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- PDB-3uj2: CRYSTAL STRUCTURE OF AN ENOLASE FROM ANAEROSTIPES CACCAE (EFI TAR... -

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Entry
Database: PDB / ID: 3uj2
TitleCRYSTAL STRUCTURE OF AN ENOLASE FROM ANAEROSTIPES CACCAE (EFI TARGET EFI-502054) WITH BOUND MG AND SULFATE
ComponentsEnolase 1
KeywordsLYASE / Enolase / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / glycolytic process / magnesium ion binding / cell surface / extracellular region
Similarity search - Function
Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase-like C-terminal domain ...Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / 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
Biological speciesAnaerostipes caccae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 1e9i / Resolution: 2 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Hillerich, B. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. ...Vetting, M.W. / Toro, R. / Bhosle, R. / 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 ANAEROSTIPES CACCAE (EFI TARGET EFI-502054) WITH BOUND MG AND SULFATE
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / 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. ...Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / 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 7, 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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 1
B: Enolase 1
C: Enolase 1
D: Enolase 1
E: Enolase 1
F: Enolase 1
G: Enolase 1
H: Enolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)390,90536
Polymers388,7898
Non-polymers2,11628
Water29,1121616
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26960 Å2
ΔGint-394 kcal/mol
Surface area110100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)282.350, 282.210, 119.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-474-

HOH

21B-560-

HOH

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Components

#1: Protein
Enolase 1 / 2-phospho-D-glycerate hydro-lyase 1 / 2-phosphoglycerate dehydratase 1


Mass: 48598.645 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaerostipes caccae (bacteria) / Strain: DSM 14662 / Gene: eno1, ANACAC_00540 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B0MAG5, phosphopyruvate hydratase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1616 / 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: 3.05 Å3/Da / Density % sol: 59.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol, 5 mM DTT, 5 mM MgCl2; Reservoir (2M Ammonium Sulfate, 100 mM Citrate pH 5.5); Cryoprotection (2M Magnesium Sulfate, 100 mM Bis-Tris ...Details: Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol, 5 mM DTT, 5 mM MgCl2; Reservoir (2M Ammonium Sulfate, 100 mM Citrate pH 5.5); Cryoprotection (2M Magnesium Sulfate, 100 mM Bis-Tris pH 5.3, 20% glycerol), VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Sep 15, 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→50 Å / Num. all: 202194 / Num. obs: 202194 / % possible obs: 63 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 23.1 Å2
Reflection shellResolution: 2→2.1 Å / % possible all: 10

