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- PDB-4gir: Crystal structure of an enolase family member from vibrio harveyi... -

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Basic information

Entry
Database: PDB / ID: 4gir
TitleCrystal structure of an enolase family member from vibrio harveyi (efi-target 501692) with homology to mannonate dehydratase, with mg, ethylene glycol and sulfate bound (ordered loops, space group P41212)
ComponentsEnolase
KeywordsLYASE / ENOLASE / putative mannonate dehydratase / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


amino acid catabolic process / magnesium ion binding
Similarity search - Function
D-mannonate dehydratase-like / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / 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 ...D-mannonate dehydratase-like / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / 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-galactonate dehydratase family member VME_00770
Similarity search - Component
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: crystal structure of an enolase family member from vibrio harveyi (efi-target 501692) with homology to mannonate dehydratase, with mg, ethylene glycol and sulfate bound (ordered loops, space group P41212)
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / ...Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionAug 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,03527
Polymers192,9014
Non-polymers1,13423
Water24,4461357
1
A: Enolase
B: Enolase
C: Enolase
D: Enolase
hetero molecules

A: Enolase
B: Enolase
C: Enolase
D: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)388,06954
Polymers385,8028
Non-polymers2,26846
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area58350 Å2
ΔGint-502 kcal/mol
Surface area89390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.836, 146.836, 169.524
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-560-

HOH

21C-734-

HOH

31C-796-

HOH

41C-818-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Enolase /


Mass: 48225.191 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (bacteria) / Strain: 1DA3 / Gene: VME_00770 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0X4R4

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Non-polymers , 6 types, 1380 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1357 / 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: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffuction / pH: 7.5
Details: Protein (10 mM Hepes pH 7.5, 150 mM NaCl, 10% glycerol, 1 mM DTT, 5 mM MgCl); Reservoir (2 M Ammonium Sulfate); Cryoprotection (Reservoir, + 20% ethylene glycol and 50 mM MgCl), sitting drop ...Details: Protein (10 mM Hepes pH 7.5, 150 mM NaCl, 10% glycerol, 1 mM DTT, 5 mM MgCl); Reservoir (2 M Ammonium Sulfate); Cryoprotection (Reservoir, + 20% ethylene glycol and 50 mM MgCl), sitting drop vapor diffuction, 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→110.99 Å / Num. all: 113621 / Num. obs: 113621 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.133 / Rsym value: 0.133 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.115.50.6731.179331143440.67380.7
2.11-2.245.40.4751.676638141120.47583.8
2.24-2.395.30.3492.174201140050.34988.2
2.39-2.585.30.262.973321137990.2692.8
2.58-2.835.50.1853.973464132970.18597
2.83-3.1660.1365.373082122550.13698.1
3.16-3.656.40.0976.970208109130.09798.6
3.65-4.477.10.0718.76602193570.07199
4.47-6.327.30.069.85348973630.0699.2
6.32-42.3866.80.0597.72840541760.05998.1

