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- PDB-1tz7: Aquifex aeolicus amylomaltase -

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Basic information

Entry
Database: PDB / ID: 1tz7
TitleAquifex aeolicus amylomaltase
Components4-alpha-glucanotransferase
KeywordsTRANSFERASE / (beta / alpha)8- barrel
Function / homology
Function and homology information


4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / : / carbohydrate metabolic process / cytoplasm
Similarity search - Function
Glycoside hydrolase, family 77 / 4-alpha-glucanotransferase / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
4-alpha-glucanotransferase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBarends, T.R.M. / Korf, H. / Kaper, T. / van der Maarel, M.J.E.C. / Dijkhuizen, L. / Dijkstra, B.W.
CitationJournal: TO BE PUBLISHED
Title: Structural influences on product specificity in amylomaltase from Aquifex aeolicus
Authors: Barends, T.R.M. / Korf, H. / Kaper, T. / van der Maarel, M.J.E.C. / Dijkhuizen, L. / Dijkstra, B.W.
History
DepositionJul 9, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: 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 / struct_ncs_dom_lim / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-alpha-glucanotransferase
B: 4-alpha-glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,7523
Polymers120,6332
Non-polymers1181
Water3,783210
1
A: 4-alpha-glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4352
Polymers60,3171
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: 4-alpha-glucanotransferase


Theoretical massNumber of molelcules
Total (without water)60,3171
Polymers60,3171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: 4-alpha-glucanotransferase
hetero molecules

A: 4-alpha-glucanotransferase
hetero molecules

B: 4-alpha-glucanotransferase

B: 4-alpha-glucanotransferase


Theoretical massNumber of molelcules
Total (without water)241,5036
Polymers241,2674
Non-polymers2362
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
crystal symmetry operation4_665-x+1,-y+1,z+1/21
crystal symmetry operation7_555y,x,-z+1/31
Buried area12620 Å2
ΔGint-65 kcal/mol
Surface area74170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.745, 156.745, 169.161
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 3 / Auth seq-ID: 1 - 485 / Label seq-ID: 21 - 505

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsMolecule A and B each represent the biologically relevant monomer

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Components

#1: Protein 4-alpha-glucanotransferase / Amylomaltase / Disproportionating enzyme / D-enzyme


Mass: 60316.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O66937, 4-alpha-glucanotransferase
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.6 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2-methyl-2,4-pentanediol, ammonium sulfate, Tris/HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2004 / Details: Sagitally focusing Ge220 and multilayer
RadiationMonochromator: Diamond (111) and Ge (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 75895 / Num. obs: 75895 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.059
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.727 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Thermus thermophilus amylomaltase

Resolution: 2.15→15 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.331 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.254 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24256 3358 5 %RANDOM
Rwork0.21469 ---
all0.21608 63203 --
obs0.21608 63203 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.124 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20.63 Å20 Å2
2--1.26 Å20 Å2
3----1.88 Å2
Refinement stepCycle: LAST / Resolution: 2.15→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8290 0 8 210 8508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0218548
X-RAY DIFFRACTIONr_bond_other_d0.0060.027660
X-RAY DIFFRACTIONr_angle_refined_deg0.6861.95311543
X-RAY DIFFRACTIONr_angle_other_deg0.711317797
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2385973
X-RAY DIFFRACTIONr_chiral_restr0.0840.21148
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.029421
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021971
X-RAY DIFFRACTIONr_nbd_refined0.1830.21797
X-RAY DIFFRACTIONr_nbd_other0.2370.28409
X-RAY DIFFRACTIONr_nbtor_other0.0870.24661
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0930.2127
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.234
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2260.2121
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.25
X-RAY DIFFRACTIONr_mcbond_it3.8361.54860
X-RAY DIFFRACTIONr_mcangle_it5.46927825
X-RAY DIFFRACTIONr_scbond_it7.90163688
X-RAY DIFFRACTIONr_scangle_it10.546103718
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 7921 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.080.05
tight thermal0.10.5
LS refinement shellResolution: 2.15→2.205 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.287 241
Rwork0.243 4486

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