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- PDB-4gin: Crystal structure of the MUTB R284C mutant from crystals soaked w... -

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Basic information

Entry
Database: PDB / ID: 4gin
TitleCrystal structure of the MUTB R284C mutant from crystals soaked with the inhibitor deoxynojirimycin
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
Sucrose isomerase / Sucrose isomerase
Similarity search - Component
Biological speciesRhizobium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionAug 8, 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)67,2246
Polymers66,8151
Non-polymers4085
Water12,899716
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.8, 89.7, 91.6
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sucrose isomerase / Trehalulose synthase


Mass: 66815.344 Da / Num. of mol.: 1 / 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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 716 / 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: 2.58 Å3/Da / Density % sol: 52.26 %
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: BM30A / Wavelength: 0.9699 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 3, 2004
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9699 Å / Relative weight: 1
ReflectionResolution: 1.9→44.85 Å / Num. all: 55036 / Num. obs: 55036 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Rsym value: 0.113 / Net I/σ(I): 10.3
Reflection shellResolution: 1.9→2.02 Å / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 5.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZJA

1zja


Resolution: 1.9→44.85 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 15.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1806 5580 10.14 %RANDOM
Rwork0.1399 ---
obs0.144 55017 99.9 %-
all-55017 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→44.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4453 0 25 716 5194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084666
X-RAY DIFFRACTIONf_angle_d1.0956351
X-RAY DIFFRACTIONf_dihedral_angle_d12.7431687
X-RAY DIFFRACTIONf_chiral_restr0.085645
X-RAY DIFFRACTIONf_plane_restr0.005840
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.92160.24141680.18941638100
1.9216-1.94420.2032010.16571618100
1.9442-1.96790.19741920.1551599100
1.9679-1.99280.19511910.14991629100
1.9928-2.01910.20951790.14951615100
2.0191-2.04670.19781790.15081662100
2.0467-2.0760.1931960.15011615100
2.076-2.10690.19251540.14851638100
2.1069-2.13990.18872010.13681622100
2.1399-2.17490.19151650.141648100
2.1749-2.21240.18311830.14371630100
2.2124-2.25270.20351940.14511613100
2.2527-2.2960.20541700.14081670100
2.296-2.34290.16812010.13381612100
2.3429-2.39380.171870.13291636100
2.3938-2.44950.19371960.13841619100
2.4495-2.51070.19781910.12941645100
2.5107-2.57860.17641780.13741622100
2.5786-2.65450.16841760.13531651100
2.6545-2.74020.17371770.13651655100
2.7402-2.83810.17922000.14191650100
2.8381-2.95170.19451960.14421628100
2.9517-3.0860.18891810.1461665100
3.086-3.24860.1962050.14361657100
3.2486-3.45210.18421720.13891668100
3.4521-3.71850.14861960.13151649100
3.7185-4.09250.15951590.12191708100
4.0925-4.68420.15191910.11551690100
4.6842-5.89940.16162040.13141704100
5.8994-44.86250.17911970.168178199
Refinement TLS params.Method: refined / Origin x: 11.4763 Å / Origin y: 12.5386 Å / Origin z: 14.8503 Å
111213212223313233
T0.0911 Å20.0085 Å20.0051 Å2-0.0764 Å2-0.0003 Å2--0.0762 Å2
L0.4872 °20.0723 °20.0739 °2-0.6844 °2-0.0711 °2--0.4728 °2
S0.0146 Å °-0.0211 Å °-0.005 Å °-0.0159 Å °0.0022 Å °-0.0731 Å °0.0068 Å °0.0178 Å °-0.0186 Å °
Refinement TLS groupSelection details: all

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