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- PDB-3ugv: Crystal structure of an enolase from alpha pretobacterium bal199 ... -

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Basic information

Entry
Database: PDB / ID: 3ugv
TitleCrystal structure of an enolase from alpha pretobacterium bal199 (EFI TARGET EFI-501650) with bound MG
ComponentsEnolase
KeywordsLYASE / Enolase / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


amino acid catabolic process / metal ion binding
Similarity search - Function
Mandelate racemase / muconate lactonizing enzyme family signature 2. / Mandelate racemase/muconate lactonizing enzyme, conserved site / 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 ...Mandelate racemase / muconate lactonizing enzyme family signature 2. / Mandelate racemase/muconate lactonizing enzyme, conserved site / 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
NICKEL (II) ION / Probable mandelate racemase
Similarity search - Component
Biological speciesalpha proteobacterium BAL199 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Wasserman, S.R. / Morisco, L.L. / Hillerich, B. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Wasserman, S.R. / Morisco, L.L. / Hillerich, B. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: to be published
Title: Crystal structure of an enolase from alpha pretobacterium bal199 (EFI TARGET EFI-501650) with bound MG
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Wasserman, S.R. / Morisco, L.L. / Hillerich, B. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / ...Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Wasserman, S.R. / Morisco, L.L. / Hillerich, B. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionNov 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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_atom_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_atom_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: Enolase
B: Enolase
C: Enolase
D: Enolase
E: Enolase
F: Enolase
G: Enolase
H: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)344,11629
Polymers343,5048
Non-polymers61321
Water15,601866
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33220 Å2
ΔGint-312 kcal/mol
Surface area83140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.711, 152.984, 173.535
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Enolase /


Mass: 42937.938 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) alpha proteobacterium BAL199 (bacteria)
Gene: BAL199_22462 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8TYI5
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 866 / 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: 2.95 Å3/Da / Density % sol: 58.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol, 5 mM DTT, 5 mM MgCl2); Reservoir (200 mM MgAcetate, 100 mM NaCac pH 6.5, 30% MPD); Cryoprotection (Reservoir), VAPOR DIFFUSION, ...Details: Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol, 5 mM DTT, 5 mM MgCl2); Reservoir (200 mM MgAcetate, 100 mM NaCac pH 6.5, 30% MPD); Cryoprotection (Reservoir), VAPOR DIFFUSION, SITTING DROP, 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: Jul 27, 2011 / 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: 2.3→173.535 Å / Num. all: 175465 / Num. obs: 175465 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 29.2 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.423.70.4811.692528251260.48196.6
2.42-2.573.90.3552.192390237940.35596.7
2.57-2.754.20.255393576224880.25597.2
2.75-2.974.40.1644.792595211700.16497.9
2.97-3.254.50.1087.188715195550.10898.1
3.25-3.644.60.07110.481502177560.07198.3
3.64-4.24.60.0491471893157620.04998.5
4.2-5.144.60.03917.261063134150.03998.7
5.14-7.274.50.03618.747699105130.03698.9
7.27-152.9844.20.02425.32483758860.02497.5

