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- PDB-7k34: Crystal structure of L-threonine transaldolase from Pseudomonas f... -

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Basic information

Entry
Database: PDB / ID: 7k34
TitleCrystal structure of L-threonine transaldolase from Pseudomonas fluorescens in internal aldimine state
ComponentsThreonine aldolase
KeywordsBIOSYNTHETIC PROTEIN / SYNTHASE / threonine transaldolase / pyridoxal phosphate / PLP / biocatalysis
Function / homology
Function and homology information


L-threonine aldolase / threonine aldolase activity / serine binding / L-serine catabolic process / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate metabolic process / cobalt ion binding / folic acid metabolic process / pyridoxal phosphate binding ...L-threonine aldolase / threonine aldolase activity / serine binding / L-serine catabolic process / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate metabolic process / cobalt ion binding / folic acid metabolic process / pyridoxal phosphate binding / one-carbon metabolic process / zinc ion binding / cytoplasm
Similarity search - Function
: / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsKumar, P. / Bingman, C.A. / Buller, A.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2-GM137417 United States
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: l-Threonine Transaldolase Activity Is Enabled by a Persistent Catalytic Intermediate.
Authors: Kumar, P. / Meza, A. / Ellis, J.M. / Carlson, G.A. / Bingman, C.A. / Buller, A.R.
History
DepositionSep 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Threonine aldolase
B: Threonine aldolase
C: Threonine aldolase
D: Threonine aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,84413
Polymers200,9794
Non-polymers8659
Water16,556919
1
A: Threonine aldolase
B: Threonine aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,9707
Polymers100,4902
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11220 Å2
ΔGint-149 kcal/mol
Surface area26870 Å2
MethodPISA
2
C: Threonine aldolase
D: Threonine aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,8746
Polymers100,4902
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10950 Å2
ΔGint-139 kcal/mol
Surface area27100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.613, 118.613, 129.976
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Threonine aldolase


Mass: 50244.836 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: obiH, CIB54_12585 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1X9LWZ7, L-threonine aldolase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 919 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.93 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: N-His-ObiH at 30 mg/ml was dissolved in 10 mM Tris pH 8.5. Two microliter of protein solution was mixed with two microliter of reservoir solution, 0.1 M Bis-Tris pH 6.75 - 7.0, 1.8 - 2.0 M ...Details: N-His-ObiH at 30 mg/ml was dissolved in 10 mM Tris pH 8.5. Two microliter of protein solution was mixed with two microliter of reservoir solution, 0.1 M Bis-Tris pH 6.75 - 7.0, 1.8 - 2.0 M ammonium sulfate and equilibrated against the reservoir at 21 C (294K)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 1.66→118.6 Å / Num. obs: 211275 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.996 / Rpim(I) all: 0.083 / Rrim(I) all: 0.216 / Net I/σ(I): 6.9
Reflection shellResolution: 1.66→1.7 Å / Redundancy: 13.1 % / Num. unique obs: 15546 / CC1/2: 0.45 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OT8
Resolution: 1.66→50.005 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.247 / WRfactor Rwork: 0.216 / SU B: 6.784 / SU ML: 0.109 / Average fsc free: 0.8546 / Average fsc work: 0.8673 / Cross valid method: FREE R-VALUE / ESU R: 0.115 / ESU R Free: 0.11
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2423 10401 4.932 %Random selection
Rwork0.2127 200497 --
all0.214 ---
obs-210898 99.849 %-
