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- PDB-2p2o: Crystal structure of maltose transacetylase from Geobacillus kaus... -

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Basic information

Entry
Database: PDB / ID: 2p2o
TitleCrystal structure of maltose transacetylase from Geobacillus kaustophilus P2(1) crystal form
ComponentsMaltose transacetylase
KeywordsTRANSFERASE / GK1921 / gka001001921.1 / MALTOSE TRANSACETYLASE / GEOBACILLUS KAUSTOPHILUS STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS / SECSG / RIKEN GENOMICS SCIENCES CENTER / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI
Function / homology
Function and homology information


maltose O-acetyltransferase / maltose O-acetyltransferase activity
Similarity search - Function
Maltose/galactoside acetyltransferase / Maltose acetyltransferase / Maltose acetyltransferase / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) ...Maltose/galactoside acetyltransferase / Maltose acetyltransferase / Maltose acetyltransferase / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Maltose transacetylase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsLiu, Z.J. / Li, Y. / Chen, L. / Zhu, J. / Rose, J.P. / Ebihara, A. / Yokoyama, S. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG) / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of Maltose Transacetylase from Geobacillus Kaustophilus at 1.8 Angstrom Resolution
Authors: Liu, Z.J. / Li, Y. / Chen, L. / Zhu, J. / Rose, J.P. / Ebihara, A. / Yokoyama, S. / Wang, B.C.
History
DepositionMar 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2012Group: Other
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 1.5Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
A: Maltose transacetylase
B: Maltose transacetylase
C: Maltose transacetylase
D: Maltose transacetylase
E: Maltose transacetylase
F: Maltose transacetylase


Theoretical massNumber of molelcules
Total (without water)123,7066
Polymers123,7066
Non-polymers00
Water21,0241167
1
A: Maltose transacetylase
B: Maltose transacetylase
C: Maltose transacetylase


Theoretical massNumber of molelcules
Total (without water)61,8533
Polymers61,8533
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-18 kcal/mol
Surface area20980 Å2
MethodPISA
2
D: Maltose transacetylase
E: Maltose transacetylase
F: Maltose transacetylase


Theoretical massNumber of molelcules
Total (without water)61,8533
Polymers61,8533
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-18 kcal/mol
Surface area20940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.472, 122.458, 72.541
Angle α, β, γ (deg.)90.00, 97.88, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit appears to be a monomer. There are two monomers in the crystallographic asymmetric unit.

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Components

#1: Protein
Maltose transacetylase / Maltose O-acetyltransferase


Mass: 20617.584 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Gene: GKB08, GK1921 / Plasmid: PET-15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RIL / References: UniProt: Q75TD0, maltose O-acetyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1167 / 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: 2.36 Å3/Da / Density % sol: 47.95 %
Description: THE STRUCTURE FACTOR FILE CONTAINS ALL COLLECTED RELECTIONS
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (10 MG/ML) AND RESERVOIR SOLUTION CONTAINING 0.1 M SODIUM HEPES, 2% V/V PEG400 IN 2.0 M AMMONIUM SULFATE, pH 7.5, VAPOR ...Details: 1 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (10 MG/ML) AND RESERVOIR SOLUTION CONTAINING 0.1 M SODIUM HEPES, 2% V/V PEG400 IN 2.0 M AMMONIUM SULFATE, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97243 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 7, 2006 / Details: ROSENBAUM
RadiationMonochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97243 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 107292 / % possible obs: 92.3 % / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Rsym value: 0.047 / Net I/σ(I): 15
Reflection shellResolution: 1.74→1.8 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 4.53 / Num. unique all: 7577 / Rsym value: 0.22 / % possible all: 65.6

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
SERGUIdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IC7

2ic7


Resolution: 1.74→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.859 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ALL COLLECTED REFLECTIONS WERE USED FOR PHASING
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 5500 5.1 %RANDOM
Rwork0.18353 ---
all0.18631 101688 --
obs0.18631 101688 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.907 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å22.41 Å2
2---0.48 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.74→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8639 0 0 1167 9806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0228837
X-RAY DIFFRACTIONr_angle_refined_deg1.441.95411977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.94951097
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83823.571420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.346151458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.291566
X-RAY DIFFRACTIONr_chiral_restr0.1120.21305
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026800
X-RAY DIFFRACTIONr_nbd_refined0.1920.24125
X-RAY DIFFRACTIONr_nbtor_refined0.3060.25978
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2949
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.231
X-RAY DIFFRACTIONr_mcbond_it0.8891.55614
X-RAY DIFFRACTIONr_mcangle_it1.33828770
X-RAY DIFFRACTIONr_scbond_it2.34133660
X-RAY DIFFRACTIONr_scangle_it3.7114.53207
LS refinement shellResolution: 1.74→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 275 -
Rwork0.257 4780 -
obs-4730 100 %

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