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- PDB-3bcf: Alpha-amylase B from Halothermothrix orenii -

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Basic information

Entry
Database: PDB / ID: 3bcf
TitleAlpha-amylase B from Halothermothrix orenii
ComponentsAlpha amylase, catalytic region
KeywordsHYDROLASE / alpha-amylase / thermostable / halophilic / N domain / raw starch binding
Function / homology
Function and homology information


glucan 1,4-alpha-maltohexaosidase / glucan 1,4-alpha-maltohexaosidase activity / alpha-amylase activity / carbohydrate metabolic process / extracellular space / metal ion binding
Similarity search - Function
Elongation Factor Tu (Ef-tu); domain 3 - #140 / Alpha-amylase C-terminal, prokaryotic / Alpha-amylase C-terminal / Immunoglobulin-like - #1220 / Copper resistance protein CopC/internalin, immunoglobulin-like / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Elongation Factor Tu (Ef-tu); domain 3 ...Elongation Factor Tu (Ef-tu); domain 3 - #140 / Alpha-amylase C-terminal, prokaryotic / Alpha-amylase C-terminal / Immunoglobulin-like - #1220 / Copper resistance protein CopC/internalin, immunoglobulin-like / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Elongation Factor Tu (Ef-tu); domain 3 / Glycosyl hydrolase, all-beta / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHalothermothrix orenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTan, T.-C. / Mijts, B.N. / Swaminathan, K. / Patel, B.K.C. / Divne, C.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal Structure of the Polyextremophilic alpha-Amylase AmyB from Halothermothrix orenii: Details of a Productive Enzyme-Substrate Complex and an N Domain with a Role in Binding Raw Starch
Authors: Tan, T.-C. / Mijts, B.N. / Swaminathan, K. / Patel, B.K.C. / Divne, C.
History
DepositionNov 12, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_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

Downloads & links

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Assembly

Deposited unit
A: Alpha amylase, catalytic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7646
Polymers68,5811
Non-polymers1835
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)226.620, 77.820, 50.330
Angle α, β, γ (deg.)90.00, 99.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Alpha amylase, catalytic region / AmyB


Mass: 68580.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothermothrix orenii (bacteria) / Strain: H 168 / Gene: amyb / Plasmid: pET-19B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q2ADF2, UniProt: B8CZ54*PLUS, alpha-amylase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 3.19 Å3/Da / Density % sol: 61.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% (w/v) monomethylether PEG 5000, 0.1M Mes-OH, 0.2M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.978 Å
DetectorType: SBC / Detector: CCD / Date: Jan 1, 2005 / Details: mirrors
RadiationMonochromator: Rosenbaum-Rock double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 58453 / Num. obs: 51305 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rsym value: 0.106 / Net I/σ(I): 9.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 5891 / Rsym value: 0.308 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VJS

1vjs


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.919 / SU B: 9.865 / SU ML: 0.149 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.255 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22869 1902 5.1 %RANDOM
Rwork0.19076 ---
all0.1927 35637 --
obs0.1927 35637 97.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å20.11 Å2
2--1.97 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4747 0 5 256 5008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224903
X-RAY DIFFRACTIONr_bond_other_d0.0010.023167
X-RAY DIFFRACTIONr_angle_refined_deg1.7961.9236645
X-RAY DIFFRACTIONr_angle_other_deg1.00837674
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9325584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.50225.055273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.66715750
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6351520
X-RAY DIFFRACTIONr_chiral_restr0.1210.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025589
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021052
X-RAY DIFFRACTIONr_nbd_refined0.2120.21016
X-RAY DIFFRACTIONr_nbd_other0.2060.23440
X-RAY DIFFRACTIONr_nbtor_refined0.1960.22375
X-RAY DIFFRACTIONr_nbtor_other0.0930.22468
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2283
X-RAY DIFFRACTIONr_metal_ion_refined0.0860.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.29
X-RAY DIFFRACTIONr_mcbond_it1.0661.52917
X-RAY DIFFRACTIONr_mcbond_other0.2681.51197
X-RAY DIFFRACTIONr_mcangle_it1.824662
X-RAY DIFFRACTIONr_scbond_it2.71432109
X-RAY DIFFRACTIONr_scangle_it3.994.51983
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 133 -
Rwork0.246 2692 -
obs--99.89 %
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)
12.4071.4004-0.8491.9069-0.79091.17050.246-0.55330.32380.3976-0.2411-0.0655-0.26310.0953-0.00490.04-0.1036-0.002-0.1269-0.1123-0.032638.05496.207322.1713
22.39360.8993-0.62520.6408-0.18191.0869-0.0492-0.0250.0683-0.03940.0426-0.17120.1263-0.31080.0066-0.0372-0.0195-0.0108-0.1424-0.0306-0.025934.3093-3.37129.4233
32.61910.06260.22462.2231-0.99333.825-0.21740.0102-0.4588-0.10270.1728-0.00820.9784-0.98420.04460.0093-0.27040.03860.069-0.0118-0.150615.1878-19.77915.0958
44.429-1.685-0.31523.95520.22133.77450.0064-0.45430.0864-0.0489-0.07140.2259-0.3024-0.37580.0649-0.2241-0.0737-0.030.266-0.0544-0.27890.7503-2.785134.5544
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A111 - 232
2X-RAY DIFFRACTION2A333 - 503
3X-RAY DIFFRACTION3A504 - 599
4X-RAY DIFFRACTION4A15 - 110

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