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- PDB-9iz5: Multifunctional PLP-dependent enzyme TM1270 -

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Basic information

Entry
Database: PDB / ID: 9iz5
TitleMultifunctional PLP-dependent enzyme TM1270
ComponentsL-alanine/L-glutamate racemase
KeywordsLYASE / Isomerase / Transferase
Function / homology
Function and homology information


carbon-sulfur lyase activity / glutamate racemase / glutamate racemase activity / alanine racemase / alanine racemase activity / transsulfuration / peptidoglycan biosynthetic process / pyridoxal phosphate binding / regulation of cell shape / cytoplasm
Similarity search - Function
: / : / Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / L-alanine/L-glutamate racemase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsNitta, S. / Miyamoto, T. / Fushinobu, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Acs Catalysis / Year: 2024
Title: Functional and Structural Analyses of a Highly Multifunctional Enzyme TM1270 from the Hyperthermophile Thermotoga maritima
Authors: Miyamoto, T. / Nitta, S. / Homma, H. / Fushinobu, S.
#1: Journal: Biosci Biotechnol Biochem / Year: 2024
Title: Multifunctional enzymes related to amino acid metabolism in bacteria.
Authors: Miyamoto, T.
History
DepositionJul 31, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-alanine/L-glutamate racemase
B: L-alanine/L-glutamate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3023
Polymers89,1962
Non-polymers1061
Water7,692427
1
A: L-alanine/L-glutamate racemase
B: L-alanine/L-glutamate racemase
hetero molecules

A: L-alanine/L-glutamate racemase
B: L-alanine/L-glutamate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,6046
Polymers178,3924
Non-polymers2122
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545x,-y-1,-z1
Buried area22090 Å2
ΔGint-109 kcal/mol
Surface area46230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.418, 120.578, 137.067
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein L-alanine/L-glutamate racemase


Mass: 44598.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Gene: aar, metC, TM_1270, Tmari_1275 / Plasmid: pET41a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9X0Z7, alanine racemase, glutamate racemase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 277.2 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 7.75% PEG 6000, 0.9M LiCl, 0.1M sodium citrate (pH 5.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 28, 2020
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→48.12 Å / Num. obs: 96442 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.034 / Net I/σ(I): 15.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4701 / CC1/2: 0.707 / Rpim(I) all: 0.383 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→48.12 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.741 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17596 4929 5.1 %RANDOM
Rwork0.15011 ---
obs0.15142 91439 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.273 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å2-0 Å20 Å2
2---0.21 Å20 Å2
3----0.48 Å2
Refinement stepCycle: 1 / Resolution: 1.7→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6084 0 7 427 6518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0126216
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165993
X-RAY DIFFRACTIONr_angle_refined_deg1.9021.8388399
X-RAY DIFFRACTIONr_angle_other_deg0.6621.76313866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3515761
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.697536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03101124
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0980.2944
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027061
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021317
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8641.8813056
X-RAY DIFFRACTIONr_mcbond_other1.8631.8813056
X-RAY DIFFRACTIONr_mcangle_it2.6213.3713813
X-RAY DIFFRACTIONr_mcangle_other2.6213.3723814
X-RAY DIFFRACTIONr_scbond_it3.512.2693160
X-RAY DIFFRACTIONr_scbond_other3.5092.273161
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3463.9644587
X-RAY DIFFRACTIONr_long_range_B_refined6.38521.637170
X-RAY DIFFRACTIONr_long_range_B_other6.33121.157092
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 362 -
Rwork0.238 6675 -
obs--100 %

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