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- PDB-2qwz: CRYSTAL STRUCTURE OF A PUTATIVE THIOESTERASE (TM1040_1390) FROM S... -

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Basic information

Entry
Database: PDB / ID: 2qwz
TitleCRYSTAL STRUCTURE OF A PUTATIVE THIOESTERASE (TM1040_1390) FROM SILICIBACTER SP. TM1040 AT 2.15 A RESOLUTION
ComponentsPhenylacetic acid degradation-related protein
KeywordsHYDROLASE / PUTATIVE THIOESTERASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


Phenylacetic acid degradation-related domain / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Phenylacetic acid degradation-related protein
Similarity search - Component
Biological speciesSilicibacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative thioesterase (YP_613385.1) from Silicibacter sp. TM1040 at 2.15 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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
Remark 300 BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAINS. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A TETRAMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phenylacetic acid degradation-related protein
B: Phenylacetic acid degradation-related protein
C: Phenylacetic acid degradation-related protein
D: Phenylacetic acid degradation-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,57816
Polymers71,6384
Non-polymers94012
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.307, 95.307, 132.634
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: LEU / End label comp-ID: PRO / Refine code: 6 / Auth seq-ID: 10 - 138 / Label seq-ID: 29 - 157

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A TETRAMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein
Phenylacetic acid degradation-related protein


Mass: 17909.439 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter sp. (bacteria) / Strain: TM1040 / Gene: YP_613385.1, TM1040_1390 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q1GGU3
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: NANODROP, 0.16M (NH4)2SO4, 20.0% Glycerol, 20.0% PEG 4000, 0.1M Acetate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97916 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 20, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.15→28.228 Å / Num. obs: 38522 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.146 / Rsym value: 0.146 / Net I/σ(I): 4.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.15-2.217.41.0240.72104528321.024100
2.21-2.277.40.90.82041227400.9100
2.27-2.337.40.8180.91981126680.818100
2.33-2.47.40.75611916125730.756100
2.4-2.487.50.6781.11856624920.678100
2.48-2.577.50.4831.61825724470.483100
2.57-2.677.40.3911.91755223630.391100
2.67-2.787.50.342.21673922450.34100
2.78-2.97.40.2682.81642222120.268100
2.9-3.047.50.2143.51529020510.214100
3.04-3.217.40.1524.91482520030.152100
3.21-3.47.40.11861410119020.118100
3.4-3.637.40.171299817610.1100
3.63-3.937.30.0877.41221416660.087100
3.93-4.37.30.0778.51123815310.077100
4.3-4.817.30.0668.91017714030.066100
4.81-5.5570.0867.4867812350.086100
5.55-6.86.80.0867.4734610790.086100
6.8-9.626.70.0657.556088420.065100
9.62-28.2286.10.055829294770.05596.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→28.228 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 12.145 / SU ML: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.19
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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. ACETATE AND GLYCEROL ARE MODELED BASED ON CRYSTALLIZATION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1926 5 %RANDOM
Rwork0.2 ---
all0.203 ---
obs0.203 38482 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.808 Å2
Baniso -1Baniso -2Baniso -3
1--2.36 Å2-1.18 Å20 Å2
2---2.36 Å20 Å2
3---3.53 Å2
Refinement stepCycle: LAST / Resolution: 2.15→28.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4099 0 62 172 4333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224232
X-RAY DIFFRACTIONr_bond_other_d0.0010.022783
X-RAY DIFFRACTIONr_angle_refined_deg1.562.0045733
X-RAY DIFFRACTIONr_angle_other_deg0.96936806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6855563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.83223.129147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.63715653
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3311527
X-RAY DIFFRACTIONr_chiral_restr0.0860.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024737
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02838
X-RAY DIFFRACTIONr_nbd_refined0.2120.2759
X-RAY DIFFRACTIONr_nbd_other0.20.22720
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21965
X-RAY DIFFRACTIONr_nbtor_other0.090.22439
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2175
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.27
X-RAY DIFFRACTIONr_mcbond_it2.15832884
X-RAY DIFFRACTIONr_mcbond_other0.5631146
X-RAY DIFFRACTIONr_mcangle_it3.41854435
X-RAY DIFFRACTIONr_scbond_it5.69981496
X-RAY DIFFRACTIONr_scangle_it6.903111296
Refine LS restraints NCS

Ens-ID: 1 / Number: 1493 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.45
2BLOOSE POSITIONAL0.375
3CLOOSE POSITIONAL0.45
4DLOOSE POSITIONAL0.385
1ALOOSE THERMAL5.4710
2BLOOSE THERMAL4.6910
3CLOOSE THERMAL5.2110
4DLOOSE THERMAL4.7910
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 149 -
Rwork0.253 2667 -
obs-2816 100 %
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)
10.4035-0.11910.48290.74560.25760.80330.0876-0.0378-0.09920.0134-0.0745-0.04870.0096-0.073-0.0131-0.01120.014-0.01390.00250.0111-0.06134.643732.97534.4188
20.31880.06940.02720.359-0.63241.3653-0.0048-0.0712-0.0124-0.08870.03620.12630.10110.0285-0.0314-0.02190.0127-0.00730.00240.0096-0.045613.0145.697532.1507
32.2728-0.68831.0911.697-1.21441.8125-0.2302-0.14840.53530.23-0.0369-0.2766-0.2185-0.00450.26710.01720.0084-0.0688-0.0601-0.0660.071829.0166.18339.3018
41.8845-0.00971.11791.3212-0.38131.4802-0.09890.24240.3472-0.0484-0.1085-0.2458-0.10420.14580.2074-0.0468-0.00820.020.01810.07390.03644.48156.345524.4851
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA-5 - 13814 - 157
22BB-5 - 13814 - 157
33CC1 - 13820 - 157
44DD2 - 13821 - 157

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