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- PDB-4e4u: Crystal structure of a putative Mandelate racemase/Muconate lacto... -

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Basic information

Entry
Database: PDB / ID: 4e4u
TitleCrystal structure of a putative Mandelate racemase/Muconate lactonizing enzyme (Target PSI-200780) from Burkholderia SAR-1
ComponentsMandalate racemase/muconate lactonizing enzyme
KeywordsISOMERASE / Racemase / Mandelate racemase / aldolase / Structural genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homologyEnolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsKumar, P.R. / Bonanno, J. / Chowdhury, S. / Foti, R. / Gizzi, A. / Hammonds, J. / Hillerich, B. / Matikainen, B. / Seidel, R. / Toro, R. ...Kumar, P.R. / Bonanno, J. / Chowdhury, S. / Foti, R. / Gizzi, A. / Hammonds, J. / Hillerich, B. / Matikainen, B. / Seidel, R. / Toro, R. / Zencheck, W. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: to be published
Title: Crystal structure of a putative MR/ML enzyme from Burkholderia SAR-1
Authors: Kumar, P.R. / Bonanno, J. / Chowdhury, S. / Foti, R. / Gizzi, A. / Hammonds, J. / Hillerich, B. / Matikainen, B. / Seidel, R. / Toro, R. / Zencheck, W. / Almo, S.C.
History
DepositionMar 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Mandalate racemase/muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8022
Polymers45,6481
Non-polymers1541
Water7,638424
1
A: Mandalate racemase/muconate lactonizing enzyme
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)366,41916
Polymers365,1858
Non-polymers1,2348
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_554-x,y,-z-11
crystal symmetry operation6_554x,-y,-z-11
crystal symmetry operation7_554y,x,-z-11
crystal symmetry operation8_554-y,-x,-z-11
Buried area48150 Å2
ΔGint-208 kcal/mol
Surface area84430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.835, 118.835, 120.839
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-601-

HOH

21A-774-

HOH

31A-776-

HOH

41A-827-

HOH

51A-1011-

HOH

DetailsThe biological assembly is an octamer generated by crystallographic symmetry operations

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Components

#1: Protein Mandalate racemase/muconate lactonizing enzyme


Mass: 45648.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: from Sargasso sea / Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Dithioerythritol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (2.5M NaCl, Sodium Acetate 4.5, 0.2M Li2SO4- Wizard II #38); Cryoprotection (LI2SO4), Sitting Drop Vapor Diffusion, ...Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (2.5M NaCl, Sodium Acetate 4.5, 0.2M Li2SO4- Wizard II #38); Cryoprotection (LI2SO4), Sitting Drop Vapor Diffusion, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2011 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionHighest resolution: 1.35 Å / Num. obs: 181393 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.261 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 16.05
Reflection shell

Rmerge(I) obs: 0.011 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.35-1.391.91166711326798.9
1.39-1.422.5414225813129100
1.42-1.463.314428212755100
1.46-1.514.5414475812370100
1.51-1.565.6614471411925100
1.56-1.617.2414636011644100
1.61-1.679.1714579311201100
1.67-1.7411.3714472410738100
1.74-1.8213.9814444010341100
1.82-1.9117.611422659872100
1.91-2.0121.96138249938899.9
2.01-2.1325.911305978831100
2.13-2.2829.141233528364100
2.28-2.4631.421154137795100
2.46-2.733.691049787132100
2.7-3.0235.92936786443100
3.02-3.4938.86819205705100
3.49-4.2742.22719094806100
4.27-6.0442.755557372999.9
6.0440.9927179195895.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
XDSdata reduction
PHENIX1.7.3_928phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→37.641 Å / Occupancy max: 1 / Occupancy min: 0.23 / FOM work R set: 0.934 / SU ML: 0.16 / σ(F): 1.34 / Phase error: 12.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1461 4719 5.02 %
Rwork0.1331 --
obs0.1338 94064 99.83 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.327 Å2 / ksol: 0.393 e/Å3
Displacement parametersBiso max: 59.07 Å2 / Biso mean: 17.8719 Å2 / Biso min: 5.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.1269 Å20 Å2-0 Å2
2--0.1269 Å20 Å2
3----0.2538 Å2
Refinement stepCycle: LAST / Resolution: 1.35→37.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3139 0 8 424 3571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053315
X-RAY DIFFRACTIONf_angle_d1.1244519
X-RAY DIFFRACTIONf_chiral_restr0.071495
X-RAY DIFFRACTIONf_plane_restr0.005591
X-RAY DIFFRACTIONf_dihedral_angle_d13.0321231
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.35-1.36530.27731370.24342900303798
1.3653-1.38140.23291770.21432926310399
1.3814-1.39830.19261420.192329633105100
1.3983-1.4160.20011630.178329163079100
1.416-1.43460.18391530.165329673120100
1.4346-1.45420.18121530.150729443097100
1.4542-1.4750.16741610.142529543115100
1.475-1.4970.16031390.135429663105100
1.497-1.52040.17241620.127129543116100
1.5204-1.54540.14231510.118629723123100
1.5454-1.5720.14271590.11529483107100
1.572-1.60060.14461570.108229433100100
1.6006-1.63140.15351760.110829493125100
1.6314-1.66470.14391490.10729743123100
1.6647-1.70090.13511660.104829583124100
1.7009-1.74040.14431480.102129633111100
1.7404-1.7840.14241530.108629983151100
1.784-1.83220.14561270.107829783105100
1.8322-1.88610.13831740.109629763150100
1.8861-1.9470.15211680.114529633131100
1.947-2.01660.13471630.117629633126100
2.0166-2.09730.15531680.118629513119100
2.0973-2.19270.14851560.120930173173100
2.1927-2.30830.13321500.123429823132100
2.3083-2.45290.1441500.126930173167100
2.4529-2.64230.13121500.134430313181100
2.6423-2.90810.15881490.145230273176100
2.9081-3.32870.151670.148330303197100
3.3287-4.19290.1261760.126430613237100
4.1929-37.65550.13821750.15853154332998

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