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- PDB-3srt: The crystal structure of a maltose O-acetyltransferase from Clost... -

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Basic information

Entry
Database: PDB / ID: 3srt
TitleThe crystal structure of a maltose O-acetyltransferase from Clostridium difficile 630
ComponentsMaltose O-acetyltransferase
KeywordsTRANSFERASE / maltose O-acetyltransferase / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


galactoside O-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
Galactoside O-acetyltransferase LacA-like / Maltose/galactoside acetyltransferase / Maltose acetyltransferase hexapeptide capping motif / Maltose acetyltransferase / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 ...Galactoside O-acetyltransferase LacA-like / Maltose/galactoside acetyltransferase / Maltose acetyltransferase hexapeptide capping motif / Maltose acetyltransferase / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.504 Å
AuthorsTan, K. / Gu, M. / Peterson, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The crystal structure of a maltose O-acetyltransferase from Clostridium difficile 630
Authors: Tan, K. / Gu, M. / Peterson, S. / Anderson, W.F. / Joachimiak, A.
History
DepositionJul 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Maltose O-acetyltransferase
B: Maltose O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,76718
Polymers42,2932
Non-polymers1,47416
Water1,78399
1
A: Maltose O-acetyltransferase
hetero molecules

A: Maltose O-acetyltransferase
hetero molecules

A: Maltose O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,20233
Polymers63,4403
Non-polymers2,76330
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
Buried area14080 Å2
ΔGint-46 kcal/mol
Surface area21710 Å2
MethodPISA
2
B: Maltose O-acetyltransferase
hetero molecules

B: Maltose O-acetyltransferase
hetero molecules

B: Maltose O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,09721
Polymers63,4403
Non-polymers1,65818
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area10660 Å2
ΔGint-31 kcal/mol
Surface area22650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.884, 152.884, 152.884
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
DetailsExperimentally unknown. It is predicted that the molecule is trimeric. The chain A and its symmetry-related molecules (z+1/2,-x+1/2,1-y) and (-y+1/2,-z,x+1/2) form a trimer. The chain B and its symmetry-related molecules (z+1,x,y) and (y,z+1,x) form a trimer.

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Components

#1: Protein Maltose O-acetyltransferase


Mass: 21146.557 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD0872, CD630_08720, maa / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic / References: UniProt: Q18A66, maltose O-acetyltransferase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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

Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.8M Ammonium Citrate Tribasic, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2011 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.5→48.5 Å / Num. all: 41225 / Num. obs: 41225 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 29
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2058 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.504→48.346 Å / SU ML: 0.28 / σ(F): 0 / Phase error: 17.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1859 1985 5 %random
Rwork0.1636 ---
all0.1647 39688 --
obs0.1647 39688 96.3 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.081 Å2 / ksol: 0.368 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.504→48.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2926 0 96 99 3121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093067
X-RAY DIFFRACTIONf_angle_d1.1314124
X-RAY DIFFRACTIONf_dihedral_angle_d17.5191154
X-RAY DIFFRACTIONf_chiral_restr0.089450
X-RAY DIFFRACTIONf_plane_restr0.004530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5036-2.56620.27411270.23692419X-RAY DIFFRACTION88
2.5662-2.63560.21941300.21482554X-RAY DIFFRACTION90
2.6356-2.71310.23171190.20272562X-RAY DIFFRACTION93
2.7131-2.80070.22871410.20672592X-RAY DIFFRACTION94
2.8007-2.90080.21881520.2022589X-RAY DIFFRACTION94
2.9008-3.01690.22981350.20142675X-RAY DIFFRACTION96
3.0169-3.15420.24341490.17832680X-RAY DIFFRACTION97
3.1542-3.32050.21151380.17322779X-RAY DIFFRACTION98
3.3205-3.52840.18121580.1612712X-RAY DIFFRACTION99
3.5284-3.80080.18891370.14192783X-RAY DIFFRACTION99
3.8008-4.18310.14711360.13722802X-RAY DIFFRACTION100
4.1831-4.78790.14471480.12452812X-RAY DIFFRACTION100
4.7879-6.03040.16941610.15812824X-RAY DIFFRACTION100
6.0304-48.35520.17561540.17082920X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 52.5243 Å / Origin y: 54.5131 Å / Origin z: 84.1058 Å
111213212223313233
T0.1957 Å2-0.0009 Å20.0582 Å2-0.1338 Å2-0.0293 Å2--0.2135 Å2
L0.4235 °20.0237 °2-0.3559 °2--0.2431 °2-0.0304 °2--0.484 °2
S-0.0049 Å °-0.0768 Å °-0.01 Å °0.0237 Å °-0.0189 Å °0.0367 Å °0.0945 Å °0.042 Å °0.0178 Å °
Refinement TLS groupSelection details: all

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