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- PDB-3r11: Crystal structure of NYSGRC enolase target 200555, a putative dip... -

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Basic information

Entry
Database: PDB / ID: 3r11
TitleCrystal structure of NYSGRC enolase target 200555, a putative dipeptide epimerase from Francisella philomiragia : Mg and Fumarate complex
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, acting on amino acids and derivatives / racemase and epimerase activity / 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
FUMARIC ACID / L-amino acid-D/L-Glu epimerase
Similarity search - Component
Biological speciesFrancisella philomiragia subsp. 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 9, 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_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
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)85,81112
Polymers84,9102
Non-polymers90110
Water12,755708
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-98 kcal/mol
Surface area27400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.930, 120.930, 149.300
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, 718 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-FUM / FUMARIC ACID


Mass: 116.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4O4
#6: 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: 3.21 Å3/Da / Density % sol: 61.73 %
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, 50 mM Fumarate, 30 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: 2→93.971 Å / Num. all: 75220 / Num. obs: 75220 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.6 % / Rsym value: 0.111 / Net I/σ(I): 16.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.1113.30.4081.8144413108370.408100
2.11-2.2413.40.3052.5137369102720.305100
2.24-2.3913.40.2312.112919796390.231100
2.39-2.5813.50.1782.412159590290.178100
2.58-2.8313.60.138511285583060.138100
2.83-3.1613.80.1264.810440875740.126100
3.16-3.6513.90.1115.49320667010.111100
3.65-4.4714.30.0688.88215957410.068100
4.47-6.3214.40.04613.16491745130.046100
6.32-30.71913.10.03715.43419126080.03799.2

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data processing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→30.323 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.9071 / SU ML: 0.16 / σ(F): 0 / Phase error: 15.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1809 3730 5.02 %random
Rwork0.1498 ---
all0.1513 74238 --
obs0.1513 74238 98.8 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.495 Å2 / ksol: 0.385 e/Å3
Displacement parametersBiso max: 84.07 Å2 / Biso mean: 24.7422 Å2 / Biso min: 4.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.3643 Å2-0 Å2-0 Å2
2---0.3643 Å2-0 Å2
3---0.7286 Å2
Refinement stepCycle: LAST / Resolution: 2→30.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5605 0 51 708 6364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085726
X-RAY DIFFRACTIONf_angle_d1.1877744
X-RAY DIFFRACTIONf_chiral_restr0.096916
X-RAY DIFFRACTIONf_plane_restr0.006983
X-RAY DIFFRACTIONf_dihedral_angle_d13.1662099
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 (%)
2-2.02530.21471530.172530268398
2.0253-2.0520.21350.15842536267198
2.052-2.08010.20381200.15462551267198
2.0801-2.10980.19591510.15552531268297
2.1098-2.14130.19951360.15362563269999
2.1413-2.17470.19291320.1462553268598
2.1747-2.21030.19151250.15532590271599
2.2103-2.24840.22621370.15272574271199
2.2484-2.28930.20631300.15172593272398
2.2893-2.33330.18981320.15272585271799
2.3333-2.38090.19251230.14712563268699
2.3809-2.43270.18171410.14462598273999
2.4327-2.48930.18651390.15272571271098
2.4893-2.55150.19831260.15152618274499
2.5515-2.62040.17781330.1472585271899
2.6204-2.69750.19151410.14832608274999
2.6975-2.78450.16851420.15142599274199
2.7845-2.8840.19441570.15112600275799
2.884-2.99930.20261620.154326082770100
2.9993-3.13570.19321440.152726302774100
3.1357-3.30080.18591380.151126512789100
3.3008-3.50730.16111680.141426182786100
3.5073-3.77770.15421400.136326722812100
3.7777-4.1570.16021290.133826962825100
4.157-4.75650.14161320.127327102842100
4.7565-5.98520.15991250.153827622887100
5.9852-30.32650.19911390.18672813295297
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)
10.12120.0360.00620.04690.06360.1010.041-0.06330.03860.0585-0.07070.01990.0328-0.112-0.01170.1196-0.0193-0.02110.1250.01270.100572.90871.803356.8318
20.07140.01270.01240.0080.01940.0657-0.00510.02310.0634-0.01250.01480.00650.0056-0.011-0.0040.0626-0.0097-0.01710.06690.00140.079982.465980.119951.1506
30.01920.00720.00780.00320.00540.0156-0.00530.0186-0.0061-0.03460.00580.01920.0107-0.0310.00780.0716-0.0066-0.0830.0833-0.05450.079871.030772.439941.9888
40.24860.02280.14230.03990.00220.08990.16040.0165-0.44380.00930.0035-0.12870.31610.01920.07890.1759-0.0719-0.1794-0.0196-0.1220.212485.987651.940647.9989
50.0140.0010.00550.0082-0.0040.0038-0.0310.02160.02140.0027-0.01860.0174-0.006-0.0566-0.00330.1727-0.0572-0.10680.2031-0.04110.204263.510364.323650.3043
60.05250.0359-0.03620.0349-0.00870.08550.0819-0.02640.08180.0548-0.02770.00210.0298-0.04360.04940.0853-0.03690.02390.07570.01260.032996.809183.636170.3776
70.0224-0.00440.00280.0138-0.01440.01540.0831-0.0302-0.0280.0693-0.0592-0.00590.081-0.0112-0.00690.1167-0.0349-0.01750.09170.01190.046194.436870.302968.1394
80.0451-0.0441-0.02420.07110.04860.10820.0862-0.01720.07670.0174-0.0109-0.08-0.045-0.0022-0.00340.0739-0.02140.01330.06680.01090.0996108.966985.940864.7206
90.07420.04380.00610.0583-0.0350.05580.09550.04740.0855-0.0923-0.0183-0.0561-0.07140.00350.02850.14670.01810.1160.14880.06450.1461110.53892.931242.269
100.01990.00430.01540.0515-0.0370.05060.02340.02160.0052-0.03880.0163-0.0204-0.00760.0360.02470.1110.01380.06910.17110.00430.0809109.726681.053841.3749
110.0232-0.0136-0.00170.04930.01210.0630.05850.04910.0401-0.0314-0.0164-0.0995-0.01110.0904-0.01640.06070.00950.00640.0881-0.00620.0832109.650574.860453.8221
120.00460.0080.01120.02070.00670.04950.0559-0.00310.03610.01450.0254-0.0118-0.01930.0483-0.02740.0587-0.02610.01170.1103-0.00280.1513110.033387.123664.7136
130.04640.01470.04860.03860.02690.05770.0281-0.05120.01480.0570.0238-0.0467-0.00750.025-0.00320.1264-0.035-0.02510.144-0.03230.1272106.740988.844675.1575
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 131:332)A0
5X-RAY DIFFRACTION5chain 'A' and (resseq 333:363)A0
6X-RAY DIFFRACTION6chain 'B' and (resseq 2:51)B0
7X-RAY DIFFRACTION7chain 'B' and (resseq 52:98)B0
8X-RAY DIFFRACTION8chain 'B' and (resseq 99:155)B0
9X-RAY DIFFRACTION9chain 'B' and (resseq 156:211)B0
10X-RAY DIFFRACTION10chain 'B' and (resseq 212:237)B0
11X-RAY DIFFRACTION11chain 'B' and (resseq 238:301)B0
12X-RAY DIFFRACTION12chain 'B' and (resseq 302:332)B0
13X-RAY DIFFRACTION13chain 'B' and (resseq 333:365)B0

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