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- PDB-3i4k: Crystal structure of Muconate lactonizing enzyme from Corynebacte... -

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Basic information

Entry
Database: PDB / ID: 3i4k
TitleCrystal structure of Muconate lactonizing enzyme from Corynebacterium glutamicum
ComponentsMuconate lactonizing enzyme
KeywordsISOMERASE / Structural genomics / NYSGXRC / target 9450d / Muconate lactonizing enzyme / Corynebacterium glutamicum / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


muconate cycloisomerase / chloromuconate cycloisomerase activity / muconate cycloisomerase activity / aromatic compound catabolic process / manganese ion binding
Similarity search - Function
Muconate/chloromuconate cycloisomerase / 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 ...Muconate/chloromuconate cycloisomerase / 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
ACETIC ACID / O-succinylbenzoate synthase and related enzymes
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 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: To be Published
Title: Crystal structure of Muconate lactonizing enzyme from Corynebacterium glutamicum
Authors: Fedorov, A.A. / Fedorov, E.V. / Sauder, J.M. / Burley, S.K. / Gerlt, J.A. / Almo, S.C.
History
DepositionJul 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 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.pdbx_leaving_atom_flag / _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_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: Muconate lactonizing enzyme
B: Muconate lactonizing enzyme
C: Muconate lactonizing enzyme
D: Muconate lactonizing enzyme
E: Muconate lactonizing enzyme
F: Muconate lactonizing enzyme
G: Muconate lactonizing enzyme
H: Muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)335,22224
Polymers334,5478
Non-polymers67516
Water9,224512
1
A: Muconate lactonizing enzyme
B: Muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8056
Polymers83,6372
Non-polymers1694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-19 kcal/mol
Surface area25550 Å2
MethodPISA
2
C: Muconate lactonizing enzyme
D: Muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8056
Polymers83,6372
Non-polymers1694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-18 kcal/mol
Surface area25700 Å2
MethodPISA
3
E: Muconate lactonizing enzyme
F: Muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8056
Polymers83,6372
Non-polymers1694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-19 kcal/mol
Surface area25610 Å2
MethodPISA
4
G: Muconate lactonizing enzyme
H: Muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8056
Polymers83,6372
Non-polymers1694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-18 kcal/mol
Surface area25790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.541, 156.709, 202.952
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Muconate lactonizing enzyme / / CHLOROMUCONATE CYCLOISOMERASE / O-succinylbenzoate synthase and related enzymes


Mass: 41818.348 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: catB, Cgl2401, cg2635 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8NN12, muconate cycloisomerase, chloromuconate cycloisomerase
#2: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H4O2
#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 / Water


Mass: 18.015 Da / Num. of mol.: 512 / 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: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG4000, 0.1M tris, 0.2M sodium acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP

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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: Jun 12, 2009
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: 174838 / Num. obs: 174838 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.086

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→24.92 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1711655.9 / 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
Rfree0.277 8816 5 %RANDOM
Rwork0.244 ---
all0.245 174838 --
obs0.244 174838 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.3952 Å2 / ksol: 0.339352 e/Å3
Displacement parametersBiso mean: 47.6 Å2
Baniso -1Baniso -2Baniso -3
1-7.31 Å20 Å20 Å2
2--1.74 Å20 Å2
3----9.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.2→24.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22472 0 8 544 23024
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it1.92
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it2.72.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.371 850 4.9 %
Rwork0.329 16464 -
obs-16464 99.8 %
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 DIFFRACTION4acy_xplor_par.txtacy_xplor_top.txt
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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