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- PDB-3tng: The crystal structure of a possible phosphate acetyl/butaryl tran... -

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Basic information

Entry
Database: PDB / ID: 3tng
TitleThe crystal structure of a possible phosphate acetyl/butaryl transferase from Listeria monocytogenes EGD-e.
ComponentsLmo1369 protein
KeywordsTRANSFERASE / phosphate acetyl/butaryl transferase / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


acyltransferase activity
Similarity search - Function
Phosphate acetyl/butyryltransferase / Phosphate acetyl/butaryl transferase / Phosphate acetyl/butaryl transferase / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / Lmo1369 protein
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.16 Å
AuthorsTan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The crystal structure of a possible phosphate acetyl/butaryl transferase from Listeria monocytogenes EGD-e.
Authors: Tan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionSep 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lmo1369 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9188
Polymers31,2701
Non-polymers6487
Water63135
1
A: Lmo1369 protein
hetero molecules

A: Lmo1369 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,83716
Polymers62,5412
Non-polymers1,29614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area6460 Å2
ΔGint-8 kcal/mol
Surface area23110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.488, 66.488, 125.133
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsExperimentally unknown. It is predicted that the chain A and its symmetry-related molecule ( y+1,x-1,-z) form a dimer.

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Components

#1: Protein Lmo1369 protein / putative phosphate acetyl/butaryl transferase


Mass: 31270.408 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: lmo1369 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) majic / References: UniProt: Q8Y7B7
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.21 Å3/Da / Density % sol: 44.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.005M Co chloride, 0.005M Ni chloride, 0.005M Cd chloride, 0.005M Mg chloride, 0.1M HEPES, 12% w/v PEG 3350, pH 7.5, 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: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2011 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.16→38 Å / Num. all: 15547 / Num. obs: 15547 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 53.2
Reflection shellResolution: 2.16→2.18 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 4.3 / Num. unique all: 756 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.16→37.586 Å / SU ML: 0.61 / σ(F): 1.36 / Phase error: 25.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2423 775 5 %random
Rwork0.1953 ---
all0.1978 15489 --
obs0.1978 15489 98.23 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.316 Å2 / ksol: 0.314 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.6318 Å20 Å20 Å2
2---0.6318 Å2-0 Å2
3---1.2636 Å2
Refinement stepCycle: LAST / Resolution: 2.16→37.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2158 0 37 35 2230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082228
X-RAY DIFFRACTIONf_angle_d1.0843008
X-RAY DIFFRACTIONf_dihedral_angle_d15.689825
X-RAY DIFFRACTIONf_chiral_restr0.067371
X-RAY DIFFRACTIONf_plane_restr0.005377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1579-2.29310.35091230.27982312X-RAY DIFFRACTION95
2.2931-2.47010.30841380.2472435X-RAY DIFFRACTION100
2.4701-2.71860.25171250.21832443X-RAY DIFFRACTION100
2.7186-3.11180.24911230.20832480X-RAY DIFFRACTION100
3.1118-3.91990.24091450.19182509X-RAY DIFFRACTION100
3.9199-37.59120.22031210.17582535X-RAY DIFFRACTION95
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)
12.6545-3.24743.04967.2393-6.93928.602-0.4412-0.305-1.3937-0.43121.18441.03750.6951-1.3383-0.8930.4787-0.0740.08320.57890.1790.95192.0111-34.044-0.1035
24.8849-1.38242.07996.9735-3.26256.32020.63381.2759-0.6372-1.7384-0.40210.4406-0.0192-0.4287-0.3370.86960.2049-0.12610.6576-0.01130.45924.4556-24.7152-20.3826
34.54980.60662.555.0683-2.79514.72910.73151.24281.3148-0.7475-0.5246-0.5437-0.8629-0.379-0.38230.60440.0680.14230.41090.20110.552911.7061-15.6682-15.2243
49.4184-1.90234.26927.7867-4.6978.0278-0.7209-0.11392.03160.73830.4034-1.2456-2.2185-0.45610.34720.7540.00140.04670.43650.13580.96820.1585-12.8347-8.6751
55.3626-2.04340.91167.01240.05864.3672-0.2683-0.3240.14250.6430.144-0.2403-0.34330.03330.14360.35020.0276-0.05820.30660.07630.33219.4255-27.89173.6709
64.758-0.22422.69744.32651.76084.1767-0.9283-1.23681.56260.88430.8141-0.8131-0.24780.2280.21710.6478-0.0044-0.2430.41990.01150.50229.4889-28.679512.4799
78.8706-2.3976-1.79613.88743.61136.4192-1.0951-1.28680.03632.07311.4037-0.3849-0.5921-0.5749-0.19010.84820.3152-0.10830.7636-0.00780.314524.4911-36.534515.9749
83.8422-2.41513.36216.2785-0.91483.0865-0.3563-1.3304-0.22150.97290.39880.53950.36580.1031-0.10340.57110.1076-0.05310.54990.08710.460122.3818-34.689813.4551
95.1284-0.10242.85114.41-0.72975.48310.31770.3967-0.0068-0.3592-0.3621-0.26020.3890.5197-0.02610.3420.0357-0.09210.38580.05650.337923.7563-37.9254-3.9329
105.2417-2.03971.01135.448-1.72815.2190.27690.3485-0.2143-0.56220.3161-0.7725-0.244-0.3186-0.45770.37440.0308-0.10490.39330.05980.44415.029-28.6413-7.4525
115.68961.13091.98944.7044.65635.20190.2195-0.3281-0.77810.1988-0.36011.19850.4531-0.39830.14850.42360.0276-0.08710.44160.1380.54546.8254-27.9243-4.7644
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:16)
2X-RAY DIFFRACTION2chain 'A' and (resseq 17:67)
3X-RAY DIFFRACTION3chain 'A' and (resseq 68:93)
4X-RAY DIFFRACTION4chain 'A' and (resseq 94:114)
5X-RAY DIFFRACTION5chain 'A' and (resseq 115:159)
6X-RAY DIFFRACTION6chain 'A' and (resseq 160:192)
7X-RAY DIFFRACTION7chain 'A' and (resseq 193:216)
8X-RAY DIFFRACTION8chain 'A' and (resseq 217:233)
9X-RAY DIFFRACTION9chain 'A' and (resseq 234:247)
10X-RAY DIFFRACTION10chain 'A' and (resseq 248:271)
11X-RAY DIFFRACTION11chain 'A' and (resseq 272:288)

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