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- PDB-3r0k: Crystal structure of NYSGRC enolase target 200555, a putative dip... -

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Basic information

Entry
Database: PDB / ID: 3r0k
TitleCrystal structure of NYSGRC enolase target 200555, a putative dipeptide epimerase from Francisella philomiragia : Tartrate bound, no Mg
ComponentsEnzyme of enolase superfamily
KeywordsMETAL BINDING PROTEIN / structural genomics / 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 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 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
SupersessionAug 31, 2011ID: 3PX5
Revision 1.2Aug 31, 2011Group: Other
Revision 1.3Feb 22, 2012Group: Database references
Revision 1.4Mar 21, 2012Group: Database references
Revision 1.5Mar 28, 2012Group: Database references
Revision 1.6Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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)85,90912
Polymers84,9102
Non-polymers99910
Water10,070559
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-84 kcal/mol
Surface area27160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.000, 121.000, 148.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#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 (bacteria) / Strain: subsp. philomiragia / Gene: Fphi_1647 / Plasmid: CHS30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)T1R-RIL / References: UniProt: B0TZW0
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


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


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


Mass: 18.015 Da / Num. of mol.: 559 / 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: 3.21 Å3/Da / Density % sol: 61.64 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / 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. ...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, 10 min, vapor diffusion, sitting drop, temperature 294K, VAPOR DIFFUSION, SITTING DROP

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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: 2→50 Å / Num. all: 75038 / Num. obs: 75038 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 28.8 % / Biso Wilson estimate: 21.61 Å2 / Rsym value: 0.093 / Net I/σ(I): 27.6
Reflection shellResolution: 2→2.11 Å / Redundancy: 27.9 % / Mean I/σ(I) obs: 11.9 / Num. unique all: 10818 / Rsym value: 0.312 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→28.103 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8895 / SU ML: 0.18 / σ(F): 0 / Phase error: 17.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1969 3740 5.04 %RANDOM
Rwork0.1653 ---
all0.1668 74276 --
obs0.1668 74276 99.08 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.201 Å2 / ksol: 0.392 e/Å3
Displacement parametersBiso max: 101.56 Å2 / Biso mean: 28.2443 Å2 / Biso min: 6.58 Å2
Baniso -1Baniso -2Baniso -3
1--1.4298 Å2-0 Å20 Å2
2---1.4298 Å20 Å2
3---2.8595 Å2
Refinement stepCycle: LAST / Resolution: 2→28.103 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5554 0 59 559 6172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085682
X-RAY DIFFRACTIONf_angle_d1.1767679
X-RAY DIFFRACTIONf_chiral_restr0.094908
X-RAY DIFFRACTIONf_plane_restr0.006973
X-RAY DIFFRACTIONf_dihedral_angle_d12.9552091
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02530.19761570.16052549270699
2.0253-2.0520.21631200.15082575269599
2.052-2.08010.16511260.14942577270399
2.0801-2.10980.20961300.15682553268399
2.1098-2.14120.20331230.15742578270198
2.1412-2.17470.18861270.15952584271199
2.1747-2.21030.20011410.16192575271699
2.2103-2.24840.21461640.15722553271799
2.2484-2.28930.20081380.15942588272699
2.2893-2.33330.20931540.16062561271599
2.3333-2.38090.19561170.1652576269399
2.3809-2.43270.21751530.16162572272599
2.4327-2.48920.22371270.16762610273799
2.4892-2.55140.21141210.17262608272999
2.5514-2.62040.18521350.16632574270999
2.6204-2.69740.20381430.1762621276499
2.6974-2.78440.23921430.1852583272699
2.7844-2.88380.22441460.17792612275899
2.8838-2.99920.21531360.1812619275599
2.9992-3.13550.1831520.173526062758100
3.1355-3.30050.22271470.168726552802100
3.3005-3.5070.17841150.163726532768100
3.507-3.77720.18231360.156226792815100
3.7772-4.15620.18471450.149426712816100
4.1562-4.75510.15381600.140226772837100
4.7551-5.98140.20031600.162427232883100
5.9814-28.10590.20861240.20362804292897
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)
10.17280.10980.04970.14670.06180.10240.035-0.05550.06520.0262-0.08210.0550.0153-0.07090.0380.1035-0.0195-0.0320.17-0.02820.155571.476673.828355.7565
20.1945-0.01270.18730.1681-0.00590.2442-0.010.00120.061-0.007-0.040.042-0.00520.00440.03430.0715-0.0011-0.02260.1045-0.02180.106979.342278.585249.8535
30.20880.05990.10730.05650.05570.08830.13940.0019-0.2910.05080.0036-0.09880.220.0011-0.00730.1664-0.0384-0.20260.0841-0.11850.223682.523153.645947.3422
40.0717-0.0263-0.03470.0241-0.0290.13760.0273-0.035-0.0310.024-0.0560.06840.0234-0.10070.02890.401-0.0317-0.01480.4677-0.01330.435662.785774.306557.8443
50.3085-0.03550.09330.13920.06950.08580.0466-0.03020.06030.0566-0.0234-0.00330.0566-0.0314-0.00230.1046-0.01080.02620.08360.01610.068295.990985.401267.4159
60.21990.03230.05840.18260.00620.01670.0431-0.0476-0.02220.1061-0.0464-0.00280.0724-0.0286-0.00580.1249-0.0264-0.00730.09120.00470.057897.148272.30270.4974
70.1057-0.03660.01220.21080.07160.13150.08660.16020.1665-0.0397-0.0361-0.1371-0.04490.05650.05420.08520.01810.03460.16280.0550.1531110.516785.403852.6525
80.22730.04250.16480.12370.06330.12980.0208-0.06690.00710.036-0.0093-0.02110.0408-0.0355-0.00640.1494-0.0043-0.0350.1631-0.01180.1282101.526185.471179.0636
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:44)A2 - 44
2X-RAY DIFFRACTION2(chain A and resid 45:116)A45 - 116
3X-RAY DIFFRACTION3(chain A and resid 117:353)A117 - 353
4X-RAY DIFFRACTION4(chain A and resid 354:363)A354 - 363
5X-RAY DIFFRACTION5(chain B and resid 2:39)B2 - 39
6X-RAY DIFFRACTION6(chain B and resid 40:115)B40 - 115
7X-RAY DIFFRACTION7(chain B and resid 116:347)B116 - 347
8X-RAY DIFFRACTION8(chain B and resid 348:365)B348 - 365

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