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- PDB-2b5d: Crystal structure of the novel alpha-amylase AmyC from Thermotoga... -

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Basic information

Entry
Database: PDB / ID: 2b5d
TitleCrystal structure of the novel alpha-amylase AmyC from Thermotoga maritima
Componentsalpha-Amylase
KeywordsHYDROLASE / (beta/alpha)7 barrel
Function / homologyimmunoglobulin/albumin-binding domain-like / Families 57/38 glycoside transferase, middle domain / Glycoside hydrolase 38, N terminal domain / 7-stranded beta/alpha barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsDickmanns, A. / Ballschmiter, M. / Liebl, W. / Ficner, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Structure of the novel alpha-amylase AmyC from Thermotoga maritima.
Authors: Dickmanns, A. / Ballschmiter, M. / Liebl, W. / Ficner, R.
History
DepositionSep 28, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: alpha-Amylase


Theoretical massNumber of molelcules
Total (without water)62,9431
Polymers62,9431
Non-polymers00
Water5,711317
1
X: alpha-Amylase

X: alpha-Amylase

X: alpha-Amylase

X: alpha-Amylase


Theoretical massNumber of molelcules
Total (without water)251,7704
Polymers251,7704
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_455y-1/2,x+1/2,-z+1/21
crystal symmetry operation10_565-x,-y+1,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
2
X: alpha-Amylase

X: alpha-Amylase


Theoretical massNumber of molelcules
Total (without water)125,8852
Polymers125,8852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_565-x,-y+1,z1
Buried area3370 Å2
ΔGint-26 kcal/mol
Surface area39920 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)112.164, 112.164, 335.544
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11X-642-

HOH

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Components

#1: Protein alpha-Amylase


Mass: 62942.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: tm1438 / Plasmid: pET24c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: alpha-amylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 4.1 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 4M Na-formiate, 5% isopropanol, 2mM DTT, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.12710, 0.97972, 0.97997, 0.98393
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 4, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.12711
20.979721
30.979971
40.983931
ReflectionResolution: 2.2→30 Å / Num. all: 54781 / Num. obs: 50618 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.4 / Biso Wilson estimate: 49.1 Å2 / Net I/σ(I): 19.1
Reflection shellResolution: 2.2→2.28 Å / % possible all: 60.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0013refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.646 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25709 2512 5.1 %RANDOM
Rwork0.21945 ---
all0.22243 54781 --
obs0.22139 47176 90.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.748 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å20 Å20 Å2
2--1.99 Å20 Å2
3----3.98 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4322 0 0 317 4639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224465
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.9446031
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4065516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.17523.389239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.25315783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4931533
X-RAY DIFFRACTIONr_chiral_restr0.1430.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023457
X-RAY DIFFRACTIONr_nbd_refined0.2420.22234
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22997
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.2286
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.215
X-RAY DIFFRACTIONr_mcbond_it1.0821.52674
X-RAY DIFFRACTIONr_mcangle_it1.80924168
X-RAY DIFFRACTIONr_scbond_it2.34132098
X-RAY DIFFRACTIONr_scangle_it3.4974.51863
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 92 -
Rwork0.279 2225 -
obs--59.03 %

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