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- PDB-4gis: crystal structure of an enolase family member from vibrio harveyi... -

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Basic information

Entry
Database: PDB / ID: 4gis
Titlecrystal structure of an enolase family member from vibrio harveyi (efi-target 501692) with homology to mannonate dehydratase, with mg, glycerol and dicarboxylates bound (mixed loops, space group I4122)
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
MALEIC ACID / MALONIC ACID / D-galactonate dehydratase family member VME_00770
Similarity search - Component
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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, glycerol and dicarboxylates bound (mixed loops, space group I4122)
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 1.1Apr 29, 2015Group: Non-polymer description
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
B: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,13713
Polymers96,4502
Non-polymers68711
Water14,196788
1
A: Enolase
B: Enolase
hetero molecules

A: Enolase
B: Enolase
hetero molecules

A: Enolase
B: Enolase
hetero molecules

A: Enolase
B: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)388,54952
Polymers385,8028
Non-polymers2,74744
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
crystal symmetry operation10_545-x,-y-1,z1
crystal symmetry operation16_445-y-1/2,-x-1/2,-z+1/21
Buried area59280 Å2
ΔGint-335 kcal/mol
Surface area89580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.195, 181.195, 115.835
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

21A-507-

HOH

31A-566-

HOH

41A-670-

HOH

51A-683-

HOH

61A-764-

HOH

71B-659-

HOH

81B-687-

HOH

91B-697-

HOH

101B-788-

HOH

111B-885-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Enolase /


Mass: 48225.191 Da / Num. of mol.: 2
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, 799 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-MAE / MALEIC ACID / Maleic acid


Mass: 116.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 788 / 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: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffuction / pH: 7
Details: Protein (10 mM Hepes pH 7.5, 150 mM NaCl, 10% glycerol, 1 mM DTT, 5 mM MgCl); Reservoir (35% Tascimate pH 7.0); Cryoprotection (Reservoir, + 20% glycerol and 50 mM MgCl), sitting drop vapor ...Details: Protein (10 mM Hepes pH 7.5, 150 mM NaCl, 10% glycerol, 1 mM DTT, 5 mM MgCl); Reservoir (35% Tascimate pH 7.0); Cryoprotection (Reservoir, + 20% glycerol 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, 2012 / 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: 1.8→128.124 Å / Num. all: 88533 / Num. obs: 88533 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.6 % / Rmerge(I) obs: 0.133 / Rsym value: 0.133 / Net I/σ(I): 14.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.9140.6831.1179753128150.683100
1.9-2.0114.20.4721.3171690120970.472100
2.01-2.1514.40.3142164691114070.314100
2.15-2.3214.70.2212156535106330.221100
2.32-2.55150.1624.614694198140.162100
2.55-2.85150.1444.613359288990.144100
2.85-3.29150.1294.811861879130.129100
3.29-4.0214.90.099610006267040.099100
4.02-5.6914.80.045127763852520.045100
5.69-29.006140.03515.84205729990.03599.3

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4GGH

4ggh


Resolution: 1.8→29.006 Å / Occupancy max: 1 / Occupancy min: 0.34 / FOM work R set: 0.885 / SU ML: 0.15 / σ(F): 0 / σ(I): 0 / Phase error: 18.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1833 4439 5.02 %RANDOM
Rwork0.1508 ---
all0.1524 88502 --
obs0.1524 88502 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.73 Å2 / Biso mean: 19.1661 Å2 / Biso min: 3.06 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6489 0 39 788 7316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076903
X-RAY DIFFRACTIONf_angle_d1.1189411
X-RAY DIFFRACTIONf_chiral_restr0.079988
X-RAY DIFFRACTIONf_plane_restr0.0051253
X-RAY DIFFRACTIONf_dihedral_angle_d14.5482557
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.82050.23311460.192327462892
1.8205-1.84190.24931520.190927802932
1.8419-1.86430.2521330.185827962929
1.8643-1.88790.22621390.190227712910
1.8879-1.91280.25041530.190527742927
1.9128-1.9390.29051410.211327732914
1.939-1.96670.23871440.172427682912
1.9667-1.9960.2371440.173527862930
1.996-2.02720.19771500.159927592909
2.0272-2.06040.21351520.163327802932
2.0604-2.09590.20221430.162228042947
2.0959-2.1340.18731490.146727822931
2.134-2.17510.19991470.148827632910
2.1751-2.21940.18711220.15328052927
2.2194-2.26770.20591480.167627932941
2.2677-2.32040.2011600.149527692929
2.3204-2.37840.19611730.148327622935
2.3784-2.44270.19111430.15127842927
2.4427-2.51450.19121540.150828132967
2.5145-2.59560.19361520.158127832935
2.5956-2.68840.18071440.156227952939
2.6884-2.79590.1841320.154128292961
2.7959-2.9230.17491710.154427942965
2.923-3.0770.17651490.152428002949
3.077-3.26950.17091370.154628472984
3.2695-3.52160.1521340.134828402974
3.5216-3.87520.1381660.123728072973
3.8752-4.43430.14871440.116328713015
4.4343-5.58020.14321580.130828823040
5.5802-29.010.18071590.157930073166

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