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- PDB-3r1z: Crystal structure of NYSGRC enolase target 200555, a putative dip... -

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Basic information

Entry
Database: PDB / ID: 3r1z
TitleCrystal structure of NYSGRC enolase target 200555, a putative dipeptide epimerase from Francisella philomiragia : Complex with L-Ala-L-Glu and L-Ala-D-Glu
ComponentsEnzyme of enolase superfamily
KeywordsISOMERASE / 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
ALANINE / D-GLUTAMIC ACID / GLUTAMIC 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 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 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
Revision 1.5Nov 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)86,32716
Polymers84,9102
Non-polymers1,41714
Water12,755708
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-89 kcal/mol
Surface area27100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.190, 121.190, 149.020
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 , 6 types, 722 molecules

#2: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2
#3: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-DGL / D-GLUTAMIC ACID


Type: D-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 708 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.22 Å3/Da / Density % sol: 61.82 %
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: 2.2 M Ammonium sulfate, 100 mM MES pH 6.0, 18% ...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: 2.2 M Ammonium sulfate, 100 mM MES pH 6.0, 18% glycerol, 50mM MgSO4, 25 mM L-Ala-L-Glu, 30 min, vapour 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: 85703 / Num. obs: 85703 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.5 % / Biso Wilson estimate: 19.31 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 16.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 5.8 / Num. unique all: 3006 / Rsym value: 0.38 / % possible all: 92.5

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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→29.69 Å / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.8984 / SU ML: 0.18 / σ(F): 0 / σ(I): 0 / Phase error: 16.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1854 4221 5 %Random
Rwork0.1571 ---
all0.1585 84359 --
obs0.1585 84359 96.28 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.043 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso max: 98.02 Å2 / Biso mean: 24.6422 Å2 / Biso min: 5.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.258 Å20 Å20 Å2
2--0.258 Å20 Å2
3---0.7469 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5605 0 84 708 6397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085765
X-RAY DIFFRACTIONf_angle_d1.2427795
X-RAY DIFFRACTIONf_chiral_restr0.1922
X-RAY DIFFRACTIONf_plane_restr0.007989
X-RAY DIFFRACTIONf_dihedral_angle_d13.3372121
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.96790.21633840.1827263764789
1.9679-2.04670.20683730.16177503787691
2.0467-2.13980.19833660.15717718808494
2.1398-2.25260.18264160.15317895831196
2.2526-2.39360.19774510.15638058850998
2.3936-2.57830.19194210.16118182860399
2.5783-2.83760.21434440.16358196864099
2.8376-3.24780.19374680.1668282875099
3.2478-4.09020.17874200.145984228842100
4.0902-29.69370.15634780.1538619909799
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)
10.18260.10090.0850.4722-0.10440.43530.0269-0.08570.04280.0529-0.09060.01330.0701-0.10220.03370.1127-0.0251-0.02470.14110.00270.133173.342571.319557.0406
20.18060.03070.15520.05520.04660.2434-0.02710.00940.0809-0.0033-0.01810.0276-0.00350.01570.02450.0747-0.0009-0.02860.0863-0.01360.096679.111678.718349.759
30.23970.0820.12560.13240.07380.1560.1232-0.0093-0.21160.0623-0.0081-0.07690.1996-00.02990.1784-0.0293-0.10480.1021-0.05970.171882.403653.740147.6126
40.00170.0022-0.00830.003-0.01010.0545-0.00340.11670.2110.00110.04860.12960.00360.0009-0.04490.2910.0114-0.01880.50830.06180.404462.806574.458158.0068
50.3324-0.128-0.00010.054-0.00150.00070.013-0.02160.06080.08570.0046-0.0170.0522-0.0178-0.00620.1104-0.02010.00050.07190.01960.045696.443184.330469.2919
60.1664-0.05440.06080.0791-0.07440.07090.0661-0.0306-0.01340.0504-0.0566-0.00970.0902-0.0241-0.00830.1074-0.0317-0.01660.07520.00580.048895.493272.020968.6162
70.0422-0.01750.00190.14310.04790.09620.04970.09690.08730.0017-0.0234-0.11250.00070.05040.01910.06880.00160.0210.12090.03810.107110.130384.187852.271
80.2379-0.14340.2540.33190.05420.44780.0095-0.09030.08570.07620.0036-0.085-0.02290.0302-0.00160.1169-0.0224-0.01970.1315-0.02370.1441106.811489.695374.4864
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 45:117)A45 - 117
3X-RAY DIFFRACTION3(chain A and resid 118:353)A118 - 353
4X-RAY DIFFRACTION4(chain A and resid 354:363)A354 - 363
5X-RAY DIFFRACTION5(chain B and resid 2:43)B2 - 43
6X-RAY DIFFRACTION6(chain B and resid 44:104)B44 - 104
7X-RAY DIFFRACTION7(chain B and resid 105:329)B105 - 329
8X-RAY DIFFRACTION8(chain B and resid 330:365)B330 - 365

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