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- PDB-8zin: Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in c... -

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Basic information

Entry
Database: PDB / ID: 8zin
TitleTerephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in complex with 2,4-dihydroxybenzoate.
Components4-hydroxythreonine-4-phosphate dehydrogenase
KeywordsLYASE / Metal-dependent oxidative Decarboxylase / OXIDOREDUCTASE / Lyase.
Function / homology4-hydroxythreonine-4-phosphate dehydrogenase / 4-hydroxythreonine-4-phosphate dehydrogenase activity / PdxA family / Pyridoxal phosphate biosynthetic protein PdxA / NAD binding / metal ion binding / CARBON DIOXIDE / 2,4-DIHYDROXYBENZOIC ACID / 4-hydroxythreonine-4-phosphate dehydrogenase
Function and homology information
Biological speciesComamonas testosteroni KF-1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKumar, K.A. / Pahwa, D. / Kumar, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)DBT-2771-BIO-CNA India
CitationJournal: To Be Published
Title: Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in complex with 2,4-dihydroxybenzoate.
Authors: Kumar, K.A. / Pahwa, D.
History
DepositionMay 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxythreonine-4-phosphate dehydrogenase
B: 4-hydroxythreonine-4-phosphate dehydrogenase
C: 4-hydroxythreonine-4-phosphate dehydrogenase
D: 4-hydroxythreonine-4-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,79520
Polymers140,6374
Non-polymers1,15816
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.295, 93.632, 165.595
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
4-hydroxythreonine-4-phosphate dehydrogenase


Mass: 35159.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni KF-1 (bacteria) / Gene: CtesDRAFT_PD2128 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B7WRJ7, 4-hydroxythreonine-4-phosphate dehydrogenase

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Non-polymers , 7 types, 139 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DOB / 2,4-DIHYDROXYBENZOIC ACID


Mass: 154.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.53 Å3/Da / Density meas: 0.539 Mg/m3 / Density % sol: 51.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Sodium malonate pH 6.0 12% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jun 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→24.934 Å / Num. obs: 47089 / % possible obs: 99.8 % / Redundancy: 7.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.162 / Rrim(I) all: 0.174 / Χ2: 1.02 / Net I/σ(I): 9
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4554 / CC1/2: 0.842 / Rrim(I) all: 0.751

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→24.934 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.858 / WRfactor Rfree: 0.274 / WRfactor Rwork: 0.236 / SU B: 0.004 / SU ML: 0 / Average fsc free: 0.9335 / Average fsc work: 0.9506 / Cross valid method: FREE R-VALUE / ESU R: 0.295 / ESU R Free: 0.338
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2896 2351 5.005 %
Rwork0.2526 44626 -
all0.254 --
obs-46977 99.521 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.62 Å2
Baniso -1Baniso -2Baniso -3
1--2.339 Å2-0 Å2-0 Å2
2--2.748 Å20 Å2
3----0.409 Å2
Refinement stepCycle: LAST / Resolution: 2.5→24.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9177 0 63 123 9363
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.5-2.5640.3551560.31632210.31733860.9080.93299.73420.304
2.564-2.6340.3181920.3131280.3133210.9280.93399.96990.297
2.634-2.7090.371540.29631110.29932670.9030.93799.93880.283
2.709-2.7920.3511470.31329820.31531330.9080.93299.87230.299
2.792-2.8820.4121600.31428920.31930570.8890.9399.83640.297
2.882-2.9820.3321380.29328200.29529620.9220.94199.8650.277
2.982-3.0930.3011260.27927150.2828450.9350.94799.85940.261
3.093-3.2170.2911470.27826120.27927650.9360.94799.7830.261
3.217-3.3570.2941400.27424960.27526380.9450.95399.92420.263
3.357-3.5180.321460.27324050.27625530.9310.95299.92170.261
3.518-3.7040.2931280.2722760.27224070.9430.95499.87540.26
3.704-3.9230.2671030.24422080.24523200.9580.96499.61210.235
3.923-4.1870.271050.22820440.2321550.9530.96699.72160.215
4.187-4.5120.255950.20619340.20920400.9570.97299.46080.199
4.512-4.9260.28810.18818080.19118990.9490.97799.47340.181
4.926-5.4810.251830.20616190.20817090.9630.97499.59040.2
5.481-6.2790.299770.23414640.23815460.9520.9799.67660.228
6.279-7.5710.243700.20912540.21113310.9660.97899.47410.203
7.571-10.2450.175550.1489950.1510750.9830.98897.67440.15
10.245-24.9340.183480.2246420.227260.9810.97695.04130.218

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