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- PDB-3m6d: The crystal structure of the d307a mutant of glycoside Hydrolase ... -

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Basic information

Entry
Database: PDB / ID: 3m6d
TitleThe crystal structure of the d307a mutant of glycoside Hydrolase (family 31) from ruminococcus obeum atcc 29174
ComponentsUncharacterized protein
KeywordsHYDROLASE / STRUCTURAL GENOMICS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / MCSG / MIDWEST CENTER FOR STRUCTURAL GENOMICS
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Immunoglobulin-like - #4040 / Glycosyl hydrolases family 31, active site / Glycosyl hydrolases family 31 active site. / glycosyl hydrolase (family 31) / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain ...Immunoglobulin-like - #4040 / Glycosyl hydrolases family 31, active site / Glycosyl hydrolases family 31 active site. / glycosyl hydrolase (family 31) / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Glycosyl hydrolase, family 31
Similarity search - Component
Biological speciesRuminococcus obeum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTan, K. / Tesar, C. / Freeman, L. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Faseb J. / Year: 2010
Title: Novel alpha-glucosidase from human gut microbiome: substrate specificities and their switch.
Authors: Tan, K. / Tesar, C. / Wilton, R. / Keigher, L. / Babnigg, G. / Joachimiak, A.
History
DepositionMar 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)154,8112
Polymers154,8112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-16 kcal/mol
Surface area46040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.856, 124.025, 87.832
Angle α, β, γ (deg.)90.00, 108.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein


Mass: 77405.453 Da / Num. of mol.: 2 / Mutation: D307A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus obeum (bacteria) / Strain: ATCC 29174 / Gene: RUMOBE_03919 / Plasmid: PMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): PPK1037 / References: UniProt: A5ZY13

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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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M BIS-TRIS, 25% PEG3350, 5MM MALTOSE, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 24, 2010 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 29095 / Num. obs: 29095 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 10.9
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 4 % / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 1.4 / Num. unique all: 1847 / % possible all: 94.1

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FFJ

3ffj
PDB Unreleased entry


Resolution: 2.9→49.78 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.834 / SU B: 53.165 / SU ML: 0.441 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.548 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29659 1481 5.1 %RANDOM
Rwork0.21799 ---
all0.22206 27591 --
obs0.22206 27591 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 mean: 54.941 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20.07 Å2
2--0.09 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10735 0 0 0 10735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02211024
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.95114866
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.87151309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45623.935582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.926151894
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2771568
X-RAY DIFFRACTIONr_chiral_restr0.1030.21493
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218616
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5721.56515
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.104210474
X-RAY DIFFRACTIONr_scbond_it1.4234509
X-RAY DIFFRACTIONr_scangle_it2.4374.54392
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.897→2.972 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 102 -
Rwork0.34 1799 -
obs--88.01 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6306-0.1608-0.33090.34210.23510.6111-0.06180.0052-0.0663-0.02620.03980.03640.04830.02040.0220.0385-0.0285-0.04340.04180.02970.1157-0.8821.89616.948
20.247-0.04650.16051.043-0.24020.47970.0110.0094-0.0290.0002-0.018-0.0415-0.02690.05610.0070.00710.005-0.01660.07360.00470.1089-2.003-2.50957.664
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 663
2X-RAY DIFFRACTION2B0 - 663

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