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- PDB-4jn7: CRYSTAL STRUCTURE OF AN ENOLASE (PUTATIVE GALACTARATE DEHYDRATASE... -

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Database: PDB / ID: 4jn7
TitleCRYSTAL STRUCTURE OF AN ENOLASE (PUTATIVE GALACTARATE DEHYDRATASE, TARGET EFI-500740) FROM AGROBACTERIUM RADIOBACTER, BOUND NA and L-MALATE, ORDERED ACTIVE SITE
ComponentsENOLASE
KeywordsLYASE / ENOLASE / PUTATIVE GALACTARATE DEHYDRATASE / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


galactarate dehydratase activity / isomerase activity
Similarity search - Function
Galactarate dehydratase 3 / : / 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 ...Galactarate dehydratase 3 / : / 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
(2S)-2-hydroxybutanedioic acid / PHOSPHATE ION / Isomerase protein
Similarity search - Component
Biological speciesAgrobacterium radiobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsVetting, M.W. / Groninger-Poe, F. / Bouvier, J.T. / Wichelecki, D. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. ...Vetting, M.W. / Groninger-Poe, F. / Bouvier, J.T. / Wichelecki, D. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Stead, M. / 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 (PUTATIVE GALACTARATE DEHYDRATASE, TARGET EFI-500740) FROM AGROBACTERIUM RADIOBACTER, BOUND NA and L-MALATE, ORDERED ACTIVE SITE
Authors: Vetting, M.W. / Groninger-Poe, F. / Bouvier, J.T. / Wichelecki, D. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, ...Authors: Vetting, M.W. / Groninger-Poe, F. / Bouvier, J.T. / Wichelecki, D. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Stead, M. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionMar 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_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_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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,30012
Polymers44,6851
Non-polymers61611
Water9,386521
1
A: ENOLASE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)362,40196
Polymers357,4778
Non-polymers4,92488
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_545-y,x-1,z1
crystal symmetry operation4_655y+1,-x,z1
crystal symmetry operation5_656-x+1,y,-z+11
crystal symmetry operation6_546x,-y-1,-z+11
crystal symmetry operation7_646y+1,x-1,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Buried area57440 Å2
ΔGint-555 kcal/mol
Surface area80530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.008, 131.008, 102.232
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-629-

HOH

21A-673-

HOH

31A-699-

HOH

41A-874-

HOH

Detailsbiological unit is an octamer

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ENOLASE


Mass: 44684.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium radiobacter (bacteria) / Strain: K84 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B9JNP7

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Non-polymers , 6 types, 532 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / 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: 2.45 Å3/Da / Density % sol: 49.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein (20 mM Tris pH 7.9, 5 mM MgCl2, 0.1 M NaCl); Reservoir (0.15 M DL-Malic Acid pH 7.0, 20 %(w/v) PEG 3350); Cryoprotection (Reservoir, + 20% ethylene glycol and 50 mM MgCl), ...Details: Protein (20 mM Tris pH 7.9, 5 mM MgCl2, 0.1 M NaCl); Reservoir (0.15 M DL-Malic Acid pH 7.0, 20 %(w/v) PEG 3350); Cryoprotection (Reservoir, + 20% ethylene glycol and 50 mM MgCl), 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: Mar 7, 2013 / 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: 1.15→92.637 Å / Num. all: 155626 / Num. obs: 155626 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Rmerge(I) obs: 0.119 / Rsym value: 0.119 / Net I/σ(I): 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.15-1.2114.10.7321318300225320.732100
1.21-1.2914.20.5561.4302131213420.556100
1.29-1.3714.20.421.8285120200720.42100
1.37-1.4814.20.2892.6266515187230.289100
1.48-1.6314.40.1854248385172900.185100
1.63-1.8214.60.1494.5228508156440.149100
1.82-2.114.90.1314.7205989138600.131100
2.1-2.57150.0956.3176708118010.095100
2.57-3.6414.90.0687.713704791940.068100
3.64-18.517140.0678.17230151680.06798.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RR1

