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- PDB-4dye: Crystal structure of an enolase (putative sugar isomerase, target... -

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Basic information

Entry
Database: PDB / ID: 4dye
TitleCrystal structure of an enolase (putative sugar isomerase, target efi-502095) from streptomyces coelicolor, no mg, ordered loop
Componentsisomerase
KeywordsISOMERASE / putative sugar isomerase / enolase family protein / EFI / enzyme function initiative / Structural Genomics
Function / homology
Function and homology information


glucarate dehydratase / isomerase activity / metal ion binding
Similarity search - Function
Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal ...Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
glucarate dehydratase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: to be published
Title: Crystal structure of an enolase (putative sugar isomerase, target efi-502095) from streptomyces coelicolor, no mg, ordered loop
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / ...Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionFeb 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
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: isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9194
Polymers42,7031
Non-polymers2163
Water6,666370
1
A: isomerase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)343,35032
Polymers341,6208
Non-polymers1,73024
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_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area35700 Å2
ΔGint-76 kcal/mol
Surface area90630 Å2
MethodPISA
2
A: isomerase
hetero molecules

A: isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8388
Polymers85,4052
Non-polymers4326
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3250 Å2
ΔGint-20 kcal/mol
Surface area28330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.670, 132.670, 111.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-520-

HOH

21A-543-

HOH

31A-550-

HOH

41A-559-

HOH

51A-619-

HOH

61A-649-

HOH

71A-696-

HOH

81A-700-

HOH

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Components

#1: Protein isomerase


Mass: 42702.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: SCO7570 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9F3A5
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.87 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffuction / pH: 4
Details: Protein (10 mM Hepes pH 7.5, 150 mM NaCl, 10% glycerol, 1 mM DTT, 5 mM MgCl); Reservoir (0.2M Amm Formate pH 6.6, 20% Peg3350); Cryoprotection (Reservoir, + 20% ethylene glycol and 50 mM ...Details: Protein (10 mM Hepes pH 7.5, 150 mM NaCl, 10% glycerol, 1 mM DTT, 5 mM MgCl); Reservoir (0.2M Amm Formate pH 6.6, 20% Peg3350); Cryoprotection (Reservoir, + 20% ethylene glycol and 50 mM MgCl), sitting drop vapor diffuction, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 3, 2012 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.6→93.812 Å / Num. all: 65168 / Num. obs: 65168 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.5 % / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 15.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.6914.40.796113570894100.796100
1.69-1.7914.50.541.412936989330.54100
1.79-1.9114.50.352.212197383970.35100
1.91-2.0714.60.213.611384278210.21100
2.07-2.2614.60.1345.510557172150.134100
2.26-2.5314.60.1016.79596365630.101100
2.53-2.9214.60.1115.58485457980.111100
2.92-3.5814.60.0986.17223649500.098100
3.58-5.0614.40.05310.85601738940.053100
5.06-26.66513.30.04114.12899321870.04198

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OQH

2oqh


Resolution: 1.6→26.665 Å / Occupancy max: 1 / Occupancy min: 0.32 / FOM work R set: 0.9074 / SU ML: 0.14 / σ(F): 0 / Phase error: 15.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1749 3294 5.05 %RANDOM
Rwork0.1568 ---
all0.1577 65164 --
obs0.1577 65164 99.93 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.67 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso max: 113.84 Å2 / Biso mean: 27.5359 Å2 / Biso min: 9.58 Å2
Baniso -1Baniso -2Baniso -3
1--2.5334 Å20 Å20 Å2
2---2.5334 Å20 Å2
3---5.0668 Å2
Refinement stepCycle: LAST / Resolution: 1.6→26.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2815 0 14 370 3199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062983
X-RAY DIFFRACTIONf_angle_d1.1394069
X-RAY DIFFRACTIONf_chiral_restr0.073463
X-RAY DIFFRACTIONf_plane_restr0.006537
X-RAY DIFFRACTIONf_dihedral_angle_d11.8881083
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.62290.23631500.229625342684100
1.6229-1.64710.24541510.214425312682100
1.6471-1.67280.23541310.203225472678100
1.6728-1.70020.20761140.187425752689100
1.7002-1.72960.20311380.179325482686100
1.7296-1.7610.23941190.167925622681100
1.761-1.79490.17741480.165125402688100
1.7949-1.83150.18281310.160125542685100
1.8315-1.87130.18791360.152725612697100
1.8713-1.91480.16411430.151325692712100
1.9148-1.96270.1861230.150625352658100
1.9627-2.01570.14741270.151426102737100
2.0157-2.0750.1741300.150425502680100
2.075-2.1420.16241390.150825782717100
2.142-2.21850.17361470.153925532700100
2.2185-2.30730.18661330.15425712704100
2.3073-2.41220.18211620.14325682730100
2.4122-2.53930.16681420.149525742716100
2.5393-2.69830.17711290.151125942723100
2.6983-2.90640.19841440.162125832727100
2.9064-3.19840.17661160.159226382754100
3.1984-3.66020.1551510.150126082759100
3.6602-4.60760.14031420.138726522794100
4.6076-26.6690.1841480.16872735288399
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)
11.60590.05261.06132.3920.27021.90790.01690.0544-0.1611-0.08550.05490.32490.2021-0.151-0.07360.1207-0.09430.00210.23210.00030.2671-39.2738-19.8724-2.8962
20.81740.1111-0.17590.5992-0.17440.6399-0.04460.2021-0.102-0.16860.03390.19140.1318-0.18430.01470.1202-0.0396-0.05740.1504-0.03280.1169-24.6057-10.8868-16.6689
30.3062-0.4042-0.10990.7573-0.12170.52930.08480.1187-0.2091-0.1687-0.00070.48250.3849-0.3143-0.05850.2043-0.0537-0.22040.3384-0.10740.4114-43.9399-20.057-14.984
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 0:82)A0 - 82
2X-RAY DIFFRACTION2chain 'A' and (resseq 83:341)A83 - 341
3X-RAY DIFFRACTION3chain 'A' and (resseq 342:375)A342 - 375

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