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- PDB-2pim: CRYSTAL STRUCTURE OF A PUTATIVE THIOESTERASE, PHENYLACETIC ACID D... -

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Entry
Database: PDB / ID: 2pim
TitleCRYSTAL STRUCTURE OF A PUTATIVE THIOESTERASE, PHENYLACETIC ACID DEGRADATION-RELATED PROTEIN (REUT_B4779) FROM RALSTONIA EUTROPHA JMP134 AT 2.20 A RESOLUTION
ComponentsPhenylacetic acid degradation-related protein
KeywordsHYDROLASE / THIOESTERASE SUPERFAMILY / PHENYLACETIC ACID DEGRADATION-RELATED PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyAcyl-CoA thioesterase N-terminal domain / Phenylacetic acid degradation-related domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / Phenylacetic acid degradation-related protein
Function and homology information
Biological speciesRalstonia eutropha JMP134 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Phenylacetic acid degradation-related protein (YP_298971.1) from Ralstonia eutropha JMP134 at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
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 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: Phenylacetic acid degradation-related protein


Theoretical massNumber of molelcules
Total (without water)14,9961
Polymers14,9961
Non-polymers00
Water99155
1
A: Phenylacetic acid degradation-related protein

A: Phenylacetic acid degradation-related protein


Theoretical massNumber of molelcules
Total (without water)29,9922
Polymers29,9922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2020 Å2
ΔGint-12 kcal/mol
Surface area11920 Å2
MethodPISA
2
A: Phenylacetic acid degradation-related protein

A: Phenylacetic acid degradation-related protein

A: Phenylacetic acid degradation-related protein

A: Phenylacetic acid degradation-related protein


Theoretical massNumber of molelcules
Total (without water)59,9854
Polymers59,9854
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation10_665-y+1,-x+1,-z1
MethodPQS
Unit cell
Length a, b, c (Å)111.774, 111.774, 46.461
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-181-

HOH

21A-189-

HOH

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Components

#1: Protein Phenylacetic acid degradation-related protein


Mass: 14996.161 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha JMP134 (bacteria) / Species: Cupriavidus necator / Gene: YP_298971.1, Reut_B4779 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q46RV7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.79 Å3/Da / Density % sol: 55.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.86
Details: NANODROP, 1.32M Sodium citrate, 0.1M Sodium cacodylate pH 6.86, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837, 0.97934
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 1, 2007 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979341
ReflectionResolution: 2.2→28.748 Å / Num. obs: 9118 / % possible obs: 100 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.141 / Rsym value: 0.141 / Net I/σ(I): 4.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.2614.30.8940.892516460.894100
2.26-2.3214.50.777193326440.777100
2.32-2.3914.50.6731.189766210.673100
2.39-2.4614.40.6571.188446140.657100
2.46-2.5414.50.491.583845780.49100
2.54-2.6314.40.4241.882545740.424100
2.63-2.7314.40.3592.178725470.359100
2.73-2.8414.40.312.575805280.31100
2.84-2.9714.30.2253.374175200.225100
2.97-3.1114.20.1784.270584960.178100
3.11-3.2814.20.1375.366074650.137100
3.28-3.48140.1155.861804430.115100
3.48-3.72140.0986.959014230.098100
3.72-4.0213.80.0828.154683970.082100
4.02-4.413.80.079.350983700.07100
4.4-4.9213.60.06110.745703360.061100
4.92-5.6813.40.0788.340763050.078100
5.68-6.96130.0798.234112630.079100
6.96-9.8412.20.05210.326402160.052100
9.84-28.7510.20.0581013491320.05896.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→28.748 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU B: 11.181 / SU ML: 0.139 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.172
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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 514 5.6 %RANDOM
Rwork0.182 ---
all0.185 ---
obs0.185 9116 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: 28.728 Å2
Baniso -1Baniso -2Baniso -3
1--2.32 Å2-1.16 Å20 Å2
2---2.32 Å20 Å2
3---3.49 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms956 0 0 55 1011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022986
X-RAY DIFFRACTIONr_bond_other_d0.0020.02948
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.9841338
X-RAY DIFFRACTIONr_angle_other_deg0.80332180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3665135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.33623.2540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.04615163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4531511
X-RAY DIFFRACTIONr_chiral_restr0.0940.2161
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021137
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02198
X-RAY DIFFRACTIONr_nbd_refined0.1940.2171
X-RAY DIFFRACTIONr_nbd_other0.1860.2921
X-RAY DIFFRACTIONr_nbtor_refined0.1670.2477
X-RAY DIFFRACTIONr_nbtor_other0.0880.2670
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.242
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2810.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.25
X-RAY DIFFRACTIONr_mcbond_it2.1733773
X-RAY DIFFRACTIONr_mcbond_other0.5183281
X-RAY DIFFRACTIONr_mcangle_it2.9951049
X-RAY DIFFRACTIONr_scbond_it5.7738345
X-RAY DIFFRACTIONr_scangle_it7.14311289
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 27 -
Rwork0.22 616 -
obs-643 100 %
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)
16.25650.33651.30654.40290.50731.97230.1252-1.1765-0.94040.7783-0.0672-0.26620.161-0.1173-0.0581-0.01430.006-0.11790.03460.25410.153230.17125.09312.705
23.1987-0.51620.11013.8870.07721.52030.1095-0.3252-0.48320.0631-0.0454-0.14790.09980.0494-0.0641-0.21910.0142-0.0382-0.20210.0721-0.104130.05534.6072.478
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
115 - 366 - 37
2237 - 13638 - 137

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