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- PDB-3thu: Crystal structure of an enolase from sphingomonas sp. ska58 (efi ... -

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Basic information

Entry
Database: PDB / ID: 3thu
TitleCrystal structure of an enolase from sphingomonas sp. ska58 (efi target efi-501683) with bound mg
ComponentsMandelate racemase / muconate lactonizing enzyme family protein
KeywordsLYASE / Enolase / mannonate dehydratase related protein / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


mannonate dehydratase / mannonate dehydratase activity / amino acid catabolic process / carbohydrate 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-mannonate dehydratase
Similarity search - Component
Biological speciesSphingomonas sp. SKA58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 sphingomonas sp. ska58 (efi target efi-501683) 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
DepositionAug 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Structure summary
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Sep 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_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.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: Mandelate racemase / muconate lactonizing enzyme family protein
B: Mandelate racemase / muconate lactonizing enzyme family protein
C: Mandelate racemase / muconate lactonizing enzyme family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,99622
Polymers143,1153
Non-polymers88119
Water20,5731142
1
A: Mandelate racemase / muconate lactonizing enzyme family protein
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)383,59356
Polymers381,6418
Non-polymers1,95248
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area52430 Å2
ΔGint-151 kcal/mol
Surface area80830 Å2
MethodPISA
2
B: Mandelate racemase / muconate lactonizing enzyme family protein
C: Mandelate racemase / muconate lactonizing enzyme family protein
hetero molecules

B: Mandelate racemase / muconate lactonizing enzyme family protein
C: Mandelate racemase / muconate lactonizing enzyme family protein
hetero molecules

B: Mandelate racemase / muconate lactonizing enzyme family protein
C: Mandelate racemase / muconate lactonizing enzyme family protein
hetero molecules

B: Mandelate racemase / muconate lactonizing enzyme family protein
C: Mandelate racemase / muconate lactonizing enzyme family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)384,18860
Polymers381,6418
Non-polymers2,54752
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area54450 Å2
ΔGint-155 kcal/mol
Surface area79250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.799, 124.799, 343.092
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-404-

CL

21A-482-

HOH

31A-540-

HOH

41A-604-

HOH

51A-632-

HOH

61A-718-

HOH

71A-726-

HOH

81A-919-

HOH

91B-876-

HOH

101B-909-

HOH

111C-925-

HOH

Detailsbiological unit is an octamer

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Mandelate racemase / muconate lactonizing enzyme family protein


Mass: 47705.160 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. SKA58 (bacteria) / Gene: SKA58_08619 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1NAJ2

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Non-polymers , 5 types, 1161 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


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


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


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 6 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1142 / 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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol, 5 mM DTT, 5 mM MgCl2; Reservoir (25% Peg3350, 100 mM TRIS pH 8.5, 200 mM MgCl2); Cryoprotection (Reservoir + 20% glycerol), sitting ...Details: Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol, 5 mM DTT, 5 mM MgCl2; Reservoir (25% Peg3350, 100 mM TRIS pH 8.5, 200 mM MgCl2); Cryoprotection (Reservoir + 20% glycerol), sitting drop vapor diffuction, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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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: Aug 1, 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: 1.8→171.546 Å / Num. all: 123065 / Num. obs: 123065 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.9 % / Rsym value: 0.077 / Net I/σ(I): 23.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.99.10.3682.1147895162410.36890.6
1.9-2.0111.70.2712.8199888170730.27199.9
2.01-2.1512.80.1824.2205878160690.182100
2.15-2.3213.30.1295.8199669149840.129100
2.32-2.5513.80.1027.2191229138360.102100
2.55-2.8514.20.0798.9178402125480.079100
2.85-3.2914.50.06410.4161722111250.064100
3.29-4.0214.60.05511.113820994890.055100
4.02-5.6914.40.05111.410691874210.051100
5.69-171.54613.50.045125777942790.04599.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2qjj