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: 27.211 Å2
Baniso -1Baniso -2Baniso -3
1-0.239 Å2-0 Å2-0 Å2
2--0.239 Å2-0 Å2
3----0.477 Å2
Refinement stepCycle: LAST / Resolution: 1.66→50.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13407 0 45 919 14371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01314007
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712421
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.6319128
X-RAY DIFFRACTIONr_angle_other_deg1.2651.56728781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49351804
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67222.925670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.304152063
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.9021559
X-RAY DIFFRACTIONr_chiral_restr0.0550.21809
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216086
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022927
X-RAY DIFFRACTIONr_nbd_refined0.1890.22986
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.211545
X-RAY DIFFRACTIONr_nbtor_refined0.1560.26748
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.25408
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2828
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.110.211
X-RAY DIFFRACTIONr_nbd_other0.1770.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1820.213
X-RAY DIFFRACTIONr_mcbond_it0.2951.3057156
X-RAY DIFFRACTIONr_mcbond_other0.2951.3057155
X-RAY DIFFRACTIONr_mcangle_it0.5181.9568971
X-RAY DIFFRACTIONr_mcangle_other0.5181.9568972
X-RAY DIFFRACTIONr_scbond_it0.3031.3496851
X-RAY DIFFRACTIONr_scbond_other0.2881.3276815
X-RAY DIFFRACTIONr_scangle_it0.4882.01210154
X-RAY DIFFRACTIONr_scangle_other0.4781.97910100
X-RAY DIFFRACTIONr_lrange_it4.63216.34615743
X-RAY DIFFRACTIONr_lrange_other4.56216.00515602
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
1.66-1.7030.3427900.326146500.327155230.6350.64599.46530.328
1.703-1.750.3128080.308142990.308151780.7440.74999.53220.307
1.75-1.8010.2987120.293140530.293148080.7780.78499.70960.29
1.801-1.8560.3057020.273136450.274143710.8310.83499.8330.265
1.856-1.9170.3056950.272131400.274138620.840.85499.80520.263
1.917-1.9840.2936320.253127920.254134430.8530.88299.85870.241
1.984-2.0590.2476710.223122820.224129600.8960.90799.9460.213
2.059-2.1430.2495950.217119050.219125060.8980.91199.9520.208
2.143-2.2380.2525330.215114680.217120090.8920.90399.93340.207
2.238-2.3470.3045750.241108510.244114440.8660.89799.84270.236
2.347-2.4730.2395300.207104130.209109450.9140.91899.98170.204
2.473-2.6230.2325140.19598040.197103180.9230.9331000.196
2.623-2.8030.2424660.291890.20296550.9140.931000.203
2.803-3.0270.2474560.20386120.20590680.9090.9281000.209
3.027-3.3150.2113960.279590.283550.9320.9371000.209
3.315-3.7040.2163890.19771450.19875350.9350.9499.98670.211
3.704-4.2730.1973290.1763290.17166580.9470.9551000.185
4.273-5.2240.2032820.17853720.17956540.9420.9491000.195
5.224-7.3480.252120.22242100.22444220.9290.9361000.237
7.348-50.0050.2341140.19623790.19724930.9580.951000.218
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.6134-0.2836-0.03290.78970.42460.6866-0.0201-0.05020.16190.08230.1479-0.16670.00560.1074-0.12780.14350.0079-0.01860.1956-0.05750.124235.311-2.3032-7.2274
23.24960.5015-1.99721.950.04513.9033-0.04130.0318-0.21750.0863-0.21210.13680.2001-0.16120.25340.1049-0.0145-0.02140.1915-0.00060.109413.5894-11.8256-17.3581
30.50210.0904-0.24713.05630.22691.1589-0.04050.0272-0.06810.1550.0128-0.0030.17110.11820.02770.1340.0097-0.01240.1612-0.02120.079125.8563-23.3972-20.0255
43.14341.588-1.5864.0895-1.19393.45530.0051-0.0612-0.07560.28380.0907-0.30130.02980.2706-0.09580.1950.0814-0.05560.1512-0.06130.102438.6525-32.65-17.8352
51.19330.7631-0.06561.5483-0.45062.5962-0.01310.096-0.14760.11640.1691-0.12160.35240.1964-0.15590.18920.0753-0.02060.176-0.09540.091940.3523-36.5889-25.6105
61.71041.7636-0.52354.484-0.40340.5306-0.09010.2492-0.1933-0.12790.1589-0.24950.21370.0774-0.06880.2030.0609-0.02050.2117-0.07480.097237.2942-32.4091-27.4129