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4GGH

4ggh


Resolution: 2→38.23 Å / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.8853 / SU ML: 0.21 / σ(F): 0 / σ(I): 0 / Phase error: 18.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1926 2826 2.49 %RANDOM
Rwork0.1481 ---
all0.1492 113452 --
obs0.1492 113452 90.94 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.26 Å2 / Biso mean: 19.6813 Å2 / Biso min: 0.43 Å2
Refinement stepCycle: LAST / Resolution: 2→38.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12973 0 54 1357 14384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913428
X-RAY DIFFRACTIONf_angle_d1.08818295
X-RAY DIFFRACTIONf_chiral_restr0.0781940
X-RAY DIFFRACTIONf_plane_restr0.0052416
X-RAY DIFFRACTIONf_dihedral_angle_d13.8964929
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.03450.26461200.21394751487179
2.0345-2.07150.25111360.20254720485679
2.0715-2.11130.26661040.19484893499781
2.1113-2.15440.26391280.18164869499781
2.1544-2.20120.21651210.18225010513183
2.2012-2.25240.2461380.17365106524485
2.2524-2.30880.24361150.16385199531486
2.3088-2.37120.241350.15575340547589
2.3712-2.44090.2051570.15645386554390
2.4409-2.51970.21331540.1595560571492
2.5197-2.60980.21641530.15175715586894
2.6098-2.71420.19551280.1525831595996
2.7142-2.83770.18911550.15165852600797
2.8377-2.98730.20071670.14975919608697
2.9873-3.17430.18221340.14495959609398
3.1743-3.41930.21490.14126002615198
3.4193-3.76310.16641490.1276035618498
3.7631-4.3070.14071610.11196090625199
4.307-5.42390.13371510.11876162631399
5.4239-38.2370.17921710.15966227639896
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)
10.5106-0.0327-0.20070.5456-0.17260.3001-0.01330.0957-0.0093-0.00620.01210.12320.0555-0.13490.01720.0961-0.03350.00020.1644-0.0220.1415-41.4512-12.5686-44.6317
20.2880.14320.25160.98970.69231.21640.0496-0.1613-0.00820.2002-0.06450.10480.0949-0.17810.02470.1599-0.04410.04420.1746-0.01640.131-30.1465-17.8852-20.0626
30.038-0.11570.07632.2337-0.75930.3037-0.028-0.0930.01270.38890.03250.2042-0.0535-0.0957-0.00780.1804-0.00180.04040.1936-0.01350.1325-27.41873.4425-13.3885
40.07040.07380.06190.50680.11680.3866-0.00620.0096-0.00090.06990.00280.08670.0439-0.06860.00230.0995-0.0140.02770.1154-0.00160.1126-27.7075-8.4372-28.3695
50.3869-0.04280.39570.3685-0.19230.4921-0.0215-0.06180.05710.03250.01660.1045-0.0994-0.13390.00990.09850.02540.01750.1687-0.01570.1443-41.734516.1726-39.4764
60.21-0.1333-0.10160.0876-0.06550.40160.00660.0488-0.0088-0.0477-0.01330.0422-0.0073-0.089-0.0020.10330.0132-0.02230.1546-0.00580.1096-30.693815.0574-62.5926
70.7270.7745-0.20173.0689-0.85980.7511-0.09730.1078-0.102-0.28240.1009-0.11890.1483-0.0565-0.01820.12220.0053-0.01880.1425-0.02950.098-23.9178-5.6779-73.0456
80.1031-0.0793-0.10030.4524-0.06740.3953-0.00560.017-0.0088-0.02760.01810.059-0.0057-0.0489-0.00930.09050.0064-0.01810.1318-0.00370.1085-26.64789.8325-58.1292
91.89180.1898-1.47791.0729-0.23933.25590.09190.0052-0.1607-0.06350.0474-0.0990.0995-0.0378-0.10180.19560.0308-0.0380.09650.0020.224113.5998-45.5133-38.4771
100.3317-0.02120.09660.3975-0.07480.20980.01770.03-0.1012-0.01550.0198-0.02610.10650.0631-0.02940.13750.0202-0.01190.1023-0.01260.129514.4216-35.6352-40.5352
110.79670.18870.25920.57710.03160.7932-0.0898-0.2022-0.26040.08630.06740.06780.1704-0.0983-0.01470.2658-0.0124-0.00070.19920.05250.19153.5782-28.9855-10.2681
122.68140.71921.00310.7540.29390.73830.0393-0.34120.05060.1169-0.08560.08040.0635-0.12230.02740.2049-0.01440.0410.15310.0390.1044-8.611-24.2255-13.6153
130.4661-0.106-0.1380.1583-0.04930.30160.0049-0.0315-0.01750.03550.0037-0.00780.00890.0048-0.00840.1502-0.0001-0.00850.10540.00460.10635.9591-19.823-28.7517
140.01160.0130.02480.48270.330.23360.0846-0.1566-0.19730.08270.00530.09380.21940.0928-0.07290.20870.0168-0.03770.14820.04070.223117.4215-35.8335-23.0519
150.82140.3006-0.36090.3153-0.27320.678-0.1052-0.0069-0.3174-0.14860.0844-0.11310.1520.15310.01060.22620.0646-0.05070.09730.03510.265221.5031-42.4605-29.46
160.9935-0.9591-0.48250.93980.41460.2069-0.0397-0.1179-0.10240.07130.0545-0.02790.1174-0.0060.00220.222-0.0151-0.00460.13750.02180.18-8.0179-37.0737-26.9509
170.5920.03610.42330.64980.04950.50760.0284-0.096-0.13410.124-0.00890.06670.1528-0.10650.01930.1451-0.03220.01010.0841-0.01170.123-17.6421-37.3558-44.8924
180.39340.31350.35570.29060.18920.60860.05750.3041-0.2826-0.0569-0.01030.01970.14070.0306-0.05320.22480.00820.00680.1968-0.06690.1773-3.5715-26.6122-76.3771
192.9646-0.96091.3521.0291-0.57711.08810.08120.42630.0665-0.0993-0.1287-0.14970.03040.13990.02840.1470.00420.01880.1702-0.04380.11135.9439-21.9152-73.0217
200.38550.12770.02320.1424-0.02520.33430.00220.0546-0.0727-0.01430.0103-0.01930.0556-0.0075-0.01350.1227-0.00340.00050.1177-0.02890.1121-8.7745-25.1172-58.6633
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 3:104)A3 - 104
2X-RAY DIFFRACTION2chain 'A' and (resseq 105:144)A105 - 144
3X-RAY DIFFRACTION3chain 'A' and (resseq 145:196)A145 - 196
4X-RAY DIFFRACTION4chain 'A' and (resseq 197:399)A197 - 399
5X-RAY DIFFRACTION5chain 'B' and (resseq -11:83)B-11 - 83
6X-RAY DIFFRACTION6chain 'B' and (resseq 84:164)B84 - 164
7X-RAY DIFFRACTION7chain 'B' and (resseq 165:196)B165 - 196
8X-RAY DIFFRACTION8chain 'B' and (resseq 197:399)B197 - 399
9X-RAY DIFFRACTION9chain 'C' and (resseq 3:28)C3 - 28
10X-RAY DIFFRACTION10chain 'C' and (resseq 29:131)C29 - 131
11X-RAY DIFFRACTION11chain 'C' and (resseq 132:164)C132 - 164
12X-RAY DIFFRACTION12chain 'C' and (resseq 165:196)C165 - 196
13X-RAY DIFFRACTION13chain 'C' and (resseq 197:326)C197 - 326
14X-RAY DIFFRACTION14chain 'C' and (resseq 327:355)C327 - 355
15X-RAY DIFFRACTION15chain 'C' and (resseq 356:376)C356 - 376
16X-RAY DIFFRACTION16chain 'C' and (resseq 377:399)C377 - 399
17X-RAY DIFFRACTION17chain 'D' and (resseq -11:131)D-11 - 131
18X-RAY DIFFRACTION18chain 'D' and (resseq 132:167)D132 - 167
19X-RAY DIFFRACTION19chain 'D' and (resseq 168:196)D168 - 196
20X-RAY DIFFRACTION20chain 'D' and (resseq 197:399)D197 - 399

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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