2qjj


Resolution: 1.8→171.546 Å / Occupancy max: 1 / Occupancy min: 0.32 / FOM work R set: 0.9188 / SU ML: 0.18 / σ(F): 0 / Phase error: 14.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1646 6189 5.03 %random
Rwork0.1384 ---
all0.1397 122968 --
obs0.1397 122968 98.45 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.732 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 139.51 Å2 / Biso mean: 19.9254 Å2 / Biso min: 5.27 Å2
Baniso -1Baniso -2Baniso -3
1--1.6602 Å20 Å20 Å2
2---1.6602 Å20 Å2
3---3.3203 Å2
Refinement stepCycle: LAST / Resolution: 1.8→171.546 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9540 0 59 1142 10741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079953
X-RAY DIFFRACTIONf_angle_d1.05713550
X-RAY DIFFRACTIONf_chiral_restr0.0751468
X-RAY DIFFRACTIONf_plane_restr0.0051760
X-RAY DIFFRACTIONf_dihedral_angle_d12.9273616
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 (%)
1.8-1.82050.24771670.22293243341083
1.8205-1.84190.25791730.22233390356387
1.8419-1.86440.26441930.21773558375191
1.8644-1.8880.23192040.19753727393196
1.888-1.91280.21322160.186138984114100
1.9128-1.9390.22712050.179838974102100
1.939-1.96670.20852380.162638664104100
1.9667-1.99610.18572200.153738984118100
1.9961-2.02730.17481910.136739474138100
2.0273-2.06050.20031720.130639354107100
2.0605-2.0960.15872070.128139274134100
2.096-2.13420.15982160.128838774093100
2.1342-2.17520.16142150.127839304145100
2.1752-2.21960.14762220.127739184140100
2.2196-2.26790.16311980.131539574155100
2.2679-2.32060.18182120.134138994111100
2.3206-2.37870.17081970.135639694166100
2.3787-2.4430.17212090.137839274136100
2.443-2.51490.16942150.135339404155100
2.5149-2.59610.17382050.137839294134100
2.5961-2.68890.1811890.138239554144100
2.6889-2.79650.15531990.136439774176100
2.7965-2.92380.15792270.133939444171100
2.9238-3.0780.1531900.136639864176100
3.078-3.27080.14622150.128739934208100
3.2708-3.52340.13692010.128539924193100
3.5234-3.8780.13722380.113939954233100
3.878-4.43920.12952210.11140244245100
4.4392-5.5930.14732280.122840664294100
5.593-172.33030.18862060.17824215442198
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)
10.00520.0071-0.0070.0059-0.01410.01450.01320.0215-0.0030.0120.04250.06480.0256-0.08720.039-0.0414-0.0842-0.00830.11680.06980.142426.364548.97118.3415
20.04950.00440.03410.037-0.02890.10210.0124-0.02030.00990.00460.02860.0595-0.0001-0.0703-0.02270.06660.00020.00880.09610.02490.132141.587560.794621.4356
30.0074-0.0030.01490.0064-0.01280.04190.027-0.02830.00340.01160.02680.04040.043-0.11520.0157-0.0067-0.06980.0050.10360.06740.145730.069949.690613.8716
40.0708-0.0207-0.02710.0641-0.01450.03120.01240.02140.0873-0.0193-0.0045-0.0487-0.03220.01070.00370.1119-0.0257-0.00320.10230.0110.106625.188728.910651.6289
50.0119-0.00430.00620.0106-0.00010.0136-0.00220.01390.0422-0.0385-0.0094-0.0027-0.01320.0025-0.00090.0911-0.01060.00280.08480.01410.0528.77918.792638.3692
60.06060.0226-0.02660.03960.00140.0210.00250.00620.0441-0.0206-0.0066-0.051-0.03640.0392-0.0070.1024-0.02320.0040.10170.01490.111623.254425.880945.9353
70.01150.00590.00180.005-0.00080.0068-0.0011-0.00480.046-0.00150.01060.0086-0.0294-0.00370.00980.13670.0017-0.01320.0673-0.02350.14982.424746.415660.1454
80.0624-0.0049-0.02190.07780.03270.02730.0108-0.08290.07410.07130.0089-0.0128-0.01130.03260.00310.1615-0.0013-0.01080.1219-0.03810.0955-1.528633.232673.5135
90.0142-0.00060.00220.0130.01040.01180.0005-0.05920.04220.0497-0.0104-0.0193-0.03680.00380.00030.1597-0.0019-0.01280.1344-0.03280.04045.744320.049681.3674
100.06320.0103-0.00310.01260.00560.04920.016-0.05470.07330.0551-0.0143-0.0011-0.0564-0.0114-0.00540.14620.0022-0.00870.0851-0.04450.0942-0.379334.813173.7451
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:161)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 162:276)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 277:403)A0
4X-RAY DIFFRACTION4chain 'B' and (resseq 1:161)B0
5X-RAY DIFFRACTION5chain 'B' and (resseq 162:276)B0
6X-RAY DIFFRACTION6chain 'B' and (resseq 277:403)B0
7X-RAY DIFFRACTION7chain 'C' and (resseq 1:63)C0
8X-RAY DIFFRACTION8chain 'C' and (resseq 64:161)C0
9X-RAY DIFFRACTION9chain 'C' and (resseq 162:276)C0
10X-RAY DIFFRACTION10chain 'C' and (resseq 277:403)C0

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