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- PDB-3p0b: Thermus thermophilus family GH57 branching enzyme: crystal struct... -

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Basic information

Entry
Database: PDB / ID: 3p0b
TitleThermus thermophilus family GH57 branching enzyme: crystal structure, mechanism of action and products formed
ComponentsTT1467 protein
KeywordsTRANSFERASE / Glycoside Hydrolase GH57 / glycogen branching
Function / homology
Function and homology information


alpha-glucan biosynthetic process / 1,4-alpha-glucan branching enzyme / 1,4-alpha-glucan branching enzyme activity (using a glucosylated glycogenin as primer for glycogen synthesis) / 1,4-alpha-glucan branching enzyme activity / glycogen biosynthetic process
Similarity search - Function
1,4-alpha-glucan branching enzyme, C-terminal / Glycoside hydrolase families 57, central domain / 1,4-alpha-glucan branching enzyme MT3115-like / 1,4-alpha-glucan branching enzyme, C-terminal / immunoglobulin/albumin-binding domain-like / Families 57/38 glycoside transferase, middle domain / Glycoside hydrolase family 57, N-terminal domain / Glycosyl hydrolase family 57 / Glycoside hydrolase 38, N terminal domain / 7-stranded beta/alpha barrel ...1,4-alpha-glucan branching enzyme, C-terminal / Glycoside hydrolase families 57, central domain / 1,4-alpha-glucan branching enzyme MT3115-like / 1,4-alpha-glucan branching enzyme, C-terminal / immunoglobulin/albumin-binding domain-like / Families 57/38 glycoside transferase, middle domain / Glycoside hydrolase family 57, N-terminal domain / Glycosyl hydrolase family 57 / Glycoside hydrolase 38, N terminal domain / 7-stranded beta/alpha barrel / Glycoside hydrolase 38, N-terminal domain superfamily / Glycoside hydrolase families 57/38, central domain superfamily / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,4-alpha-glucan branching enzyme TTHA1902 / 1,4-alpha-glucan branching enzyme TTHA1902
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsPijning, T. / Dijkstra, B.W.
Citation
Journal: To be Published
Title: Thermus thermophilus GLYCOSYL HYDROLASE FAMILY 57 branching enzyme: crystal structure, mechanism of action and products formed
Authors: Palomo-Reixach, M. / Pijning, T. / Booiman, T. / Dobruchowska, J. / van der Vlist, J. / Kralj, S. / Planas, A. / Loos, K. / Kamerling, J.P. / Dijkstra, B.W. / van der Maarel, M.J.E.C. / ...Authors: Palomo-Reixach, M. / Pijning, T. / Booiman, T. / Dobruchowska, J. / van der Vlist, J. / Kralj, S. / Planas, A. / Loos, K. / Kamerling, J.P. / Dijkstra, B.W. / van der Maarel, M.J.E.C. / Dijkhuizen, L. / Leemhuis, H.
#1: Journal: To be Published / Year: 2003
Title: Crystal structure of TT1467 from Thermus thermophilus HB8
Authors: Idaka, M. / Terada, T. / Murayama, K. / Yamaguchi, H. / Nureki, O. / Ishitani, R. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S.
History
DepositionSep 28, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TT1467 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5152
Polymers61,4231
Non-polymers921
Water12,322684
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.532, 119.532, 74.097
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein TT1467 protein


Mass: 61423.191 Da / Num. of mol.: 1 / Fragment: branching enzyme
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: tthHB8IM / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P84162, UniProt: Q5SH28*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 684 / 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: 2.15 Å3/Da / Density % sol: 42.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% (w/v) PEG 3350, 8% (v/v) Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 3, 2008
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.3→40 Å / Num. all: 117389 / Num. obs: 116916 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.7 %
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 2.5 / Num. unique all: 16811 / % possible all: 99.1