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: 1e9i
Starting model: 1e9i

1e9i


Resolution: 2→46.029 Å / Occupancy max: 1 / Occupancy min: 0.43 / FOM work R set: 0.7862 / SU ML: 0.26 / σ(F): 0 / Phase error: 27.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2309 1301 0.64 %RANDOM
Rwork0.1724 ---
all0.1728 202194 --
obs0.1728 202194 63.59 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.13 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 136.83 Å2 / Biso mean: 33.0003 Å2 / Biso min: 0.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.0167 Å2-0 Å2-0 Å2
2--1.2917 Å2-0 Å2
3----3.9438 Å2
Refinement stepCycle: LAST / Resolution: 2→46.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25624 0 108 1616 27348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00926165
X-RAY DIFFRACTIONf_angle_d1.04535384
X-RAY DIFFRACTIONf_chiral_restr0.0653939
X-RAY DIFFRACTIONf_plane_restr0.0044624
X-RAY DIFFRACTIONf_dihedral_angle_d14.1959612
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.080.3269250.28073354337910
2.08-2.17470.3302640.25669575963927
2.1747-2.28930.3133830.2459140811416440
2.2893-2.43280.31711240.2356187501887454
2.4328-2.62060.29761560.2249233802353667
2.6206-2.88430.29891860.2173291302931683
2.8843-3.30150.25792130.1878328883310194
3.3015-4.15920.2042240.1413342713449597
4.1592-46.04090.16192260.1315354643569099
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)
10.0062-0.00990.01490.0003-0.0060.0218-0.0170.0247-0.0112-0.01490.00860.01760.00620.0227-0.01090.041-0.00320.0702-0.0033-0.0751-0.2694-77.26233.00116.9037
20.0867-0.00130.00310.010.00120.03460.01580.0107-0.23180.0169-0.04080.09680.1156-0.0482-0.01910.0251-0.13610.0923-0.17930.1159-0.073-87.0711-16.821329.2876
30.03280.0182-0.00190.0040.00660.06430.01-0.0739-0.02150.02740.0018-0.0070.0022-0.03790.00610.049-0.00680.05990.01180.0985-0.2625-60.43873.108842.8494
40.03140.0006-0.02360.00380.00370.02190.00850.0025-0.02720.0123-0.0035-0.00480.0188-0.00190.0030.14980.02490.040.109-0.02670.1393-52.3522-20.294127.3375
50.04770.01630.02060.01320.03170.07060.03-0.002-0.19050.0445-0.024-0.10920.10350.0841-0.02750.01060.10620.0234-0.0664-0.086-0.0738-47.8316-13.817329.3726
60.03310.0058-0.03030.0482-0.00770.06280.04890.01570.0553-0.07440.0463-0.0579-0.06260.00250.0645-0.005-0.03430.13990.04550.0802-0.0103-40.513626.347617.7965
70.0186-0.00250.02850.12060.01070.07230.00040.0019-0.0096-0.00710.0476-0.33270.04480.2103-0.0255-0.30210.0531-0.02020.1048-0.05560.1674-21.279515.842230.6236
80.02280.0002-0.01260.0194-0.01450.04040.0183-0.01790.06070.00690.0459-0.0467-0.01570.020.00660.0288-0.0333-0.02860.0642-0.06570.1418-41.750842.075744.5491
90.03320.0367-0.0270.0325-0.03250.0318-0.0213-0.02340.1078-0.00420.0107-0.2078-0.10340.1368-0.0447-0.0763-0.2350.1280.0216-0.06530.4552-23.747654.764732.1446
100.08250.04070.02480.0885-0.00130.07890.03070.01840.0767-0.03240.01660.10090.0064-0.0144-0.01650.06240.0014-0.01530.1260.02270.126-100.581339.42318.0474
110.0717-0.0049-0.03160.01650.01730.0351-0.04220.05250.1443-0.0195-0.04130.2412-0.0494-0.1317-0.0608-0.15080.09860.11360.1246-0.03460.4898-119.89448.876131.325
120.0289-0.0135-0.02620.01180.00770.01950.026-0.04240.03070.08710.02310.0628-0.00860.0130.04360.02460.02170.16730.0835-0.0963-0.0577-99.649521.801943.5511
130.0207-0.0253-0.02180.1514-0.00120.0449-0.06780.0162-0.08440.0576-0.00950.29980.0923-0.162-0.0849-0.2242-0.18460.10110.02370.01360.1128-117.529210.045930.1065
140.0378-0.009-0.01670.00330.00260.00960.00990.05760.0599-0.0410.04690.0086-0.0211-0.01440.03090.1752-0.05860.02410.03810.04810.2438-63.925462.756419.1233
15-0.00610.0104-0.00460.02640.0130.00320.0258-0.01040.1476-0.0081-0.0049-0.0737-0.05350.0108-0.03270.0717-0.17910.0861-0.3135-0.1020.4122-54.094781.542432.917
160.030.0152-0.01590.0738-0.00950.0170.0595-0.04380.0803-0.0138-0.00720.0366-0.03160.0087-0.01260.1058-0.040.03720.0819-0.03030.2073-80.932860.844144.9807
170.0026-0.00960.00810.0354-0.00780.03340.0294-0.01040.18490.003-0.02050.0866-0.1233-0.0758-0.03120.12360.09030.0731-0.08870.03990.5444-93.000679.207832.5862
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:152)A1 - 152
2X-RAY DIFFRACTION2chain 'A' and (resseq 153:426)A153 - 426
3X-RAY DIFFRACTION3chain 'B' and (resseq 1:152)B1 - 152
4X-RAY DIFFRACTION4chain 'B' and (resseq 153:175)B153 - 175
5X-RAY DIFFRACTION5chain 'B' and (resseq 176:426)B176 - 426
6X-RAY DIFFRACTION6chain 'C' and (resseq 1:152)C1 - 152
7X-RAY DIFFRACTION7chain 'C' and (resseq 153:426)C153 - 426
8X-RAY DIFFRACTION8chain 'D' and (resseq 1:152)D1 - 152
9X-RAY DIFFRACTION9chain 'D' and (resseq 153:426)D153 - 426
10X-RAY DIFFRACTION10chain 'E' and (resseq 1:152)E1 - 152
11X-RAY DIFFRACTION11chain 'E' and (resseq 153:426)E153 - 426
12X-RAY DIFFRACTION12chain 'F' and (resseq 1:152)F1 - 152
13X-RAY DIFFRACTION13chain 'F' and (resseq 153:426)F153 - 426
14X-RAY DIFFRACTION14chain 'G' and (resseq 1:152)G1 - 152
15X-RAY DIFFRACTION15chain 'G' and (resseq 153:426)G153 - 426
16X-RAY DIFFRACTION16chain 'H' and (resseq 1:152)H1 - 152
17X-RAY DIFFRACTION17chain 'H' and (resseq 153:426)H153 - 426

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