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- PDB-9zau: Pel polysaccharide deacetylase PelA from Bacillus cereus ATCC 10987 -

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Basic information

Entry
Database: PDB / ID: 9zau
TitlePel polysaccharide deacetylase PelA from Bacillus cereus ATCC 10987
ComponentsPredicted membrane protein, putative
KeywordsMEMBRANE PROTEIN / Carbohydrate esterase / Carbohydrate binding module (CBM)
Function / homologyProtein of unknown function DUF2194 / Uncharacterised protein conserved in bacteria (DUF2194) / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Class I glutamine amidotransferase-like / carbohydrate metabolic process / Predicted membrane protein, putative
Function and homology information
Biological speciesBacillus cereus ATCC 10987 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsShankara Subramanian, A. / Pfoh, R. / Howell, P.L.
Funding support Canada, 3items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT 191979 Canada
Canadian Institutes of Health Research (CIHR)FDN154327 Canada
Canadian Institutes of Health Research (CIHR)FDN159902 Canada
CitationJournal: J.Biol.Chem. / Year: 2026
Title: Bacillus cereus PelA DA is a polysaccharide de-N-acetylase required for Pel-dependent biofilm formation.
Authors: Subramanian, A.S. / Le Mauff, F. / Kitova, E.N. / Pfoh, R. / Panjalingam, M. / Wu, D.Y. / Gilbert, S. / Morrison, Z.A. / Jacobsen-Perez, C.A. / Razvi, E. / Nitz, M. / Codee, J. / Klassen, J. ...Authors: Subramanian, A.S. / Le Mauff, F. / Kitova, E.N. / Pfoh, R. / Panjalingam, M. / Wu, D.Y. / Gilbert, S. / Morrison, Z.A. / Jacobsen-Perez, C.A. / Razvi, E. / Nitz, M. / Codee, J. / Klassen, J.S. / Sheppard, D.C. / Howell, P.L.
History
DepositionNov 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Predicted membrane protein, putative
B: Predicted membrane protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,2044
Polymers134,0732
Non-polymers1312
Water1,38777
1
A: Predicted membrane protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1022
Polymers67,0371
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Predicted membrane protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1022
Polymers67,0371
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.238, 112.033, 100.509
Angle α, β, γ (deg.)90.000, 90.890, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Predicted membrane protein, putative


Mass: 67036.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Construct was the mature protein without a signal sequence. It includes residues 27-610 and an N-terminal methionine residue. Residues 27-46 are not visible in the structure. The first ...Details: Construct was the mature protein without a signal sequence. It includes residues 27-610 and an N-terminal methionine residue. Residues 27-46 are not visible in the structure. The first residue in the above alignment should begin at "47"
Source: (gene. exp.) Bacillus cereus ATCC 10987 (bacteria) / Gene: BCE_5585 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q72WZ3
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.15 M Ammonium fluoride, 27.5% (v/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 1.28377 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28377 Å / Relative weight: 1
ReflectionResolution: 2.51→29.64 Å / Num. obs: 40986 / % possible obs: 98.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 53.85 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 7.8
Reflection shellResolution: 2.51→2.58 Å / Rmerge(I) obs: 0.6 / Num. unique obs: 2720

