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- PDB-3r0u: Crystal structure of NYSGRC enolase target 200555, a putative dip... -

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Basic information

Entry
Database: PDB / ID: 3r0u
TitleCrystal structure of NYSGRC enolase target 200555, a putative dipeptide epimerase from Francisella philomiragia : Tartrate and Mg complex
ComponentsEnzyme of enolase superfamily
KeywordsLYASE / enolase / structural genomics / putative epimerase / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


racemase and epimerase activity / racemase and epimerase activity, acting on amino acids and derivatives / Isomerases; Racemases and epimerases; Acting on amino acids and derivatives / peptide metabolic process / magnesium ion binding
Similarity search - Function
Dipeptide epimerase / 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 ...Dipeptide epimerase / 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
D(-)-TARTARIC ACID / L-amino acid-D/L-Glu epimerase
Similarity search - Component
Biological speciesFrancisella philomiragia subsp. philomiragia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsVetting, M.W. / Hillerich, B. / Seidel, R.D. / Zencheck, W.D. / Toro, R. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.
Authors: Lukk, T. / Sakai, A. / Kalyanaraman, C. / Brown, S.D. / Imker, H.J. / Song, L. / Fedorov, A.A. / Fedorov, E.V. / Toro, R. / Hillerich, B. / Seidel, R. / Patskovsky, Y. / Vetting, M.W. / ...Authors: Lukk, T. / Sakai, A. / Kalyanaraman, C. / Brown, S.D. / Imker, H.J. / Song, L. / Fedorov, A.A. / Fedorov, E.V. / Toro, R. / Hillerich, B. / Seidel, R. / Patskovsky, Y. / Vetting, M.W. / Nair, S.K. / Babbitt, P.C. / Almo, S.C. / Gerlt, J.A. / Jacobson, M.P.
History
DepositionMar 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Database references
Revision 1.3Mar 21, 2012Group: Database references
Revision 1.4Mar 28, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enzyme of enolase superfamily
B: Enzyme of enolase superfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,05815
Polymers84,9102
Non-polymers1,14713
Water11,223623
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-121 kcal/mol
Surface area27390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.070, 121.070, 149.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Enzyme of enolase superfamily


Mass: 42455.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella philomiragia subsp. philomiragia (bacteria)
Strain: ATCC 25017 / Gene: Fphi_1647 / Plasmid: CHS30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)T1R-RIL / References: UniProt: B0TZW0

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Non-polymers , 5 types, 636 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 623 / 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: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 294 K / pH: 5.6
Details: Protein: 10 mM HEPES pH 7.5, 150 mM Nacl, 10% glycerol, 5 mM DTT; Reservoir: 2M Ammonium Sulfate, 100 mM NaCitrate, 200 mM KNaTartrate; Soak: 2.4 M Ammonium sulfate, 100 mM NaCitrate pH 5.6, ...Details: Protein: 10 mM HEPES pH 7.5, 150 mM Nacl, 10% glycerol, 5 mM DTT; Reservoir: 2M Ammonium Sulfate, 100 mM NaCitrate, 200 mM KNaTartrate; Soak: 2.4 M Ammonium sulfate, 100 mM NaCitrate pH 5.6, KNaTartrate, 20% glycerol, 5mM MgSO4, 10 min, vapor diffusion, sitting drop, temperature 294K

