-3.81610.23511480.1941271392
3.8161-3.95140.19161640.1811270291
3.9514-4.10830.23851450.1811270291
4.1083-4.29360.23191450.1704271191
4.2936-4.51750.19111410.1704273291
4.5175-4.79680.17071260.1604271890
4.7968-5.16130.18551370.1676269990
5.1613-5.66990.231700.1876268189
5.6699-6.46590.21181260.1974270289
6.4659-8.05660.23131590.1887268888
8.0566-19.98660.16991570.1746274286
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)
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

Refinement-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection details
11(CHAIN A AND RESID 13:117)
22(CHAIN A AND RESID 118:138)
33(CHAIN A AND RESID 139:269)
44(CHAIN A AND RESID 270:487)
55(CHAIN A AND RESID 488:511)
66(CHAIN A AND RESID 512:529)
77(CHAIN A AND RESID 530:702)
88(CHAIN A AND RESID 703:740)
99(CHAIN B AND RESID 54:92)
1010(CHAIN B AND RESID 93:187)
1111(CHAIN B AND RESID 188:286)
1212(CHAIN B AND RESID 287:317)
1313(CHAIN B AND RESID 318:401)
1414(CHAIN B AND RESID 402:420)
1515(CHAIN B AND RESID 421:492)
1616(CHAIN B AND RESID 493:528)
1717(CHAIN B AND RESID 529:582)
1818(CHAIN B AND RESID 583:597)
1919(CHAIN B AND RESID 598:666)
2020(CHAIN B AND RESID 667:720)
2121(CHAIN D AND RESID 169:177)

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