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- PDB-8zhy: Magnesium substituted Terephthalate 1,2-cis-dihydrodioldehydrogen... -

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Basic information

Entry
Database: PDB / ID: 8zhy
TitleMagnesium substituted Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in complex with CO2.
Components4-hydroxythreonine-4-phosphate dehydrogenase
KeywordsLYASE / Metal-dependent oxidative Decarboxylase / OXIDOREDUCTASE.
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 / 4-hydroxythreonine-4-phosphate dehydrogenase
Function and homology information
Biological speciesComamonas testosteroni KF-1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKumar, K.A. / Pahwa, D. / Kumar, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)DBT-2271-BIO-CNA India
CitationJournal: To Be Published
Title: Magnesium substituted Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in complex with CO2.
Authors: Kumar, K.A. / Pahwa, D.
History
DepositionMay 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_struct_assembly ...pdbx_entry_details / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_entry_details.has_protein_modification

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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)141,30918
Polymers140,6374
Non-polymers67114
Water2,756153
1
A: 4-hydroxythreonine-4-phosphate dehydrogenase
hetero molecules

D: 4-hydroxythreonine-4-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,70610
Polymers70,3192
Non-polymers3878
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_644-x+1,-y-1/2,z-1/21
Buried area3870 Å2
ΔGint-126 kcal/mol
Surface area24120 Å2
MethodPISA
2
B: 4-hydroxythreonine-4-phosphate dehydrogenase
C: 4-hydroxythreonine-4-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6038
Polymers70,3192
Non-polymers2846
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-66 kcal/mol
Surface area23600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.729, 93.776, 166.309
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A
74A
84A
95A
105A
116A
126A

NCS domain segments:

Auth asym-ID: A / Label asym-ID: A

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth seq-IDLabel seq-ID
111THRTHRGLNGLN2 - 31322 - 333
211THRTHRGLNGLN2 - 31322 - 333
322METMETGLYGLY1 - 31121 - 331
422METMETGLYGLY1 - 31121 - 331
533METMETPROPRO1 - 31421 - 334
633METMETPROPRO1 - 31421 - 334
744THRTHRGLYGLY2 - 31122 - 331
844THRTHRGLYGLY2 - 31122 - 331
955THRTHRGLNGLN2 - 31322 - 333
1055THRTHRGLNGLN2 - 31322 - 333
1166METMETGLYGLY1 - 31121 - 331
1266METMETGLYGLY1 - 31121 - 331

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
4-hydroxythreonine-4-phosphate dehydrogenase / Terephthalate 1 / 2-cis-dihydrodioldehydrogenase/Decarboxylase


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 , 6 types, 167 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.56 Å3/Da / Density meas: 0.51 Mg/m3 / Density % sol: 52.08 % / Description: tabular plates
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 4% v/v TacsimateTM pH 6.0 12% w/v Polyethylene glycol 3,350
PH range: 7-8

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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: Nov 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→26.22 Å / Num. obs: 42297 / % possible obs: 99.6 % / Redundancy: 6.7 % / CC1/2: 0.969 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.094 / Rrim(I) all: 0.25 / Χ2: 1.02 / Net I/σ(I): 6.2
Reflection shellResolution: 2.7→9.73 Å / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4389 / CC1/2: 0.785 / Rpim(I) all: 0.241 / Rrim(I) all: 0.685 / Χ2: 0.72 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→20.001 Å / Cor.coef. Fo:Fc: 0.819 / Cor.coef. Fo:Fc free: 0.745 / SU B: 20.531 / SU ML: 0.42 / Cross valid method: FREE R-VALUE / ESU R: 0.847 / ESU R Free: 0.464
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3303 1855 4.914 %
Rwork0.2829 35893 -
all0.285 --
obs-37748 99.217 %
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: 31.117 Å2
Baniso -1Baniso -2Baniso -3
1--2.756 Å20 Å2-0 Å2
2--2.567 Å20 Å2
3---0.189 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9148 0 32 153 9333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0129311
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169174
X-RAY DIFFRACTIONr_angle_refined_deg1.31.80212655
X-RAY DIFFRACTIONr_angle_other_deg0.4461.72321086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.66651242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.901556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4101525
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.10510344
X-RAY DIFFRACTIONr_chiral_restr0.0620.21537
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210951
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021893
X-RAY DIFFRACTIONr_nbd_refined0.2240.21944
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.28658
X-RAY DIFFRACTIONr_nbtor_refined0.1650.24447
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.25086
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2257
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1530.228
X-RAY DIFFRACTIONr_nbd_other0.1770.2166
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1680.211
X-RAY DIFFRACTIONr_ncsr_local_group_10.0780.059204
X-RAY DIFFRACTIONr_ncsr_local_group_20.0780.059028
X-RAY DIFFRACTIONr_ncsr_local_group_30.0810.059258
X-RAY DIFFRACTIONr_ncsr_local_group_40.0810.058907
X-RAY DIFFRACTIONr_ncsr_local_group_50.0760.059168
X-RAY DIFFRACTIONr_ncsr_local_group_60.0810.059003
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.078240.05009
12AX-RAY DIFFRACTIONLocal ncs0.078240.05009
23AX-RAY DIFFRACTIONLocal ncs0.078320.05009
24AX-RAY DIFFRACTIONLocal ncs0.078320.05009
35AX-RAY DIFFRACTIONLocal ncs0.080970.05009
36AX-RAY DIFFRACTIONLocal ncs0.080970.05009
47AX-RAY DIFFRACTIONLocal ncs0.081310.05009
48AX-RAY DIFFRACTIONLocal ncs0.081310.05009
59AX-RAY DIFFRACTIONLocal ncs0.075560.05009
510AX-RAY DIFFRACTIONLocal ncs0.075560.05009
611AX-RAY DIFFRACTIONLocal ncs0.080850.05009
612AX-RAY DIFFRACTIONLocal ncs0.080850.05009
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
2.7-2.7690.361300.31726040.31927340.8890.931000.31
2.769-2.8430.3441190.32925360.3326550.8980.9221000.321
2.843-2.9240.3741480.3124070.31425550.9040.9341000.301
2.924-3.0120.3961300.32823830.33225140.8810.92199.96020.319
3.012-3.1080.3741080.31123350.31324450.8930.93199.91820.301
3.108-3.2150.3421130.30522580.30723710.920.9331000.299
3.215-3.3330.3691130.30621810.30922960.8960.9499.91290.303
3.333-3.4650.3071120.30220900.30222080.9330.94199.72830.299
3.465-3.6140.3681190.31319930.31621130.8860.92499.95270.31
3.614-3.7840.4061080.3519200.35320310.8780.91899.85230.346
3.784-3.9810.332970.2818490.28319540.9230.94399.59060.278
3.981-4.2120.319840.26117330.26418330.9220.9599.12710.258
4.212-4.4880.335630.26816730.27117520.9220.94399.08680.267
4.488-4.8280.281810.23615420.23816440.950.95998.72260.239
4.828-5.2580.254690.23414360.23515140.9560.96299.40550.233
5.258-5.8290.297620.25913420.26114070.9420.95899.78680.259
5.829-6.6370.309610.25711870.25912510.9510.96199.76020.254
6.637-7.9140.247610.20710180.2110960.9660.97298.44890.21
7.914-10.4070.181450.168250.1618970.980.98396.990.169
10.407-20.0010.307300.2275650.2316310.9660.97494.29480.239

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