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- PDB-2yoc: Crystal structure of PulA from Klebsiella oxytoca -

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Basic information

Entry
Database: PDB / ID: 2yoc
TitleCrystal structure of PulA from Klebsiella oxytoca
ComponentsPULLULANASE
KeywordsHYDROLASE / GLYCOSYL HYDROLASE / TYPE 2 SECRETION SYSTEMS
Function / homology
Function and homology information


pullulanase / pullulanase activity / carbohydrate binding / carbohydrate metabolic process / plasma membrane
Similarity search - Function
Pullulanase, Ins domain / Pullulanase Ins domain / Pullulanase, carbohydrate-binding module 41 / Bacterial pullanase-associated domain / Alpha-1,6-glucosidases, pullulanase-type / Alpha-1,6-glucosidases, pullulanase-type, C-terminal / Pullulanase, N2 domain / Alpha-1,6-glucosidases, pullulanase-type, C-terminal / Pullulanase N2 domain / Rab geranylgeranyltransferase alpha-subunit, insert domain ...Pullulanase, Ins domain / Pullulanase Ins domain / Pullulanase, carbohydrate-binding module 41 / Bacterial pullanase-associated domain / Alpha-1,6-glucosidases, pullulanase-type / Alpha-1,6-glucosidases, pullulanase-type, C-terminal / Pullulanase, N2 domain / Alpha-1,6-glucosidases, pullulanase-type, C-terminal / Pullulanase N2 domain / Rab geranylgeranyltransferase alpha-subunit, insert domain / Immunoglobulin-like - #1110 / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Carbohydrate-binding-like fold / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesKLEBSIELLA OXYTOCA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.88 Å
AuthorsFrancetic, O. / Mechaly, A.E. / Tello-Manigne, D. / Buschiazzo, A. / Bernarde, C. / Nadeau, N. / Pugsley, A.P. / Alzari, P.M.
CitationJournal: Structure / Year: 2016
Title: Structural Basis of Pullulanase Membrane Binding and Secretion Revealed by X-Ray Crystallography, Molecular Dynamics and Biochemical Analysis
Authors: East, A. / Mechaly, A.E. / Huysmans, G.H.M. / Bernarde, C. / Tello-Manigne, D. / Nadeau, N. / Pugsley, A.P. / Buschiazzo, A. / Alzari, P.M. / Bond, P.J. / Francetic, O.
History
DepositionOct 23, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3Jan 20, 2016Group: Database references
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AI" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AI" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BI" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PULLULANASE
B: PULLULANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,21524
Polymers236,5502
Non-polymers1,66622
Water5,549308
1
A: PULLULANASE
B: PULLULANASE
hetero molecules

A: PULLULANASE
B: PULLULANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)476,43148
Polymers473,1004
Non-polymers3,33144
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area15410 Å2
ΔGint-571.3 kcal/mol
Surface area140100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.150, 179.150, 334.690
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein PULLULANASE / / ALPHA-DEXTRIN ENDO-1 / 6-ALPHA-GLUCOSIDASE / PULLULAN 6-GLUCANOHYDROLASE


Mass: 118274.914 Da / Num. of mol.: 2 / Fragment: RESIDUES 21-1089
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) KLEBSIELLA OXYTOCA (bacteria) / Strain: UNF5023 / Plasmid: PCHA4486 / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834 / References: UniProt: P07206, pullulanase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64 % / Description: NONE
Crystal growDetails: 1.8 M AMMONIUM SULPHATE, 2 % MPD AND 100 MM SODIUM CITRATE (PH 7.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.88→58.64 Å / Num. obs: 71937 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 14.5 % / Biso Wilson estimate: 76.13 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 20.4
Reflection shellResolution: 2.88→3.04 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 4 / % possible all: 98.5

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.88→42.17 Å / Cor.coef. Fo:Fc: 0.9432 / Cor.coef. Fo:Fc free: 0.9215 / SU R Cruickshank DPI: 0.85 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.936 / SU Rfree Blow DPI: 0.292 / SU Rfree Cruickshank DPI: 0.295
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=16565. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=16565. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=8.
RfactorNum. reflection% reflectionSelection details
Rfree0.2131 3633 5.06 %RANDOM
Rwork0.1711 ---
obs0.1733 71862 99.45 %-
Displacement parametersBiso mean: 81.16 Å2
Baniso -1Baniso -2Baniso -3
1-4.4003 Å20 Å20 Å2
2--4.4003 Å20 Å2
3----8.8006 Å2
Refine analyzeLuzzati coordinate error obs: 0.399 Å
Refinement stepCycle: LAST / Resolution: 2.88→42.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16104 0 78 308 16490
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0116496HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2222466HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5556SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes468HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2404HARMONIC5
X-RAY DIFFRACTIONt_it16496HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion20.44
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2157SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact19496SEMIHARMONIC4
LS refinement shellResolution: 2.88→2.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2845 251 5.18 %
Rwork0.2196 4594 -
all0.223 4845 -
obs--99.45 %
Refinement TLS params.Method: refined / Origin x: 54.7012 Å / Origin y: 113.1728 Å / Origin z: 203.917 Å
111213212223313233
T0.428 Å2-0.0376 Å20.1432 Å2-0.6341 Å20.0779 Å2--0.3745 Å2
L0.9637 °2-0.578 °2-0.3417 °2-0.8567 °20.2481 °2--0 °2
S-0.1644 Å °-0.2066 Å °-0.267 Å °0.2388 Å °0.0933 Å °0.279 Å °0.0609 Å °-0.0016 Å °0.0712 Å °
Refinement TLS groupSelection details: ALL

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