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- PDB-3om4: Crystal structure of B. megaterium levansucrase mutant K373A -

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Basic information

Entry
Database: PDB / ID: 3om4
TitleCrystal structure of B. megaterium levansucrase mutant K373A
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 / molecular replacement / Resolution: 1.75 Å
AuthorsStrube, C.P. / Homann, A. / Gamer, M. / Jahn, D. / Seibel, J. / Heinz, D.W.
CitationJournal: To be Published
Title: Crystal structure of B. megaterium levansucrase mutant K373A
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)205,84721
Polymers204,0594
Non-polymers1,78817
Water26,2481457
1
A: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4075
Polymers51,0151
Non-polymers3924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4515
Polymers51,0151
Non-polymers4364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5916
Polymers51,0151
Non-polymers5775
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3975
Polymers51,0151
Non-polymers3824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.585, 100.075, 95.544
Angle α, β, γ (deg.)90.000, 90.670, 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: 51014.801 Da / Num. of mol.: 4 / Fragment: Levansucrase SacB, UNP residues 29-484 / Mutation: K373A
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, 1474 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1457 / 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: 2.19 Å3/Da / Density % sol: 43.9 %
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: 14.2 / Wavelength: 0.91841 Å
DetectorType: MX-225 ccd-detector from Rayonics (Evanston, USA) / Detector: CCD / Date: Apr 24, 2009
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.75→47.77 Å / Num. all: 174958 / Num. obs: 172859 / % possible obs: 98.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 1.75→1.84 Å / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
DNAdata collection
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→47.77 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.279 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2133 8763 5 %RANDOM
Rwork0.2015 ---
all0.202 174958 --
obs0.202 174956 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 46.51 Å2 / Biso mean: 13.2493 Å2 / Biso min: 3.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0.38 Å2
2--0.04 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.75→47.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14152 0 104 1457 15713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02214672
X-RAY DIFFRACTIONr_angle_refined_deg1.0231.94519864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06151822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36525.855743
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.563152473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5191536
X-RAY DIFFRACTIONr_chiral_restr0.0710.22109
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02111320
X-RAY DIFFRACTIONr_mcbond_it0.391.58934
X-RAY DIFFRACTIONr_mcangle_it0.727214431
X-RAY DIFFRACTIONr_scbond_it0.86535738
X-RAY DIFFRACTIONr_scangle_it1.4674.55425
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 643 -
Rwork0.292 12145 -
all-12788 -
obs--97.92 %

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