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- PDB-4isx: The crystal structure of maltose o-acetyltransferase from clostri... -

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Basic information

Entry
Database: PDB / ID: 4isx
TitleThe crystal structure of maltose o-acetyltransferase from clostridium difficile 630 in complex with acetyl-coa
ComponentsMaltose O-acetyltransferase
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / NIAID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
Function / homology
Function and homology information


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 proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat ...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 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
ACETYL COENZYME *A / Acetyltransferase
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.702 Å
AuthorsTan, K. / Gu, G. / Peterson, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The crystal structure of maltose o-acetyltransferase from clostridium difficile 630 in complex with acetyl-coa
Authors: Tan, K. / Gu, G. / Peterson, S. / Anderson, W.F. / Joachimiak, A.
History
DepositionJan 17, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionJan 30, 2013ID: 4EBH
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_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
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)44,1075
Polymers42,2932
Non-polymers1,8143
Water50428
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)66,4549
Polymers63,4403
Non-polymers3,0146
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation23_544y,-z-1/2,-x-1/21
crystal symmetry operation32_454-z-1/2,x,-y-1/21
Buried area10950 Å2
ΔGint-19 kcal/mol
Surface area21200 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)65,8686
Polymers63,4403
Non-polymers2,4293
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation33_554y+1/2,z,x-1/21
crystal symmetry operation41_545z+1/2,x-1/2,y1
Buried area11640 Å2
ΔGint-8 kcal/mol
Surface area21250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.896, 167.896, 167.896
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11B-303-

HOH

21B-306-

HOH

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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: Clostridium difficile, maa / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL(21)MAGIC / References: UniProt: Q18A66, maltose O-acetyltransferase
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M MGCL2, 0.1M MES:NAOH, 10% (W/V)PEG4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 19, 2012 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.7→39 Å / Num. all: 10868 / Num. obs: 10868 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 36.9
Reflection shellResolution: 2.7→2.76 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 3.3 / Num. unique all: 722 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY:3SRT

3srt


Resolution: 2.702→38.518 Å / SU ML: 0.35 / σ(F): 1.35 / Phase error: 27.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.252 522 4.81 %Random
Rwork0.1945 ---
obs0.1972 10861 99.84 %-
all-10861 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.702→38.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2913 0 114 28 3055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033081
X-RAY DIFFRACTIONf_angle_d0.7154183
X-RAY DIFFRACTIONf_dihedral_angle_d15.2471180
X-RAY DIFFRACTIONf_chiral_restr0.049457
X-RAY DIFFRACTIONf_plane_restr0.003531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7024-2.97420.36011280.27062576X-RAY DIFFRACTION100
2.9742-3.40440.30521320.23792556X-RAY DIFFRACTION100
3.4044-4.28830.22711350.18852566X-RAY DIFFRACTION100
4.2883-38.52190.23141270.17062641X-RAY DIFFRACTION99
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)
13.27211.07160.76533.6271-0.63693.72810.1639-0.69850.5430.556-0.2666-0.0236-0.47840.0904-0.00260.4131-0.0089-0.01020.4941-0.0660.32-7.1551-6.6383-41.8393
20.7191-0.1404-0.10642.31352.45564.3374-0.18490.17920.1837-0.036-0.49610.0177-0.1056-0.12610.55250.3367-0.06750.00410.40340.01250.436-3.5891-7.02-59.9248
31.727-0.1112-0.53622.54751.04526.85760.10470.9983-0.1644-0.4772-0.0504-1.05150.65541.4801-0.21640.42530.0240.0320.77320.0630.54012.7238-18.4642-69.0764
46.6222-0.54133.07792.1761-2.28253.74380.21020.2926-1.4003-0.31830.0696-0.75580.65340.5292-0.02020.3805-0.06270.05020.38550.02490.64342.4515-24.3223-60.5728
52.23590.97380.15152.2353-0.05371.7936-0.225-0.3154-0.25840.19360.1721-0.05070.3040.09550.08260.3468-0.02340.02480.34620.12090.2648-11.3314-22.7366-53.0065
64.57-2.81190.62486.8288-0.34782.9141-0.0137-0.362-0.51250.70470.10390.02560.74410.0553-0.04170.6578-0.11730.02090.40050.19810.4051-18.2844-39.1677-50.9474
70.1142-0.1707-0.73660.2251.02354.6071-0.31050.3390.5339-0.06830.1780.5483-1.3065-0.68420.23840.96180.06670.41080.59660.25261.494310.3174-38.3353-73.3752
83.2055-1.2553-0.90630.56150.10952.20010.1919-0.76261.72771.22440.2888-0.6155-0.71930.77050.16531.5538-0.2570.1850.4843-0.48831.581219.7777-44.8152-52.3628
92.40480.0127-0.01710.45481.07342.4174-0.0157-0.20591.03820.82320.2930.4343-0.61330.0994-0.24530.7205-0.02060.19870.3939-0.13250.899411.3147-51.3399-55.5281
101.5338-1.0725-1.13312.32430.03741.5626-0.0735-0.33180.04411.2384-0.05780.8517-0.1641-0.2568-0.08320.94380.30890.41230.1111-0.35310.51077.9401-60.1215-54.2126
111.2112-1.0458-0.1251.73910.81492.43970.24690.46341.10250.18930.21120.624-0.1216-0.2091-0.28150.378-0.01450.0950.48770.1930.77157.5875-56.6836-68.7024
125.7141-2.14560.5182.9360.88790.75570.27760.1390.29980.43540.42920.62520.1974-0.4128-0.21970.4997-0.09690.15490.53720.07070.796-1.4243-69.9107-63.5422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 36 )
3X-RAY DIFFRACTION3chain 'A' and (resid 37 through 52 )
4X-RAY DIFFRACTION4chain 'A' and (resid 53 through 62 )
5X-RAY DIFFRACTION5chain 'A' and (resid 63 through 169 )
6X-RAY DIFFRACTION6chain 'A' and (resid 170 through 185 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 17 )
8X-RAY DIFFRACTION8chain 'B' and (resid 18 through 52 )
9X-RAY DIFFRACTION9chain 'B' and (resid 53 through 96 )
10X-RAY DIFFRACTION10chain 'B' and (resid 97 through 106 )
11X-RAY DIFFRACTION11chain 'B' and (resid 107 through 167 )
12X-RAY DIFFRACTION12chain 'B' and (resid 168 through 185 )

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