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UFA
Resolution: 1.35→33 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.91 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18905 5862 5 %RANDOM
Rwork0.16945 ---
all0.17 116835 --
obs0.17043 110973 99.51 %-
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: 22.214 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2---0.42 Å20 Å2
3---0.84 Å2
Refinement stepCycle: LAST / Resolution: 1.35→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4124 0 6 684 4814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0214450
X-RAY DIFFRACTIONr_angle_refined_deg1.311.9486070
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3075547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40422.165231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.2615702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8671550
X-RAY DIFFRACTIONr_chiral_restr0.0890.2607
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213580
X-RAY DIFFRACTIONr_mcbond_it0.6371.52652
X-RAY DIFFRACTIONr_mcangle_it1.06324252
X-RAY DIFFRACTIONr_scbond_it1.82131798
X-RAY DIFFRACTIONr_scangle_it2.7794.51816
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 471 -
Rwork0.254 7944 -
obs--98.38 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.07720.2444-0.80651.9388-1.31313.9309-0.0975-0.0188-0.05790.03120.07560.12560.0576-0.22470.02190.07080.01380.04520.06660.00810.0621-0.2-25.4-22.751
21.1074-0.3709-0.3031.3999-0.27531.2677-0.054-0.09630.01660.14710.0218-0.026-0.10330.03880.03220.08920.00110.01350.06230.00690.01252.268-15.365-19.606
33.8504-0.3419-0.25342.1015-0.31951.03360.0037-0.03930.12660.10440.00740.1843-0.0571-0.1463-0.01120.11110.02080.0210.09540.00140.0666-17.741-2.484-20.967
42.7524-1.4402-0.02291.9117-0.13590.6398-0.0314-0.1390.05850.12310.0349-0.0394-0.00980.0478-0.00350.1060.00610.00280.06580.00320.00211.974-8.311-18.073
50.8743-0.25860.06371.60140.42652.1619-0.0495-0.0634-0.12940.05370.0087-0.04530.19690.14870.04070.11020.01960.04460.06470.03650.0511.192-32.356-24.87
66.76682.1275-1.25396.0523-0.22394.711-0.0353-0.1291-0.19890.1834-0.0833-0.36880.0880.22960.11870.09960.0160.010.08360.02840.03217.542-23.371-21.439
71.1699-0.5495-0.25513.4475-0.22271.0249-0.08840.0761-0.2806-0.2575-0.00550.13860.31770.10420.09390.22850.02350.08890.08830.0160.11268.84-44.51-27.728
86.14370.6304-1.49342.7539-0.56862.2948-0.2750.0165-0.33060.20690.08450.03230.35520.12560.19060.220.04590.11360.08120.05330.08547.985-40.961-17.483
93.98471.7857-5.651217.4059-18.353524.7551-1.1616-0.189-0.8806-0.78041.90381.27061.4807-2.5023-0.74210.7142-0.06660.45680.44750.19690.6888-8.933-46.516-13.359
106.288-2.0004-1.40282.73210.27261.2713-0.3911-0.1987-0.51290.30580.1290.26710.36350.06320.26210.28290.04980.15460.11150.07590.14641.43-42.685-10.263
113.8031-1.42032.40386.3441-2.60262.91790.10730.0711-0.3926-0.45240.04360.07350.1481-0.0599-0.1510.2033-0.01070.08110.13230.05860.217-16.978-29.658-12.754
122.1339-0.77880.88962.6591-1.28373.3486-0.0177-0.0874-0.1754-0.04050.08890.2980.1364-0.2519-0.07120.11140.00380.04820.10990.02370.0871-21.451-16.342-17.875
132.9473-2.8087-0.06597.888-1.27792.8632-0.3195-0.3396-0.20150.36810.28860.32230.0166-0.11050.03090.20660.06310.08950.19910.08610.0724-12.456-25.74-1.542
141.3096-0.2964-0.1962.9831-2.49943.0716-0.1486-0.2995-0.22890.26610.15730.13870.0493-0.0683-0.00870.18740.04490.09030.14130.07740.092-4-34.82-5.988
152.362-0.98531.01522.191-1.06422.2892-0.1622-0.2778-0.1040.32780.09490.02880.01940.14940.06730.17690.05330.0680.14470.04930.0395-4.842-23.494-5.144
160.8990.1658-0.13792.6129-0.113.0165-0.2518-0.0775-0.26540.07820.10950.23990.44490.02170.14240.20160.01930.15040.10480.06320.18442.032-42.156-17.945
172.64070.7326-1.32542.2446-1.13223.2795-0.07920.1948-0.1152-0.3976-0.00130.10020.65460.08280.08050.27350.04880.00350.0768-0.02690.06999.761-37.6-44.189
181.2796-0.2779-0.20681.6066-0.69712.72650.03610.0513-0.1136-0.06120.04570.3180.1637-0.3205-0.08180.1025-0.00660.01470.0749-0.00680.07730.419-29.931-38.98
191.52660.7658-0.82671.9466-0.88752.2561-0.02670.1857-0.0692-0.2226-0.01180.03840.14450.00680.03850.09880.02090.00850.0801-0.01490.02558.089-24.918-48.365
201.0462-0.67760.01493.3467-0.58412.5732-0.0365-0.0567-0.07290.0198-0.0604-0.27560.28650.4020.0970.11550.04180.03250.11560.01790.051617.48-29.522-35.623
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 23
2X-RAY DIFFRACTION2A24 - 80
3X-RAY DIFFRACTION3A81 - 105
4X-RAY DIFFRACTION4A106 - 129
5X-RAY DIFFRACTION5A130 - 168
6X-RAY DIFFRACTION6A169 - 175
7X-RAY DIFFRACTION7A176 - 213
8X-RAY DIFFRACTION8A214 - 226
9X-RAY DIFFRACTION9A227 - 246
10X-RAY DIFFRACTION10A247 - 273
11X-RAY DIFFRACTION11A274 - 283
12X-RAY DIFFRACTION12A284 - 323
13X-RAY DIFFRACTION13A324 - 335
14X-RAY DIFFRACTION14A336 - 358
15X-RAY DIFFRACTION15A359 - 382
16X-RAY DIFFRACTION16A383 - 415
17X-RAY DIFFRACTION17A416 - 443
18X-RAY DIFFRACTION18A444 - 476
19X-RAY DIFFRACTION19A477 - 503
20X-RAY DIFFRACTION20A504 - 517

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