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- PDB-4go8: Crystal Structure of the TREHALULOSE SYNTHASE MUTB, MUTANT A258V,... -

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Basic information

Entry
Database: PDB / ID: 4go8
TitleCrystal Structure of the TREHALULOSE SYNTHASE MUTB, MUTANT A258V, in complex with TRIS
ComponentsSucrose isomerase
KeywordsISOMERASE / MUTANT ENZYME / TIM-BARREL / (BETA/ALPHA)8 / SUCROSE ISOMERASE / GLYCOSIDE HYDROLASE / TREHALULOSE SYNTHASE / GH13 FAMILY (CAZY DATABASE) / CALCIUM BINDING
Function / homology
Function and homology information


oligosaccharide catabolic process / alpha-amylase activity / isomerase activity / metal ion binding
Similarity search - Function
Glycosyl hydrolase, C-terminal (DUF3459) / Domain of unknown function (DUF3459) / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta ...Glycosyl hydrolase, C-terminal (DUF3459) / Domain of unknown function (DUF3459) / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas mesoacidophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å
AuthorsLipski, A. / Haser, R. / Aghajari, N.
CitationJournal: To be Published / Year: 2013
Title: Crystal structure of MUTB A258V mutant in complex with TRIS
Authors: Lipski, A. / Watzlawick, H. / Ravaud, S. / Robert, X. / Haser, R. / Mattes, R. / Aghajari, N.
History
DepositionAug 19, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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

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Assembly

Deposited unit
A: Sucrose isomerase
B: Sucrose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,2586
Polymers127,9342
Non-polymers3244
Water19,1501063
1
A: Sucrose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1293
Polymers63,9671
Non-polymers1622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sucrose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1293
Polymers63,9671
Non-polymers1622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.51, 71.31, 81.53
Angle α, β, γ (deg.)68.04, 72.72, 70.10
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Sucrose isomerase / Trehalulose synthase


Mass: 63966.902 Da / Num. of mol.: 2 / Fragment: MUTB fragment, UNP residues 28-584 / Mutation: A258V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mesoacidophila (bacteria) / Gene: mutB / Plasmid: PHWG660.7 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q2PS28, EC: 5.4.11.99
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1063 / 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: 2.47 Å3/Da / Density % sol: 50.18 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl, 12%(w/v) PEG20000, 0.01M L-Cysteine, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97559 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2008
RadiationMonochromator: Toroidal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97559 Å / Relative weight: 1
ReflectionResolution: 2.15→14.82 Å / Num. all: 66682 / Num. obs: 62687 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 21.3 Å2 / Rsym value: 0.108 / Net I/σ(I): 7.6
Reflection shellResolution: 2.15→2.3 Å / Redundancy: 1.86 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 3.46 / Num. unique all: 11394 / % possible all: 93.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMACrefinement
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1ZJB

1zjb


Resolution: 2.15→14.82 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 25.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2495 3184 5.08 %RANDOM
Rwork0.1904 ---
obs0.194 62658 94.5 %-
all-62658 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→14.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8900 0 18 1063 9981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039214
X-RAY DIFFRACTIONf_angle_d0.66512546
X-RAY DIFFRACTIONf_dihedral_angle_d10.8893313
X-RAY DIFFRACTIONf_chiral_restr0.0521282
X-RAY DIFFRACTIONf_plane_restr0.0031653
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.15-2.1820.28431260.2085258494
2.182-2.2160.27551310.2008258794
2.216-2.25220.29941500.2078254094
2.2522-2.29090.26081430.2104251492
2.2909-2.33240.29221140.2039259294
2.3324-2.37710.30221330.199259495
2.3771-2.42540.26011360.1903262595
2.4254-2.47790.25531250.1883260695
2.4779-2.53530.2521470.1979258794
2.5353-2.59830.28141280.2009258895
2.5983-2.66820.30011490.2087261596
2.6682-2.74620.30231370.206263095
2.7462-2.83430.23781400.186258196
2.8343-2.93480.23981520.1797262296
2.9348-3.05140.24761520.1877258195
3.0514-3.18890.29511380.1877261495
3.1889-3.35520.21341620.1775258895
3.3552-3.56270.22461380.1778262695
3.5627-3.83340.23591430.1719252294
3.8334-4.21110.20181220.1642257793
4.2111-4.80220.21731370.1787250492
4.8022-5.98340.22371530.1945259295
5.9834-14.82450.23491280.2229260595

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