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- PDB-2dsl: Mutant N33D structure of phenylacetic acid degradation protein Pa... -

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Basic information

Entry
Database: PDB / ID: 2dsl
TitleMutant N33D structure of phenylacetic acid degradation protein PaaI from Thermus thermophilus HB8
ComponentsPhenylacetic acid degradation protein PaaI
KeywordsHYDROLASE / THIOESTERASE / HOT DOG FOLD / PHENYLACETIC ACID DEGRADATION / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


acyl-CoA hydrolase activity
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
Phenylacetic acid degradation protein PaaI
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsShimizu, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Mutant N33D structure of phenylacetic acid degradation protein PaaI from Thermus thermophilus HB8
Authors: Shimizu, K. / Sugahara, M. / Kunishima, N.
History
DepositionJun 30, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Nov 10, 2021Group: 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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)28,6224
Polymers28,5622
Non-polymers602
Water4,197233
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)57,2448
Polymers57,1254
Non-polymers1204
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
Buried area8240 Å2
ΔGint-61 kcal/mol
Surface area16520 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)57.670, 57.670, 139.696
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-1001-

CL

21A-1002-

MG

31A-1046-

HOH

41A-1047-

HOH

51A-1106-

HOH

61B-229-

HOH

DetailsThe biological assembly is a tetramer generated from the dimer A and B in the asymmetric unit.

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Components

#1: Protein Phenylacetic acid degradation protein PaaI


Mass: 14281.208 Da / Num. of mol.: 2 / Mutation: N33D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SJP3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.03 Å3/Da / Density % sol: 39.48 %
Crystal growTemperature: 295 K / Method: microbach / pH: 7.5
Details: 20% PEG 400, 0.2M Magnesium Chloride, 0.1M HEPES, pH 7.5, Microbach, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jul 23, 2002 / Details: Mirror
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 26557 / Num. obs: 26557 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.39 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.056 / Net I/σ(I): 12.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.55 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 3.3 / Num. unique all: 26557 / Rsym value: 0.384 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J1Y

1j1y


Resolution: 1.7→22.56 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1626023.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1361 5.1 %RANDOM
Rwork0.19 ---
obs0.19 26557 98.8 %-
all-26557 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.115 Å2 / ksol: 0.393909 e/Å3
Displacement parametersBiso mean: 24.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2--0.25 Å20 Å2
3----0.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→22.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1722 0 2 233 1957
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it1.862
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it3.032.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.317 224 5.2 %
Rwork0.31 4109 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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