3rr1


Resolution: 1.15→18.517 Å / Occupancy max: 1 / Occupancy min: 0.32 / FOM work R set: 0.93 / SU ML: 0.08 / σ(F): 0 / σ(I): 0 / Phase error: 13.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1446 7811 5.02 %RANDOM
Rwork0.1356 ---
all0.1361 155622 --
obs0.1361 155622 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.21 Å2 / Biso mean: 12.7696 Å2 / Biso min: 4.07 Å2
Refinement stepCycle: LAST / Resolution: 1.15→18.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3154 0 32 521 3707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083385
X-RAY DIFFRACTIONf_angle_d1.3284621
X-RAY DIFFRACTIONf_chiral_restr0.077473
X-RAY DIFFRACTIONf_plane_restr0.008620
X-RAY DIFFRACTIONf_dihedral_angle_d11.8221265
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 (%)
1.15-1.16310.20982690.204248675136100
1.1631-1.17670.19582540.191548835137100
1.1767-1.19110.20032350.188648945129100
1.1911-1.20620.19112670.178748565123100
1.2062-1.2220.17812600.174948885148100
1.222-1.23880.18562520.169248835135100
1.2388-1.25650.16232530.168249035156100
1.2565-1.27520.16812540.159448985152100
1.2752-1.29510.16752440.154949105154100
1.2951-1.31640.16992500.156448885138100
1.3164-1.33910.17572460.148549225168100
1.3391-1.36340.15892540.146249115165100
1.3634-1.38960.17372630.14548735136100
1.3896-1.4180.15512720.139748885160100
1.418-1.44880.15722720.134749015173100
1.4488-1.48250.14072590.130449075166100
1.4825-1.51950.14822690.122848995168100
1.5195-1.56060.12342470.12149195166100
1.5606-1.60650.12812600.116749205180100
1.6065-1.65830.13222540.115849275181100
1.6583-1.71760.12782700.118449165186100
1.7176-1.78630.12182600.119649265186100
1.7863-1.86750.13822540.122849575211100
1.8675-1.96580.13542640.121349375201100
1.9658-2.08890.13642760.120649255201100
2.0889-2.24990.12842430.116949975240100
2.2499-2.47580.11962830.118749615244100
2.4758-2.8330.13642730.126649975270100
2.833-3.56510.13972740.128350535327100
3.5651-18.51960.14852800.15345205548599
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)
10.32980.1220.04470.31320.03240.31860.0125-0.01650.02010.001-0.00530.081-0.0371-0.2289-0.00240.03550.06180.00830.16030.01250.083226.0657-49.862550.4515
20.1801-0.2024-0.08010.29290.09840.43670.05890.1072-0.0183-0.0747-0.04290.0751-0.0243-0.1458-0.0180.09390.0431-0.01680.12840.0150.079835.9652-51.685620.541
30.3157-0.13690.03640.4755-0.050.35290.03450.0425-0.0282-0.0644-0.00960.03090.0113-0.0613-0.01770.05680.0061-0.00750.06810.01170.062846.5411-64.726926.1546
40.48560.0386-0.05690.08540.04110.5193-0.0005-0.0454-0.00540.00430.01490.0165-0.0241-0.0549-0.01810.04840.01360.00190.0590.01380.059545.6571-56.222443.9818
51.0119-0.1859-0.04140.4038-0.21670.3748-0.01270.126-0.1102-0.15510.04550.0678-0.0447-0.2212-0.02670.07430.0659-0.02770.14090.0260.071631.5436-48.912832.6892
60.7658-0.7383-0.1591.45630.10340.20410.10970.14370.0489-0.2228-0.11120.092-0.0094-0.2330.00790.10330.0053-0.0290.19470.00670.112225.4291-68.477235.0634
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 115 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 116 through 143 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 231 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 232 through 284 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 285 through 368 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 369 through 395 )A0

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