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- PDB-2zad: Crystal Structure of Muconate Cycloisomerase from Thermotoga mari... -

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Basic information

Entry
Database: PDB / ID: 2zad
TitleCrystal Structure of Muconate Cycloisomerase from Thermotoga maritima MSB8
ComponentsMuconate cycloisomeraseMuconate lactonizing enzyme
KeywordsISOMERASE / Muconate lactonizing enzyme (MLE) / TM0006 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


L-Ala-D/L-Glu epimerase activity / L-Ala-D/L-Glu epimerase / racemase and epimerase activity, acting on amino acids and derivatives / cell wall organization / cell wall macromolecule catabolic process / metal ion binding
Similarity search - Function
Dipeptide epimerase / 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 ...Dipeptide epimerase / 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
: / DI(HYDROXYETHYL)ETHER / L-Ala-D/L-Glu epimerase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsPadmanabhan, B. / Bessho, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of Muconate Cycloisomerase from Thermotoga maritima MSB8
Authors: Padmanabhan, B. / Bessho, Y. / Yokoyama, S.
History
DepositionOct 3, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,82323
Polymers156,5574
Non-polymers3,26519
Water21,9421218
1
A: Muconate cycloisomerase
B: Muconate cycloisomerase
hetero molecules

A: Muconate cycloisomerase
B: Muconate cycloisomerase
hetero molecules

A: Muconate cycloisomerase
B: Muconate cycloisomerase
hetero molecules

A: Muconate cycloisomerase
B: Muconate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,59348
Polymers313,1158
Non-polymers6,47940
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
Buried area37020 Å2
ΔGint-101.6 kcal/mol
Surface area89010 Å2
MethodPISA
2
C: Muconate cycloisomerase
D: Muconate cycloisomerase
hetero molecules

C: Muconate cycloisomerase
D: Muconate cycloisomerase
hetero molecules

C: Muconate cycloisomerase
D: Muconate cycloisomerase
hetero molecules

C: Muconate cycloisomerase
D: Muconate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,69744
Polymers313,1158
Non-polymers6,58336
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 area39980 Å2
ΔGint-144.9 kcal/mol
Surface area89290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.770, 112.770, 122.526
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

#1: Protein
Muconate cycloisomerase / Muconate lactonizing enzyme


Mass: 39139.336 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta834(DE3) / References: UniProt: Q9WXM1, muconate cycloisomerase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1218 / 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: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growTemperature: 293 K / Method: oil-batch / pH: 4.5
Details: 40%(v/v) PEG 400, 0.1M Acetate, pH 4.5 (Wizard Cryo II-38), OIL-BATCH, temperature 293.0K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9781, 0.900, 0.9793
DetectorType: RIGAKU JUPITER 210 / Detector: CCD
RadiationMonochromator: Si double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97811
20.91
30.97931
ReflectionResolution: 1.6→50 Å / Num. all: 201326 / Num. obs: 200701 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.108
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.28 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.448 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20084 9899 5 %RANDOM
Rwork0.17486 ---
obs0.17617 186624 97.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.454 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--0.41 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10808 0 193 1218 12219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02211278
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.251.9815108
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48851417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06923.988519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14152111
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.091590
X-RAY DIFFRACTIONr_chiral_restr0.0890.21684
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028278
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.25651
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.27740
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.21110
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.2207
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.285
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8341.57076
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.19211087
X-RAY DIFFRACTIONr_scbond_it2.24334623
X-RAY DIFFRACTIONr_scangle_it3.54.53999
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 693 -
Rwork0.202 12469 -
obs--89.02 %

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