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- PDB-4gak: Crystal structure of acyl-ACP thioesterase from Spirosoma linguale -

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Basic information

Entry
Database: PDB / ID: 4gak
TitleCrystal structure of acyl-ACP thioesterase from Spirosoma linguale
ComponentsAcyl-ACP thioesterase
KeywordsHYDROLASE / MCSG / PSI-BIOLOGY / STRUCTURAL GENOMICS / Midwest Center for Structural Genomics
Function / homology
Function and homology information


thiolester hydrolase activity / fatty acid biosynthetic process
Similarity search - Function
Acyl-ACP thioesterase / Acyl-ACP thioesterase N-terminal domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Acyl-ACP thioesterase
Similarity search - Component
Biological speciesSpirosoma linguale (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsChang, C. / Wu, R. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of acyl-ACP thioesterase from Spirosoma linguale
Authors: Chang, C. / Wu, R. / Endres, M. / Joachimiak, A.
History
DepositionJul 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-ACP thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1894
Polymers28,9691
Non-polymers2203
Water3,693205
1
A: Acyl-ACP thioesterase
hetero molecules

A: Acyl-ACP thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3788
Polymers57,9392
Non-polymers4396
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4520 Å2
ΔGint-31 kcal/mol
Surface area22450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.657, 61.657, 155.945
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Acyl-ACP thioesterase


Mass: 28969.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spirosoma linguale (bacteria) / Strain: ATCC 33905 / DSM 74 / LMG 10896 / Gene: Slin_6353 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D2QU30
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M MES, 1.26M Ammonium Sulfate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2012
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 24520 / Num. obs: 24494 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 42.9
Reflection shellResolution: 1.9→1.92 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 4 / Num. unique all: 614 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDEphasing
ARP/wARPmodel building
RESOLVEphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 6.693 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.136
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2236 1237 5.1 %RANDOM
Rwork0.1854 ---
all0.1872 24327 --
obs0.1872 24327 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.89 Å2 / Biso mean: 43.048 Å2 / Biso min: 24.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20 Å2
2---0.82 Å20 Å2
3---1.64 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2008 0 13 205 2226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022105
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.942866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1125257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.50623.431102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91815350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1141518
X-RAY DIFFRACTIONr_chiral_restr0.1050.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211618
LS refinement shellResolution: 1.901→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 82 -
Rwork0.319 1409 -
all-1491 -
obs-14327 93.13 %
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)
10.21240.3118-0.5120.5834-0.48322.78670.0890.00270.04010.1474-0.03230.0155-0.17230.1324-0.05680.04450.00740.0010.07290.01990.071815.96029.406471.7498
20.5443-0.0532-0.0660.1647-0.10210.15510.0420.05450.06530.0217-0.0446-0.00350.040.01430.00260.065-0.00070.00260.06020.00740.07289.110611.091564.4679
31.2135-0.25070.02680.6312-0.52220.4670.01540.14950.0014-0.0244-0.01720.00520.0322-0.01070.00180.05670.0213-0.020.0704-0.02840.04515.77265.373257.645
40.4076-0.3389-0.1870.4121-0.16070.8860.00390.05920.0074-0.028-0.0585-0.04660.06940.01160.05460.0324-0.0092-0.00950.0689-0.00460.064116.60334.839363.1397
52.46430.3211.42090.1987-1.067910.8633-0.212-0.03570.3014-0.0492-0.06310.02560.0380.39330.27510.03150.0185-0.01370.0748-0.00860.079825.62135.37669.654
60.4511-0.1215-0.28210.70420.28640.24650.02210.0513-0.0103-0.0091-0.03860.02050.0022-0.02540.01650.07430.0469-0.00060.0792-0.00150.052515.25122.514760.9852
79.93652.32274.25197.4935-1.64652.82260.5057-0.3424-0.8648-0.36030.1740.60230.4017-0.2415-0.67970.08380.0118-0.10350.11160.05270.1689-7.5579.20250.3893
83.87360.1719-0.77950.2799-0.06390.16270.04280.48260.0337-0.152-0.0468-0.06230.0004-0.07580.0040.10770.00530.02380.14920.04390.023210.28912.658248.6222
93.61713.40041.3745.93781.58160.72280.01050.2555-0.2002-0.1505-0.0435-0.0470.16250.13540.03310.19180.09020.08370.0818-0.00180.085215.6759-3.046153.5568
101.4458-0.6869-0.30772.509-0.20360.74590.03820.1933-0.2845-0.12180.02460.19920.1438-0.3816-0.06290.0441-0.0757-0.0140.20140.00970.1292-2.2614-11.423465.2607
110.7583-0.8487-0.00783.9124-0.8360.24290.01010.0346-0.0751-0.0352-0.01010.06910.0115-0.019600.0542-0.0203-0.0250.06850.01060.0453-0.24190.919769.9103
120.13310.38450.23521.13880.55271.3126-0.01370.0138-0.0468-0.05790.0389-0.11250.1258-0.0036-0.02520.05340.01230.0010.0156-0.01270.11939.556-10.677769.372
130.6704-1.1673-2.63348.6462-1.690716.30770.11950.021-0.0095-0.27940.19720.3986-0.3431-0.3163-0.31670.0531-0.0338-0.00910.0489-0.00060.0757-10.13492.141466.7911
141.9643-0.2412-0.49341.8145-0.22740.1848-0.1260.1822-0.23540.03080.07240.08570.0765-0.07360.05360.1677-0.0473-0.00710.0376-0.04080.12990.8388-13.505466.1678
155.21780.08861.15980.17840.11661.1265-0.20550.1549-0.0628-0.0327-0.04170.00580.2247-0.06990.24710.1552-0.02060.0380.0246-0.03670.15084.0821-10.41563.8874
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 21
2X-RAY DIFFRACTION2A22 - 50
3X-RAY DIFFRACTION3A51 - 64
4X-RAY DIFFRACTION4A65 - 93
5X-RAY DIFFRACTION5A94 - 99
6X-RAY DIFFRACTION6A100 - 112
7X-RAY DIFFRACTION7A113 - 118
8X-RAY DIFFRACTION8A119 - 136
9X-RAY DIFFRACTION9A137 - 146
10X-RAY DIFFRACTION10A147 - 165
11X-RAY DIFFRACTION11A166 - 187
12X-RAY DIFFRACTION12A188 - 206
13X-RAY DIFFRACTION13A207 - 211
14X-RAY DIFFRACTION14A212 - 233
15X-RAY DIFFRACTION15A234 - 247

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