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- PDB-3es8: Crystal structure of divergent enolase from Oceanobacillus Iheyen... -

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Basic information

Entry
Database: PDB / ID: 3es8
TitleCrystal structure of divergent enolase from Oceanobacillus Iheyensis complexed with Mg and L-malate.
ComponentsMuconate cycloisomerase
KeywordsIsomerase / lyase / Structural genomics / NYSGRC / target 9375a / enolase superfamily / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


galactarate dehydratase (D-threo-forming) / lyase activity / metal ion binding
Similarity search - Function
Galactarate dehydratase 2 / 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 ...Galactarate dehydratase 2 / 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
(2S)-2-hydroxybutanedioic acid / Galactarate dehydratase (D-threo-forming)
Similarity search - Component
Biological speciesOceanobacillus iheyensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Sauder, J.M. / Burley, S.K. / Gerlt, J.A. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Biochemistry / Year: 2009
Title: Computation-facilitated assignment of the function in the enolase superfamily: a regiochemically distinct galactarate dehydratase from Oceanobacillus iheyensis .
Authors: Rakus, J.F. / Kalyanaraman, C. / Fedorov, A.A. / Fedorov, E.V. / Mills-Groninger, F.P. / Toro, R. / Bonanno, J. / Bain, K. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / Jacobson, M.P. / Gerlt, J.A.
History
DepositionOct 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Muconate cycloisomerase
B: Muconate cycloisomerase
C: Muconate cycloisomerase
D: Muconate cycloisomerase
E: Muconate cycloisomerase
F: Muconate cycloisomerase
G: Muconate cycloisomerase
H: Muconate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)356,49424
Polymers355,2278
Non-polymers1,26716
Water9,116506
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28740 Å2
ΔGint-97 kcal/mol
Surface area88260 Å2
MethodPISA
2
A: Muconate cycloisomerase
B: Muconate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1246
Polymers88,8072
Non-polymers3174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-19 kcal/mol
Surface area26360 Å2
MethodPISA
3
C: Muconate cycloisomerase
D: Muconate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1246
Polymers88,8072
Non-polymers3174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-19 kcal/mol
Surface area26310 Å2
MethodPISA
4
E: Muconate cycloisomerase
F: Muconate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1246
Polymers88,8072
Non-polymers3174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-19 kcal/mol
Surface area26310 Å2
MethodPISA
5
G: Muconate cycloisomerase
H: Muconate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1246
Polymers88,8072
Non-polymers3174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-19 kcal/mol
Surface area26350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.584, 105.695, 105.718
Angle α, β, γ (deg.)109.31, 109.47, 109.66
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a dimer

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Components

#1: Protein
Muconate cycloisomerase / divergent enolase


Mass: 44403.367 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oceanobacillus iheyensis (bacteria) / Gene: OB2843 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EMJ9
#2: Chemical
ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H6O5
#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.: 506 / 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: 2.56 Å3/Da / Density % sol: 51.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3350, 0.15 M DL-malic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 3, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. all: 170773 / Num. obs: 170773 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.079

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→24.94 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 733121.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 8568 5 %RANDOM
Rwork0.224 ---
all0.226 170773 --
obs0.224 170773 95.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.8644 Å2 / ksol: 0.338332 e/Å3
Displacement parametersBiso mean: 43.5 Å2
Baniso -1Baniso -2Baniso -3
1-6.74 Å24.56 Å29.51 Å2
2---6.73 Å2-4.92 Å2
3----0.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.2→24.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24776 0 80 506 25362
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.82
X-RAY DIFFRACTIONc_scbond_it1.82
X-RAY DIFFRACTIONc_scangle_it2.662.5
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.442 707 4.9 %
Rwork0.43 13862 -
obs-13862 82.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4MLT_par.txtMLT_top.txt
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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