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- PDB-2ess: Crystal structure of an acyl-ACP thioesterase (NP_810988.1) from ... -

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Basic information

Entry
Database: PDB / ID: 2ess
TitleCrystal structure of an acyl-ACP thioesterase (NP_810988.1) from Bacteroides thetaiotaomicron VPI-5482 at 1.90 A resolution
Componentsacyl-ACP thioesterase
KeywordsHYDROLASE / NP_810988.1 / Acyl-ACP thioesterase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


fatty acyl-[ACP] hydrolase activity / acyl carrier activity / metal ion binding
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 speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an acyl-ACP thioesterase (NP_810988.1) from Bacteroides thetaiotaomicron VPI-5482 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE PROTEIN WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG, MGSDKIHHHHHHDYDIPTTENLYFQG. ...SEQUENCE THE PROTEIN WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG, MGSDKIHHHHHHDYDIPTTENLYFQG. THE TAG WAS REMOVED WITH TEV-PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: acyl-ACP thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,46810
Polymers28,7311
Non-polymers7379
Water2,846158
1
A: acyl-ACP thioesterase
hetero molecules

A: acyl-ACP thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,93620
Polymers57,4612
Non-polymers1,47518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area7580 Å2
ΔGint-226 kcal/mol
Surface area20720 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.150, 91.150, 64.770
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein acyl-ACP thioesterase


Mass: 28730.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: bt2075 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A611
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.54 Å3/Da / Density % sol: 51.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4.6
Details: 30.0% MPD, 0.2M NaCl, 0.1M Acetate, pH 4.6 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.000, 0.9796
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 9, 2005
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97961
ReflectionResolution: 1.9→30 Å / Num. obs: 24794 / % possible obs: 99.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.096 / Χ2: 0.96 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsΧ2% possible all
1.9-1.951005.40.0961.717331.028100
1.95-21005.40.78917560.965
2-2.061005.40.61717431.073
2.06-2.1398.64.80.54917180.956
2.13-2.21005.40.37317620.932
2.2-2.291005.40.32517540.956
2.29-2.391005.40.2717700.96
2.39-2.521005.40.22717580.983
2.52-2.681005.50.16817740.926
2.68-2.881005.40.13717560.957
2.88-3.171005.40.1117840.913
3.17-3.631005.40.08217990.98
3.63-4.581005.30.0617941.003
4.58-5099.75.20.0418930.813

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PDB_EXTRACT1.601data extraction
HKL-2000data reduction
SOLVEphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MAD / Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 6.378 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.122
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. DISORDERED MODEL BETWEEN RESIDUES 124-129 WAS NOT MODELED. 4. CA MODELED BASED ON ANOMALOUS DIFFERENCE MAP. 5. CHLORINE AND MPD MODELED BASED UPON CRYSTALLIZTION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1260 5.1 %RANDOM
Rwork0.166 ---
all0.168 ---
obs0.16834 23470 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.781 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1948 0 43 158 2149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222072
X-RAY DIFFRACTIONr_bond_other_d0.0020.021390
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.9532820
X-RAY DIFFRACTIONr_angle_other_deg0.97933367
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2535254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.27323.592103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62415338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3821514
X-RAY DIFFRACTIONr_chiral_restr0.0960.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022298
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02449
X-RAY DIFFRACTIONr_nbd_refined0.1950.2339
X-RAY DIFFRACTIONr_nbd_other0.1960.21454
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2976
X-RAY DIFFRACTIONr_nbtor_other0.0870.21114
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2110
X-RAY DIFFRACTIONr_metal_ion_refined0.3350.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2710.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.218
X-RAY DIFFRACTIONr_mcbond_it2.11831279
X-RAY DIFFRACTIONr_mcbond_other0.5173498
X-RAY DIFFRACTIONr_mcangle_it3.1351997
X-RAY DIFFRACTIONr_scbond_it5.3518917
X-RAY DIFFRACTIONr_scangle_it7.47811816
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 96 -
Rwork0.253 1666 -
obs--99.66 %
Refinement TLS params.Method: refined / Origin x: 43.426 Å / Origin y: 6.51 Å / Origin z: 8.631 Å
111213212223313233
T-0.0947 Å20.0045 Å2-0.0205 Å2--0.1547 Å2-0.0017 Å2---0.1369 Å2
L1.0543 °20.0403 °20.1983 °2-1.5093 °2-0.2997 °2--1.1892 °2
S-0.021 Å °0.0472 Å °0.0489 Å °-0.0725 Å °0.047 Å °0.0944 Å °0.1028 Å °-0.0139 Å °-0.026 Å °
Refinement TLS groupSelection: all

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