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- PDB-3qmw: RedJ with PEG molecule bound in the active site -

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Basic information

Entry
Database: PDB / ID: 3qmw
TitleRedJ with PEG molecule bound in the active site
ComponentsThioesterase
KeywordsHYDROLASE / Alpha/Beta hydrolase fold
Function / homology
Function and homology information


lipid biosynthetic process / hydrolase activity
Similarity search - Function
Thioesterase type II, NRPS/PKS/S-FAS / Polyketide synthase, thioesterase domain / Thioesterase / Thioesterase / Thioesterase domain / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWhicher, J.R. / Smith, J.L.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure and Function of the RedJ Protein, a Thioesterase from the Prodiginine Biosynthetic Pathway in Streptomyces coelicolor.
Authors: Whicher, J.R. / Florova, G. / Sydor, P.K. / Singh, R. / Alhamadsheh, M. / Challis, G.L. / Reynolds, K.A. / Smith, J.L.
History
DepositionFeb 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Thioesterase
B: Thioesterase
C: Thioesterase
D: Thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,7525
Polymers114,5584
Non-polymers1941
Water2,720151
1
A: Thioesterase
D: Thioesterase


Theoretical massNumber of molelcules
Total (without water)57,2792
Polymers57,2792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-24 kcal/mol
Surface area21390 Å2
MethodPISA
2
B: Thioesterase
C: Thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4733
Polymers57,2792
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-20 kcal/mol
Surface area21820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.545, 45.013, 156.403
Angle α, β, γ (deg.)90.00, 109.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Thioesterase / RedJ


Mass: 28639.441 Da / Num. of mol.: 4 / Fragment: UNP residues 6-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: SCO5894, SC3F7.14 / Production host: Escherichia coli (E. coli)
References: UniProt: O54157, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG3350, 0.22 M sodium chloride, 2 mM DTT, 0.1 M HEPES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 35740 / Num. obs: 33414 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rsym value: 0.101 / Net I/σ(I): 11.02
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.359 / % possible all: 83.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QMV

3qmv


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.873 / Cross valid method: THROUGHOUT / ESU R: 3.878 / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28436 1621 4.9 %RANDOM
Rwork0.21446 ---
obs0.21798 33414 --
all-35740 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.475 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å20 Å2-0.11 Å2
2--2.91 Å20 Å2
3----2.06 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7692 0 13 151 7856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0217946
X-RAY DIFFRACTIONr_bond_other_d00.025637
X-RAY DIFFRACTIONr_angle_refined_deg1.2011.97110835
X-RAY DIFFRACTIONr_angle_other_deg4.006313443
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5985974
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.34420.551381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.353151136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.29215117
X-RAY DIFFRACTIONr_chiral_restr0.0730.21143
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218974
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021823
X-RAY DIFFRACTIONr_mcbond_it0.5721.54929
X-RAY DIFFRACTIONr_mcbond_other01.51939
X-RAY DIFFRACTIONr_mcangle_it1.09227888
X-RAY DIFFRACTIONr_scbond_it1.32533017
X-RAY DIFFRACTIONr_scangle_it2.2994.52947
LS refinement shellResolution: 2.499→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 86 -
Rwork0.31 1827 -
obs--73.69 %

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