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- PDB-1j1y: Crystal Structure of PaaI from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 1j1y
TitleCrystal Structure of PaaI from Thermus thermophilus HB8
ComponentsPaaI protein
KeywordsHYDROLASE / THIOESTERASE / HOT DOG FOLD / PHENYLACETIC ACID DEGRADATION / Structural Genomics / 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 / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsKunishima, N. / Sugahara, M. / Kuramitsu, S. / Yokoyama, S. / Miyano, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 2005
Title: A Novel Induced-fit Reaction Mechanism of Asymmetric Hot Dog Thioesterase PaaI
Authors: Kunishima, N. / Asada, Y. / Sugahara, M. / Ishijima, J. / Nodake, Y. / Sugahara, M. / Miyano, M. / Kuramitsu, S. / Yokoyama, S. / Sugahara, M.
History
DepositionDec 24, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PaaI protein
B: PaaI protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6204
Polymers28,5602
Non-polymers602
Water3,603200
1
A: PaaI protein
B: PaaI protein
hetero molecules

A: PaaI protein
B: PaaI protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2408
Polymers57,1214
Non-polymers1204
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
Buried area8140 Å2
ΔGint-64 kcal/mol
Surface area17090 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)57.877, 57.877, 139.607
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-1003-

HOH

41A-1004-

HOH

51A-1077-

HOH

61A-1099-

HOH

71B-215-

HOH

DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operation: 1-x, y, -z.

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Components

#1: Protein PaaI protein


Mass: 14280.224 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SJP3
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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 / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.16 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7.5
Details: PEG 400, magnesium chloride, HEPES-Na, pH 7.5, MICROBATCH, temperature 295K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
130.0 mg/mlprotein11
250 mM11NaCl
320 mMTris-HCl11pH8.0
430 %(v/v)PEG40011
50.2 M11MgCl2
60.1 MHEPES-NaOH11pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 0.97950, 0.97945, 1.02000
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 12, 2001
RadiationMonochromator: UNDULATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.979451
31.021
ReflectionResolution: 1.7→30 Å / Num. all: 26981 / Num. obs: 26981 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.07 / Net I/σ(I): 5.9
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 4.2 / Num. unique all: 3841 / Rsym value: 0.176 / % possible all: 100
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.7→30 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.193 1349 -RANDOM
Rwork0.181 ---
all0.182 26981 --
obs0.182 26981 100 %-
Displacement parametersBiso mean: 18 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1733 0 2 200 1935
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_bond_d0.004
LS refinement shellResolution: 1.7→1.76 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.198 129 -
Rwork0.202 --
obs-2624 100 %
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.005
LS refinement shell
*PLUS
Rfactor obs: 0.202

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