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- PDB-2hlj: CRYSTAL STRUCTURE OF A PUTATIVE THIOESTERASE (KT2440) FROM PSEUDO... -

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Basic information

Entry
Database: PDB / ID: 2hlj
TitleCRYSTAL STRUCTURE OF A PUTATIVE THIOESTERASE (KT2440) FROM PSEUDOMONAS PUTIDA KT2440 AT 2.00 A RESOLUTION
ComponentsHypothetical protein
KeywordsHYDROLASE / PUTATIVE THIOESTERASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


fatty acyl-CoA hydrolase activity / acyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
: / Thioesterase-like superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Betainyl-CoA thiolase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (NP_742468.1) from Pseudomonas putida KT2440 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / 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 ...database_2 / 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 / _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 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE 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 (0) 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: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0102
Polymers17,9181
Non-polymers921
Water3,063170
1
A: Hypothetical protein
hetero molecules

A: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0194
Polymers35,8352
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area4470 Å2
ΔGint-17 kcal/mol
Surface area15080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)53.809, 73.613, 39.752
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Hypothetical protein


Mass: 17917.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: KT2440 / Gene: NP_742468.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q88R33
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.21 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.9
Details: 0.2M K2NO3, 20.0% PEG-3350, No Buffer, pH 6.9, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97934, 0.97915, 0.91837
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 18, 2006 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979341
20.979151
30.918371
ReflectionResolution: 2→29.323 Å / Num. obs: 11181 / % possible obs: 99.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.053.60.2872.628557850.287100
2.05-2.113.60.2762.728927950.276100
2.11-2.173.60.2293.328277770.229100
2.17-2.243.70.2243.327537520.224100
2.24-2.313.60.193.626327280.19100
2.31-2.393.60.164.625046880.16100
2.39-2.483.60.1544.625206960.154100
2.48-2.583.60.1455.123336410.145100
2.58-2.73.60.135.623326430.13100
2.7-2.833.60.0957.421856070.095100
2.83-2.983.60.0868.320345650.086100
2.98-3.163.60.0719.319815500.071100
3.16-3.383.50.0689.318475210.068100
3.38-3.653.60.0629.217474910.062100
3.65-43.50.05810.215974500.058100
4-4.473.50.04911.514294100.049100
4.47-5.163.50.04812.412573630.048100
5.16-6.323.40.061110653170.06100
6.32-8.943.20.0559.98202560.05599.6
8.94-29.3330.04413.14331460.04494.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→29.323 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.727 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.169
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. 4. RESIDUES 117-119 ARE DISORDERED AND WERE NOT MODELED. 5. GLYCEROL ADDED BASED ON CRYSTALLIZATION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.227 531 4.8 %RANDOM
Rwork0.167 ---
obs0.17 11154 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.701 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å20 Å20 Å2
2---1.85 Å20 Å2
3---3.17 Å2
Refinement stepCycle: LAST / Resolution: 2→29.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1224 0 6 170 1400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211273
X-RAY DIFFRACTIONr_bond_other_d0.0020.021145
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.9431731
X-RAY DIFFRACTIONr_angle_other_deg0.85632645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3545158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23523.65163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03615206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.386158
X-RAY DIFFRACTIONr_chiral_restr0.0910.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021429
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02269
X-RAY DIFFRACTIONr_nbd_refined0.2110.2203
X-RAY DIFFRACTIONr_nbd_other0.1820.21106
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2610
X-RAY DIFFRACTIONr_nbtor_other0.0850.2750
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2118
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2870.2109
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.214
X-RAY DIFFRACTIONr_mcbond_it2.2193837
X-RAY DIFFRACTIONr_mcbond_other0.5243320
X-RAY DIFFRACTIONr_mcangle_it3.02151238
X-RAY DIFFRACTIONr_scbond_it5.228550
X-RAY DIFFRACTIONr_scangle_it6.70911490
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 38 -
Rwork0.178 745 -
obs-783 100 %
Refinement TLS params.Method: refined / Origin x: 46.597 Å / Origin y: 7.897 Å / Origin z: 7.062 Å
111213212223313233
T-0.0614 Å20.0123 Å20.0008 Å2--0.0376 Å2-0.001 Å2---0.029 Å2
L1.0167 °2-0.2942 °20.1113 °2-1.6542 °20.0984 °2--0.649 °2
S-0.058 Å °-0.08 Å °0.0868 Å °0.1033 Å °0.0462 Å °0.0254 Å °0.0015 Å °0.014 Å °0.0119 Å °
Refinement TLS groupSelection: ALL

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