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- PDB-3om5: Crystal structure of B. megaterium levansucrase mutant N252A -

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Basic information

Entry
Database: PDB / ID: 3om5
TitleCrystal structure of B. megaterium levansucrase mutant N252A
ComponentsLevansucrase
KeywordsTRANSFERASE / five fold beta-propeller / levansucrase
Function / homology
Function and homology information


levansucrase / levansucrase activity / carbohydrate utilization / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 68 / Levansucrase/Invertase / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Levansucrase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsStrube, C.P. / Homann, A. / Gamer, M. / Jahn, D. / Seibel, J. / Heinz, D.W.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Polysaccharide Synthesis of the Levansucrase SacB from Bacillus megaterium Is Controlled by Distinct Surface Motifs.
Authors: Strube, C.P. / Homann, A. / Gamer, M. / Jahn, D. / Seibel, J. / Heinz, D.W.
History
DepositionAug 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Levansucrase
B: Levansucrase
C: Levansucrase
D: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,83719
Polymers204,1204
Non-polymers1,71815
Water20,8251156
1
A: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3523
Polymers51,0301
Non-polymers3222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3523
Polymers51,0301
Non-polymers3222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6697
Polymers51,0301
Non-polymers6396
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4646
Polymers51,0301
Non-polymers4345
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.368, 100.186, 95.195
Angle α, β, γ (deg.)90.000, 90.680, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Levansucrase


Mass: 51029.879 Da / Num. of mol.: 4 / Fragment: Levansucrase SacB, UNP residues 29-484 / Mutation: N252A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: sacB / Production host: Escherichia coli (E. coli) / References: UniProt: D5DC07, levansucrase

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Non-polymers , 6 types, 1171 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1156 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: USING 3 uL OF A 8 MG/ML PROTEIN SOLUTION MIXED WITH 3 uL RESERVOIR BUFFER (0.1 M Na-Phosphate-citrate pH 4.1; 0.2 M lithiumsulfate; 20% (w/v) PEG 1000) IN THE DROPLET. , VAPOR DIFFUSION, ...Details: USING 3 uL OF A 8 MG/ML PROTEIN SOLUTION MIXED WITH 3 uL RESERVOIR BUFFER (0.1 M Na-Phosphate-citrate pH 4.1; 0.2 M lithiumsulfate; 20% (w/v) PEG 1000) IN THE DROPLET. , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MX225 (Rayonics LLC) / Detector: CCD / Date: Aug 21, 2008
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.714
11h,-k,-l20.106
11L, -K, H30.088
11-L, K, H40.091
ReflectionResolution: 1.95→50.01 Å / Num. all: 117898 / Num. obs: 117544 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 1.95→2.11 Å / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.1data extraction
DNAdata collection
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→50.01 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.228 / WRfactor Rwork: 0.1966 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8587 / SU B: 3.717 / SU ML: 0.102 / SU R Cruickshank DPI: 0.0493 / SU Rfree: 0.0384 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2084 5928 5 %RANDOM
Rwork0.1811 ---
all0.1825 117898 --
obs0.1825 117876 93.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 51.84 Å2 / Biso mean: 25.7455 Å2 / Biso min: 10.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å2-14.73 Å2
2---6.92 Å20 Å2
3---6.1 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14156 0 101 1156 15413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02214579
X-RAY DIFFRACTIONr_angle_refined_deg1.0281.94519709
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95351794
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.07425.804734
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.713152463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5381536
X-RAY DIFFRACTIONr_chiral_restr0.070.22091
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02111204
X-RAY DIFFRACTIONr_mcbond_it0.4271.58874
X-RAY DIFFRACTIONr_mcangle_it0.775214313
X-RAY DIFFRACTIONr_scbond_it0.91735705
X-RAY DIFFRACTIONr_scangle_it1.4814.55396
LS refinement shellResolution: 1.955→2.006 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 40 -
Rwork0.248 969 -
all-1009 -
obs--10.82 %

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