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- PDB-2fs2: Structure of the E. coli PaaI protein from the phyenylacetic acid... -

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Basic information

Entry
Database: PDB / ID: 2fs2
TitleStructure of the E. coli PaaI protein from the phyenylacetic acid degradation operon
ComponentsPhenylacetic acid degradation protein paaI
KeywordsHYDROLASE / T820 / PHENYLACETIC ACID / DEGRADATION / OPERON / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


acyl-CoA hydrolase activity / phenylacetate catabolic process / Hydrolases; Acting on ester bonds; Thioester hydrolases
Similarity search - Function
Phenylacetic acid degradation protein PaaD / : / 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
Acyl-coenzyme A thioesterase PaaI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKniewel, R. / Buglino, J.A. / Solorzano, V. / Wu, J. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structure, Function, and Mechanism of the Phenylacetate Pathway Hot Dog-fold Thioesterase PaaI
Authors: Song, F. / Zhuang, Z. / Finci, L. / Dunaway-Mariano, D. / Kniewel, R. / Buglino, J.A. / Solorzano, V. / Wu, J. / Lima, C.D.
History
DepositionJan 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn ...audit_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag ..._audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _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 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phenylacetic acid degradation protein paaI
B: Phenylacetic acid degradation protein paaI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8515
Polymers32,5632
Non-polymers2883
Water1,42379
1
A: Phenylacetic acid degradation protein paaI
B: Phenylacetic acid degradation protein paaI
hetero molecules

A: Phenylacetic acid degradation protein paaI
B: Phenylacetic acid degradation protein paaI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,70210
Polymers65,1264
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+5/31
Unit cell
Length a, b, c (Å)69.847, 69.847, 117.168
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-169-

HOH

21A-171-

HOH

DetailsTetramer by translating the dimer by 1 0 0 0 -1 0 0 0 -1 trans 0, 121.0, 195.3

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Components

#1: Protein Phenylacetic acid degradation protein paaI


Mass: 16281.526 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: paaI / Plasmid: Topo-adapted C-term hexahistidine tag / Production host: Escherichia coli (E. coli) / Strain (production host): B834DE3 / References: UniProt: P76084
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.51 Å3/Da / Density % sol: 50.92 %
Description: THE NUMBER OF UNIQUE REFLECTIONS FOR THE DATA COLLECTION INCLUDES FRIEDEL PAIRS USED TO PHASE THE STRUCTURE.
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 13% PEG 4000, 0.1M BIS-TRIS, 20% MPD, 0.2M LITHIUM SULFATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9798 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 7, 2003
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionRedundancy: 2.5 % / Av σ(I) over netI: 6.9 / Number: 99872 / Rmerge(I) obs: 0.093 / Χ2: 1 / D res high: 2 Å / D res low: 20 Å / Num. obs: 40460 / % possible obs: 93.5
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)Rmerge(I) obsChi squaredRedundancy
4.320423397.50.0612.0332.8
3.424.3426998.40.0721.8042.8
2.993.42419697.20.0931.172.7
2.712.99415395.70.130.8162.5
2.522.71405893.90.1560.6652.5
2.372.52398692.20.2110.5832.4
2.252.37394591.40.2630.5452.3
2.152.25394290.90.2950.5352.3
2.072.15384989.20.3550.4812.2
22.07382988.90.4620.4012.2
ReflectionResolution: 2→20 Å / Num. all: 43273 / Num. obs: 40460 / % possible obs: 93.5 % / Observed criterion σ(F): -0.5 / Observed criterion σ(I): -0.5 / Redundancy: 2.5 % / Rmerge(I) obs: 0.093 / Χ2: 1 / Net I/σ(I): 6.9
Reflection shellResolution: 2→2.07 Å / % possible obs: 88.9 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3829 / Χ2: 0.401 / % possible all: 88.9

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se36.1270.6570.0590.0781.287
2Se28.1260.5650.1310.030.933
3Se21.5730.3670.5820.1680.623
4Se32.8330.3170.4410.0370.544
5Se6.3550.2640.4590.0270.295
6Se36.7510.3930.6380.1440.867
7Se36.5510.6470.1730.0180.501
8Se34.0560.6770.9980.1330.599
9Se22.8710.3990.3240.1270.203
10Se10.8830.8980.1530.019

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.03phasing
RESOLVE2.02phasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
MAR345data collection
RefinementMethod to determine structure: SAD / Resolution: 2→19.88 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.145 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23 981 5.1 %RANDOM
Rwork0.187 ---
all0.189 22978 --
obs-19072 83.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.946 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20.53 Å20 Å2
2--1.06 Å20 Å2
3----1.59 Å2
Refinement stepCycle: LAST / Resolution: 2→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 15 79 2108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0212062
X-RAY DIFFRACTIONr_angle_refined_deg2.3291.9162790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1435268
X-RAY DIFFRACTIONr_chiral_restr0.1670.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021560
X-RAY DIFFRACTIONr_nbd_refined0.2470.2866
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2109
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.210
X-RAY DIFFRACTIONr_mcbond_it1.6081.51328
X-RAY DIFFRACTIONr_mcangle_it3.08722102
X-RAY DIFFRACTIONr_scbond_it5.5063734
X-RAY DIFFRACTIONr_scangle_it8.8144.5688
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.366 51
Rwork0.319 920
obs-971

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