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97905 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Details: Undulator Source
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97905 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 87501 / Num. obs: 87501 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Biso Wilson estimate: 22.48 Å2 / Rsym value: 0.117 / Net I/σ(I): 13.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 12592 / Rsym value: 0.557 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
MOSFLMdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→30.614 Å / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.9021 / SU ML: 0.17 / σ(F): 0 / Phase error: 16.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1947 1996 2.28 %random
Rwork0.1613 ---
obs0.1613 87353 99.87 %-
all-87353 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.763 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso max: 91.29 Å2 / Biso mean: 28.7856 Å2 / Biso min: 7.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.3534 Å2-0 Å20 Å2
2---0.3534 Å20 Å2
3---0.7068 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.614 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5605 0 65 623 6293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.025773
X-RAY DIFFRACTIONf_angle_d1.6287814
X-RAY DIFFRACTIONf_chiral_restr0.131922
X-RAY DIFFRACTIONf_plane_restr0.008994
X-RAY DIFFRACTIONf_dihedral_angle_d13.6952114
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.94750.25481410.211260096150100
1.9475-2.00020.2351400.186260026142100
2.0002-2.0590.20551410.1760276168100
2.059-2.12540.18231420.160960246166100
2.1254-2.20140.18711410.155160476188100
2.2014-2.28950.20411410.149560436184100
2.2895-2.39370.18411400.146960356175100
2.3937-2.51980.2081430.156160856228100
2.5198-2.67760.21351420.160760656207100
2.6776-2.88420.1951430.167561006243100
2.8842-3.17420.18931430.163561186261100
3.1742-3.63280.18231430.149661646307100
3.6328-4.57450.16471470.141862206367100
4.5745-30.61830.21181490.18216418656799
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)
10.30090.15390.07810.20920.14240.29920.0642-0.20450.02670.1438-0.15360.06250.0907-0.18050.01540.183-0.0395-0.03190.21630.01540.176972.992171.97356.7595
20.18990.0450.10850.01910.05780.2702-0.00970.01490.114-0.0296-0.0179-0.02020.0280.01960.00750.0758-0.0073-0.02410.0883-0.0010.096682.752480.141451.2897
30.0460.0252-0.02090.0240.01160.0448-0.0007-0.0335-0.0435-0.0419-0.03440.06550.0367-0.06740.00870.1307-0.0102-0.06140.1544-0.04790.153871.055372.602341.92
40.001-0.00470.01180.0051-0.0039-0.00220.0064-0.0857-0.13890.1037-0.059-0.0480.11910.0134-0.11250.3619-0.2487-0.401-0.01070.02650.471381.90742.401855.2167
50.0048-0.0088-0.00820.03570.02470.03150.14260.0638-0.2488-0.02490.0421-0.06090.19660.05870.03360.36810.0822-0.2891-0.0443-0.23750.555693.302746.452647.9513
60.26440.01390.02260.0905-0.02790.17030.20750.1312-0.3161-0.0058-0.0218-0.0270.20080.04540.12450.17980.0055-0.06980.1684-0.08540.16483.233260.852844.1138
70.10290.03090.03960.05450.01790.0466-0.0520.04220.0888-0.0022-0.01850.0549-0.0343-0.11470.03720.239-0.0474-0.08860.2655-0.05270.265763.485464.468350.2383
80.2640.00450.07030.13950.15470.18370.07990.00560.10120.0365-0.0341-0.03280.0724-0.06080.00470.1509-0.01090.03840.13820.03290.135996.321886.307766.3302
90.13630.0210.0390.11560.00260.18930.0923-0.0709-0.02540.0992-0.05990.00160.1393-0.03450.00590.1556-0.0343-0.01620.12340.00570.083795.489373.296970.2913
100.0652-0.06710.03550.28840.0950.2250.11820.0040.22670.0606-0.022-0.1940.00170.01370.0640.0869-0.01550.02890.09830.0490.2109.175686.196264.4791
110.0310.00610.0380.0093-0.00680.05770.10850.07910.0962-0.0829-0.0437-0.0718-0.1202-0.0201-0.00110.23730.03070.13170.28090.17930.2996109.625196.718743.3721
120.06010.0193-0.04730.0068-0.02290.07420.11560.10920.1208-0.0755-0.0169-0.104-0.0776-0.00880.03810.0813-0.0070.27990.27830.27930.067111.610489.68240.5404
130.06320.0575-0.00110.0825-0.03740.14570.13150.20320.0415-0.1123-0.0607-0.1105-0.00830.07880.02830.13410.03560.05530.22340.02570.1371109.351777.80344.2798
140.2978-0.1764-0.06270.23730.00250.21640.05550.13480.123-0.0756-0.0443-0.1123-0.05290.1085-0.00550.08940.0058-0.00090.1290.00550.1182110.199877.115158.6889
150.00760.0090.01630.02530.0230.10210.0387-0.01990.12810.04470.0247-0.123-0.01180.1473-0.03730.1128-0.02840.00710.1616-0.01490.2548111.181591.46766.0072
160.15660.0230.11740.13780.03660.22580.0368-0.06650.0180.1-0.0058-0.0827-0.02960.0633-0.00840.1657-0.0187-0.04340.194-0.02530.1474102.306285.786579.0364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:51)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 52:98)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 99:130)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 131:182)A0
5X-RAY DIFFRACTION5chain 'A' and (resseq 183:237)A0
6X-RAY DIFFRACTION6chain 'A' and (resseq 238:332)A0
7X-RAY DIFFRACTION7chain 'A' and (resseq 333:363)A0
8X-RAY DIFFRACTION8chain 'B' and (resseq 2:29)B0
9X-RAY DIFFRACTION9chain 'B' and (resseq 30:98)B0
10X-RAY DIFFRACTION10chain 'B' and (resseq 99:156)B0
11X-RAY DIFFRACTION11chain 'B' and (resseq 157:182)B0
12X-RAY DIFFRACTION12chain 'B' and (resseq 183:211)B0
13X-RAY DIFFRACTION13chain 'B' and (resseq 212:259)B0
14X-RAY DIFFRACTION14chain 'B' and (resseq 260:314)B0
15X-RAY DIFFRACTION15chain 'B' and (resseq 315:346)B0
16X-RAY DIFFRACTION16chain 'B' and (resseq 347:365)B0

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