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- PDB-4h2c: Trehalulose synthase MutB R284C mutant -

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Basic information

Entry
Database: PDB / ID: 4h2c
TitleTrehalulose synthase MutB R284C mutant
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


alpha-amylase activity / oligosaccharide catabolic process / 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
Sucrose isomerase / Sucrose isomerase
Similarity search - Component
Biological speciesRhizobium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLipski, A. / Ravaud, S. / Robert, X. / Haser, R. / Aghajari, N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Mutations inducing an active-site aperture in Rhizobium sp. sucrose isomerase confer hydrolytic activity
Authors: Lipski, A. / Watzlawick, H. / Ravaud, S. / Robert, X. / Rhimi, M. / Haser, R. / Mattes, R. / Aghajari, N.
History
DepositionSep 12, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Nov 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_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.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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3857
Polymers63,8851
Non-polymers5016
Water15,349852
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.09, 90.08, 91.57
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sucrose isomerase / Trehalulose synthase


Mass: 63884.793 Da / Num. of mol.: 1 / Fragment: TREHALULOSE SYNTHASE MUTB, UNP residues 28-584 / Mutation: R284C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium (bacteria) / Strain: MX-45 / Gene: mutB / Plasmid: PHWG659.3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: Q2PS28, UniProt: M1E1F6*PLUS, EC: 5.4.11.99
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 852 / 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: 2.71 Å3/Da / Density % sol: 54.69 %
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: ID14-3 / Wavelength: 0.931 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 4, 2004
RadiationMonochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.7→16.8 Å / Num. obs: 92087 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 7.4 % / Biso Wilson estimate: 11.4 Å2 / Rsym value: 0.16 / Net I/σ(I): 9
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 5.3 / Num. unique all: 11131 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GIN

4gin


Resolution: 1.7→16.8 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 15.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.173 3865 5.02 %RANDOM
Rwork0.1419 ---
obs0.1435 76945 99.97 %-
all-76945 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→16.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4483 0 31 852 5366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134746
X-RAY DIFFRACTIONf_angle_d1.436466
X-RAY DIFFRACTIONf_dihedral_angle_d13.211743
X-RAY DIFFRACTIONf_chiral_restr0.11656
X-RAY DIFFRACTIONf_plane_restr0.008856
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.72070.19951330.14942566100
1.7207-1.74250.17811400.14822574100
1.7425-1.76540.19591380.1472614100
1.7654-1.78950.19841400.15152557100
1.7895-1.81510.17721330.14512558100
1.8151-1.84210.17661360.1492581100
1.8421-1.87090.20921270.15082627100
1.8709-1.90150.19731230.14922570100
1.9015-1.93430.1871360.15462580100
1.9343-1.96940.18451270.14212611100
1.9694-2.00720.1951270.14972620100
2.0072-2.04810.17271470.1362570100
2.0481-2.09250.1831380.14052576100
2.0925-2.14110.15041290.14182611100
2.1411-2.19460.1731480.14442599100
2.1946-2.25380.1741340.14512599100
2.2538-2.31990.19191430.14782574100
2.3199-2.39460.18761500.14042598100
2.3946-2.47990.17891250.14292641100
2.4799-2.57890.16811360.14342593100
2.5789-2.69580.16651440.14722630100
2.6958-2.83730.18421470.1442595100
2.8373-3.01410.17641450.1472628100
3.0141-3.24520.15581290.14032645100
3.2452-3.5690.16461390.13262642100
3.569-4.07890.1531400.12792657100
4.0789-5.11470.15531720.1222670100
5.1147-16.76560.17081390.1608279499
Refinement TLS params.Method: refined / Origin x: 11.5779 Å / Origin y: 102.683 Å / Origin z: 14.7788 Å
111213212223313233
T0.0778 Å20.0096 Å20.0064 Å2-0.0657 Å2-0.001 Å2--0.0688 Å2
L0.5626 °20.0698 °20.1122 °2-0.6935 °2-0.0722 °2--0.508 °2
S0.0101 Å °-0.0186 Å °-0.0115 Å °-0.0163 Å °0 Å °-0.0876 Å °0.0093 Å °0.0175 Å °-0.0118 Å °
Refinement TLS groupSelection details: ALL

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