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MDR

1mdr


Resolution: 2.3→114.642 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.8616 / SU ML: 0.29 / σ(F): 0 / σ(I): 0 / Phase error: 20.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2077 8248 4.97 %RANDOM
Rwork0.1605 ---
all0.1628 166037 --
obs0.1628 166037 92.19 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.086 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso max: 159.43 Å2 / Biso mean: 36.7372 Å2 / Biso min: 5.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.7403 Å20 Å2-0 Å2
2--1.8742 Å2-0 Å2
3----2.6145 Å2
Refinement stepCycle: LAST / Resolution: 2.3→114.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22354 0 21 866 23241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01223048
X-RAY DIFFRACTIONf_angle_d1.05431539
X-RAY DIFFRACTIONf_chiral_restr0.073443
X-RAY DIFFRACTIONf_plane_restr0.0054065
X-RAY DIFFRACTIONf_dihedral_angle_d13.6678334
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.32610.3192440.24964578482281
2.3261-2.35350.32382410.254632487382
2.3535-2.38220.31032470.24264697494483
2.3822-2.41240.30552510.22384803505485
2.4124-2.44410.29452440.22584795503985
2.4441-2.47760.2852480.21824863511185
2.4776-2.5130.26042340.21535000523488
2.513-2.55050.28112500.20864918516887
2.5505-2.59040.27522690.25073534289
2.5904-2.63280.26912400.2015069530989
2.6328-2.67820.26142390.19465081532090
2.6782-2.72690.27272700.19725175544591
2.7269-2.77940.25642710.1865227549892
2.7794-2.83610.2532820.18085257553993
2.8361-2.89780.22982440.18155328557293
2.8978-2.96520.24893000.17735383568395
2.9652-3.03940.2112760.1745405568195
3.0394-3.12160.24022940.17445430572496
3.1216-3.21340.21322710.17075497576896
3.2134-3.31720.21962780.16375488576696
3.3172-3.43570.1943000.1635475577597
3.4357-3.57330.19293140.15625544585898
3.5733-3.73590.19073200.14215581590198
3.7359-3.93290.15832800.13175597587798
3.9329-4.17930.15713010.12355599590098
4.1793-4.5020.1632860.11775677596398
4.502-4.95510.15323060.11095631593798
4.9551-5.67210.17663110.13075696600798
5.6721-7.14610.18773280.13695709603798
7.1461-114.78480.16483090.15145581589092
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)
10.01790.0070.00120.0051-0.00090.00460.0088-0.02570.0160.0023-0.00240.0325-0.0157-0.0425-0.00230.07820.0829-0.00020.2072-0.01980.225190.1683106.3253116.8793
20.01940.0132-0.01430.0163-0.00580.01630.01710.07330.0101-0.0450.02520.05190.0212-0.0820.06070.0418-0.0208-0.08090.14180.06070.046198.486291.3875100.548
30.0001-00.00070.0104-0.01420.0208-0.0135-0.00080.0221-0.01080.00030.0216-0.0157-0.0184-0.01220.06880.0714-0.03180.11360.0340.130394.5798109.8356101.4492
40.05070.0365-0.00170.0385-0.00690.0017-0.00060.00760.01230.024-0.00310.05780.0429-0.0412-0.00880.2529-0.23860.02870.28850.01490.283178.279150.8878121.2141
50.02080.00840.00260.0275-0.00630.0057-0.00110.0337-0.0519-0.0560.0320.03620.0445-0.03470.02610.1782-0.1672-0.0530.216-0.04450.145591.528458.4443103.1355
60.0070.00190.00620.00060.00160.0054-0.00420.00970.0079-0.0018-0.00230.01370.0058-0.0066-0.00260.1761-0.1654-0.03110.2586-0.00630.22372.003855.2141109.1644
70.01330.00790.00240.0934-0.01930.0111-0.0122-0.0093-0.0083-0.00190.00310.02670.01130.0117-0.00130.5590.14180.09090.37890.04590.4633137.57435.714102.4518
80.0882-0.0053-0.03450.0103-0.00710.0467-0.07580.0455-0.1737-0.0511-0.00550.02670.18590.0486-0.05570.37740.02460.04150.0665-0.06160.1904125.529644.0166102.4465
90.01190.01850.00090.0496-0.01550.03070.0006-0.0156-0.01360.013-0.0192-0.069-0.01150.02280.01510.2178-0.0639-0.0560.23590.03410.2791145.984297.266597.412
100.0373-0.0272-0.03290.1847-0.01920.0953-0.03270.06240.039-0.06610.0041-0.1112-0.05510.05570.00820.0622-0.01510.00470.11040.00480.0687137.373585.391897.7827
110.00120.0032-0.00170.0071-0.00470.0034-0.0240.0101-0.0472-0.02110.0053-0.00660.0579-0.0160.0010.4664-0.15620.05370.17780.01610.381698.628933.514126.0874
120.03890.00150.03020.1118-0.02970.0371-0.0006-0.0816-0.06460.0187-0.0279-0.02120.05040.0041-0.02150.22670.00190.04610.13370.09720.1222109.577151.9661141.3185
130.0007-0.0032-0.00240.01860.01460.0124-0.005-0.0257-0.05050.0114-0.00840.00160.0429-0.0106-0.01260.3036-0.03520.03040.08550.08150.2236110.736337.6908133.5808
140.0319-0.029-0.02570.0420.00230.0663-0.0370.0280.0007-0.02450.03010.0808-0.02-0.14720.00250.15440.0192-0.03510.3360.05780.297976.584988.3021127.8196
150.0594-0.0033-0.06470.0827-0.01980.1496-0.0223-0.00420.00750.07820.06790.0953-0.024-0.08860.0150.0715-0.0180.03640.16670.04280.087191.500580.6114140.2482
160.02180.01-0.00840.008-0.00110.00510.00960.01270.0332-0.00360.00970.0088-0.00210.0046-0.00290.1934-0.0478-0.01760.20180.01150.228134.9765111.7115123.0168
170.17920.0367-0.01820.0904-0.00810.0890.0472-0.00830.08930.05760.0218-0.0323-0.0270.10580.00490.0881-0.0121-0.01570.1008-0.03460.0846125.6096101.3832127.4432
180.0017-0.0027-0.00090.0030.00140.00070.01440.0116-0.0063-0.0060.0035-0.0110.00840.0115-0.00240.21620.1480.02880.23310.02450.2543155.048352.7165122.0352
190.048-0.02660.00820.034-0.00930.0361-0.0217-0.048-0.04280.03630.0188-0.07290.07810.07250.00480.06180.1472-0.04720.1050.02360.0899145.230162.8204125.4105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 4:119)A4 - 119
2X-RAY DIFFRACTION2chain 'A' and (resseq 120:316)A120 - 316
3X-RAY DIFFRACTION3chain 'A' and (resseq 317:366)A317 - 366
4X-RAY DIFFRACTION4chain 'B' and (resseq 4:139)B4 - 139
5X-RAY DIFFRACTION5chain 'B' and (resseq 140:316)B140 - 316
6X-RAY DIFFRACTION6chain 'B' and (resseq 317:366)B317 - 366
7X-RAY DIFFRACTION7chain 'C' and (resseq 4:42)C4 - 42
8X-RAY DIFFRACTION8chain 'C' and (resseq 43:366)C43 - 366
9X-RAY DIFFRACTION9chain 'D' and (resseq 4:42)D4 - 42
10X-RAY DIFFRACTION10chain 'D' and (resseq 43:366)D43 - 366
11X-RAY DIFFRACTION11chain 'E' and (resseq 4:119)E4 - 119
12X-RAY DIFFRACTION12chain 'E' and (resseq 120:267)E120 - 267
13X-RAY DIFFRACTION13chain 'E' and (resseq 268:366)E268 - 366
14X-RAY DIFFRACTION14chain 'F' and (resseq 4:119)F4 - 119
15X-RAY DIFFRACTION15chain 'F' and (resseq 120:367)F120 - 367
16X-RAY DIFFRACTION16chain 'G' and (resseq 4:42)G4 - 42
17X-RAY DIFFRACTION17chain 'G' and (resseq 43:366)G43 - 366
18X-RAY DIFFRACTION18chain 'H' and (resseq 4:42)H4 - 42
19X-RAY DIFFRACTION19chain 'H' and (resseq 43:366)H43 - 366

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