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX1.21.2_5419refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→29.64 Å / SU ML: 0.4039 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.7967
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2565 2100 5.13 %
Rwork0.1942 38847 -
obs0.1975 40947 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.38 Å2
Refinement stepCycle: LAST / Resolution: 2.51→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8751 0 2 77 8830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00848961
X-RAY DIFFRACTIONf_angle_d0.991412173
X-RAY DIFFRACTIONf_chiral_restr0.05481361
X-RAY DIFFRACTIONf_plane_restr0.00761555
X-RAY DIFFRACTIONf_dihedral_angle_d19.36193289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.570.39141360.34542273X-RAY DIFFRACTION88.4
2.57-2.640.37491610.31582645X-RAY DIFFRACTION99.5
2.64-2.710.35671280.2892589X-RAY DIFFRACTION99.45
2.71-2.790.35991340.28062615X-RAY DIFFRACTION99.28
2.79-2.880.35731180.28122616X-RAY DIFFRACTION99.38
2.88-2.980.371400.27572586X-RAY DIFFRACTION98.95
2.98-3.10.34391280.24752596X-RAY DIFFRACTION98.16
3.1-3.240.29151470.22092588X-RAY DIFFRACTION98.81
3.24-3.410.29841690.21762576X-RAY DIFFRACTION98.92
3.41-3.620.27451200.20572620X-RAY DIFFRACTION99.28
3.63-3.90.21891690.1732610X-RAY DIFFRACTION99.32
3.9-4.30.24991570.15552597X-RAY DIFFRACTION99.31
4.3-4.920.1821210.14322629X-RAY DIFFRACTION99.13
4.92-6.180.22311320.16572650X-RAY DIFFRACTION99.04
6.18-29.640.19261400.15672657X-RAY DIFFRACTION98.66
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)
11.19554956419-0.198027072721-0.005317339201941.74169611952-0.1283088478461.873401737290.0110552168617-0.287354977101-0.06972995777550.4396400395740.0260707490524-0.2267020854340.1306628592820.143137567172-0.03931570557720.471443979463-0.0409907105276-0.05383608269920.468397039501-0.051268500080.3630785167588.86428572351-10.710225908145.686776424
22.49629441678-2.04753113145-0.5531936516675.039124864361.444381616953.589465989780.1877981233610.2836825749930.193627570391-0.393247983917-0.152602033590.270835680081-0.704166079586-0.613909490576-0.02442457485580.5451796429080.02797851102840.03021116599850.4990456895890.05960264142660.367593971152-11.18656398639.3856140932615.983849317
31.53948479236-1.044353756050.2387178847223.06026499976-0.2430884806875.301050360810.1092750563790.2692226495860.138693444853-0.446240884381-0.0323381932408-0.0872059901851-0.17635336254-0.168853450846-0.0578626922540.440927049434-0.06201821905190.02612562694640.396675527918-0.0002834899982050.3180110242971.054468977811.7229539767915.5971390665
45.92522239648-5.18454382706-0.4311657130946.33226036666-1.69885926012.579353867610.4954158610970.281098925302-0.743084709196-0.171464749693-0.1692945397380.7718092970510.245555885298-0.409009003338-0.3290184606710.506011516318-0.07757664737260.002087175439240.440724929003-0.02149945838680.393723291494-10.4638350614-0.90067387582931.4574242608
52.71539332699-0.4293663390430.0009882672798611.67869957285-0.2289444347024.30646909447-0.0914600747303-0.3325305191760.4388342137680.3602330489860.166340796369-0.209735773872-0.7077544166550.232055563682-0.06482366309720.577199475719-0.04702642353220.004845778765850.325278738154-0.07818672399140.4324642425215.476863444149.8133818339844.9109973955
62.21301806450.1598225633430.3922049577733.56520625331-0.6873945751692.71405364788-0.04198570106240.5354257353960.231819078664-0.964624734560.127036407734-0.368527105626-0.146924058130.261818112131-0.07600399552490.616885346417-0.08146221424970.1367703590080.5030491635980.01394831213850.40110433504920.3609955879-18.39782613352.73660476944
71.34669166838-0.293706382744-0.8527226775023.50936450158-0.3104284470772.62357137898-0.175864972905-0.0603715156241-0.41897604857-0.485837157581-0.0879260047957-0.04923373890521.13449423120.2845158346010.2922927553430.5948964276030.0966778759153-0.07854092720460.484964151135-0.01042369799910.42102207740215.5711874892-51.424173173423.8221568468
82.2244034714-0.046572581163-0.82055440183.25751141637-0.8280097520434.460630278960.0328847724311-0.21869117584-0.2172661957110.1199954750730.0101945654818-0.1438395811270.3529666646540.0222130152844-0.04389600916970.3125659245850.0180432192097-0.05990706833760.338346683222-0.0002381193376820.32469940957815.1993061352-42.026997726132.7479256416
91.233085348330.9213207309511.064053150196.437059511470.5630201854724.952680792790.02813509340520.258647716390.0947076039522-0.7932123614260.165319635580.3662124419040.398006876223-0.255830743949-0.1549274952220.6536423700110.0936505560244-0.02626104475660.3992588952060.002011212558350.32878688390711.2604910307-43.548901091613.8302332401
102.443256997580.679350604543-0.8454905688642.644397109460.1250611169472.86712454177-0.05820492779840.417401766782-0.105807453766-0.7901909783460.034807333387-0.6887124661720.388881179020.5708182503870.09085912571420.6848499423370.1709922324380.194799147610.5976495996160.01165685484150.61529179507131.9228171361-39.00576563897.0227436468
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 47 through 282 )AA47 - 2821 - 228
22chain 'A' and (resid 283 through 365 )AA283 - 365229 - 311
33chain 'A' and (resid 366 through 466 )AA366 - 466312 - 412
44chain 'A' and (resid 467 through 502 )AA467 - 502413 - 448
55chain 'A' and (resid 503 through 610 )AA503 - 610449 - 556
66chain 'B' and (resid 47 through 244 )BB47 - 2441 - 198
77chain 'B' and (resid 245 through 329 )BB245 - 329199 - 269
88chain 'B' and (resid 330 through 466 )BB330 - 466270 - 406
99chain 'B' and (resid 467 through 502 )BB467 - 502407 - 439
1010chain 'B' and (resid 503 through 608 )BB503 - 608440 - 545

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