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- PDB-3bbj: CRYSTAL STRUCTURE OF A PUTATIVE THIOESTERASE II (TFU_2367) FROM T... -

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Basic information

Entry
Database: PDB / ID: 3bbj
TitleCRYSTAL STRUCTURE OF A PUTATIVE THIOESTERASE II (TFU_2367) FROM THERMOBIFIDA FUSCA YX AT 2.45 A RESOLUTION
ComponentsPutative thioesterase II
KeywordsHYDROLASE / PUTATIVE THIOESTERASE II / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


: / : / Acyl-CoA thioesterase C-terminal domain / Acyl-CoA thioesterase, double hotdog domain / Acyl-CoA thioesterase, double hotdog domain / : / Acyl-CoA thioesterase N-terminal domain / Porin / HotDog domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
TesB-like acyl-CoA thioesterase 3
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.16 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative thioesterase II (YP_290423.1) from Thermobifida fusca YX at 2.45 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 9, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. 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

Downloads & links

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Assembly

Deposited unit
A: Putative thioesterase II
B: Putative thioesterase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,52110
Polymers60,0282
Non-polymers4928
Water2,954164
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.818, 103.654, 54.734
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTYRTYRAA5 - 1186 - 119
21THRTHRTYRTYRBB5 - 1186 - 119
32ILEILEARGARGAA125 - 133126 - 134
42ILEILEARGARGBB125 - 133126 - 134
53GLYGLYARGARGAA145 - 164146 - 165
63GLYGLYARGARGBB145 - 164146 - 165
74PROPROLEULEUAA171 - 208172 - 209
84PROPROLEULEUBB171 - 208172 - 209
95PROPROALAALAAA215 - 267216 - 268
105PROPROALAALABB215 - 267216 - 268

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Components

#1: Protein Putative thioesterase II


Mass: 30014.225 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (bacteria) / Strain: YX / Gene: YP_290423.1, Tfu_2367 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q47MC2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsREMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: NANODROP, 22.2% PEG 3350, 0.171M Sodium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0000, 0.9796, 0.9794
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2007
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
30.97941
ReflectionResolution: 2.15→48.393 Å / Num. obs: 22595 / % possible obs: 73.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 24.52 Å2 / Rmerge(I) obs: 0.067 / Χ2: 0.987 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.15-2.233.20.2417930.657126.2
2.23-2.323.10.20110280.65133.9
2.32-2.423.10.18614250.762146.4
2.42-2.553.30.16718130.776159.6
2.55-2.713.50.13922290.901172.8
2.71-2.923.40.10927431.107189.6
2.92-3.213.60.09730841.03199.8
3.21-3.683.60.07631051.128199.9
3.68-4.633.50.06731221.119199.6
4.63-48.3933.40.03432820.984199.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALEPACKdata scaling
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.16→48.393 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / SU B: 11.258 / SU ML: 0.15 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.44 / ESU R Free: 0.266
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION 4. EDO, CL AND SO4 MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED. 5. THE NOMINAL RESOLUTION IS 2.45 A WITH 3406 OBSERVED REFLECTIONS BETWEEN 2.45-2.16 (35.7% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1140 5 %RANDOM
Rwork0.181 ---
obs0.184 22593 72.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.805 Å2
Baniso -1Baniso -2Baniso -3
1-9.27 Å20 Å20 Å2
2---6.8 Å20 Å2
3----2.47 Å2
Refinement stepCycle: LAST / Resolution: 2.16→48.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4066 0 23 164 4253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224220
X-RAY DIFFRACTIONr_bond_other_d0.0020.022803
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.9635788
X-RAY DIFFRACTIONr_angle_other_deg0.89236795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6065537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.76622.5180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70515608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9591539
X-RAY DIFFRACTIONr_chiral_restr0.0810.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024753
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02874
X-RAY DIFFRACTIONr_nbd_refined0.1970.2777
X-RAY DIFFRACTIONr_nbd_other0.2040.22884
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21959
X-RAY DIFFRACTIONr_nbtor_other0.0870.22269
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2169
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1250.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2510.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.24
X-RAY DIFFRACTIONr_mcbond_it1.50832763
X-RAY DIFFRACTIONr_mcbond_other0.24131062
X-RAY DIFFRACTIONr_mcangle_it2.34954332
X-RAY DIFFRACTIONr_scbond_it3.98381680
X-RAY DIFFRACTIONr_scangle_it5.426111453
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1369TIGHT POSITIONAL0.10.1
1616MEDIUM POSITIONAL0.370.75
1369TIGHT THERMAL0.110.5
1616MEDIUM THERMAL0.732
LS refinement shellResolution: 2.16→2.22 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 21 -
Rwork0.231 536 -
all-557 -
obs--24.77 %
Refinement TLS params.Method: refined / Origin x: 73.454 Å / Origin y: 19.2302 Å / Origin z: 40.1787 Å
111213212223313233
T-0.0689 Å20.013 Å20.0221 Å2--0.0117 Å20.0102 Å2---0.0424 Å2
L0.2215 °20.0484 °20.0348 °2-1.1617 °2-0.0406 °2--0.3795 °2
S-0.0059 Å °-0.0498 Å °0.0173 Å °0.0411 Å °0.0059 Å °-0.0026 Å °-0.0342 Å °-0.0116 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 2715 - 272
2X-RAY DIFFRACTION1BB0 - 2711 - 272

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