73.15481.5197-0.757610.0037-1.67666.5781-0.09480.0698-0.25880.0678-0.00940.1550.2323-0.21840.10420.18860.0078-0.01030.1799-0.07070.115530.6486-35.3516-34.7062
80.7274-0.05290.01551.07420.52760.7650.01940.1431-0.0031-0.10240.0592-0.05860.01060.089-0.07860.1631-0.0027-0.00330.209-0.02240.0732.1834-15.7074-25.076
92.6619-0.4847-0.13462.07451.16321.875-0.00580.0606-0.05370.08220.4152-0.51830.24470.4904-0.40940.04310.0731-0.04350.336-0.21370.182555.5833-19.6637-21.5808
101.6859-0.8974-0.16341.34230.53350.97520.05360.08780.3269-0.13490.1936-0.4138-0.16420.3284-0.24720.0762-0.07870.06840.2251-0.08170.154147.2052-1.2373-20.896
111.0920.5316-0.62211.4914-0.32642.0541-0.03930.12580.2411-0.18320.09330.0602-0.07-0.113-0.0540.14050.01230.00130.14450.01540.12118.56751.9978-14.2346
121.1010.8004-0.96860.7758-0.04933.91170.06020.00630.08170.03330.1308-0.05510.09520.1755-0.19090.149-0.0067-0.00130.2391-0.1130.202737.1847-8.1872-6.5318
132.38712.8179-4.93283.3438-5.850710.2438-0.02760.27490.157-0.09470.33960.15880.2016-0.5694-0.3120.550.1766-0.14680.3656-0.06680.231648.5387-21.0517-6.192
146.10111.5011-5.85291.9762-1.94546.8861-0.0251-0.28770.00660.34830.0876-0.19630.07330.2457-0.06250.16690.0772-0.0720.2016-0.0880.067440.2862-10.32824.4337
151.2409-0.0455-1.11732.2008-0.02541.1744-0.2605-0.003-0.09060.25320.24530.28330.39960.03620.01520.32490.0726-0.00340.14220.02520.062826.5187-27.04011.3995
160.9105-1.3648-0.47178.36981.03296.0668-0.13050.0763-0.0453-0.30330.01510.1201-0.18170.05590.11540.2971-0.04480.04070.05850.04670.141719.0564-33.0359-3.0585
171.2206-1.7823-1.72113.89971.52423.7909-0.4439-0.1411-0.38011.11560.14240.66230.63520.07070.30150.79950.0750.27320.16050.19240.300116.4807-34.938611.6913
180.6796-0.3854-0.06931.47230.21350.4559-0.1687-0.2253-0.03890.45280.19620.04430.2770.0907-0.02750.3030.0937-0.00230.17590.01090.005527.1554-19.4086.912
192.1105-0.2567-0.27951.06520.58821.1269-0.149-0.0772-0.10870.2927-0.00560.32830.2032-0.19070.15460.1913-0.02020.11040.1682-0.01370.10925.0976-10.01536.6862
202.43610.6226-0.01651.44170.57990.76410.0653-0.0050.38180.1069-0.02560.1773-0.0511-0.1177-0.03970.15180.0450.01610.1547-0.00140.12315.56084.52660.1078
212.4164-1.93443.16343.388-3.91818.17930.07340.1203-0.0866-0.1309-0.04690.31670.1518-0.1497-0.02650.1257-0.0105-0.03220.137-0.05970.196353.3622-41.195714.2852
220.3893-0.1156-0.0111.9482-0.52350.8605-0.0364-0.0354-0.0140.03490.01950.14230.0451-0.00910.01690.1697-0.0081-0.0070.1659-0.01210.067863.8115-29.588729.7177
232.1552-0.01742.86446.4067-5.88319.174-0.23240.2337-0.00630.25870.0467-0.1911-0.56490.30330.18570.3239-0.09920.00370.2923-0.05690.26275.5851-8.899626.6219
241.3783-0.60450.40420.8528-0.15730.7255-0.01510.0112-0.0260.06990.0497-0.02560.05260.1452-0.03450.18-0.0122-0.01740.1986-0.01790.069377.6237-25.982435.6972
258.07210.8444-1.42235.9471-2.70919.17140.02840.3960.163-0.05610.15470.31350.12930.1914-0.18310.14360.052-0.01780.2448-0.04360.115690.7074-35.298827.4652
261.63320.7192-0.48691.64130.00061.26880.0288-0.0101-0.11160.26960.0597-0.18750.24910.3272-0.08850.19960.0987-0.09510.2167-0.03530.052490.2175-39.475944.0617
2710.62180.3162-1.16481.6914-0.928710.0104-0.00710.12970.16790.0534-0.126-0.2872-0.20650.34710.13310.17680.0135-0.08860.2224-0.02530.118392.756-30.397149.7806
281.14320.05990.46440.74040.1390.8245-0.027-0.0380.02570.11730.048-0.01390.04720.1051-0.02090.18160.0053-0.02160.1809-0.0050.06275.111-27.978837.9213
290.8786-0.3838-0.08872.18720.13730.8253-0.0381-0.0837-0.1790.2540.0381-0.12580.22890.071-00.23650.0383-0.00360.12020.03390.065370.969-51.356840.2961
300.7644-0.80740.04272.2844-0.12420.6428-0.0748-0.0724-0.21320.14790.08550.31660.2046-0.1-0.01070.1847-0.0530.05160.12650.0210.111755.4746-46.735536.1792
310.83610.3481-0.40951.5246-0.45632.0320.0639-0.1031-0.00820.0951-0.06080.26-0.1952-0.0963-0.00310.1502-0.0075-0.00750.1636-0.01120.11655.0344-18.309828.9756
320.28180.4286-0.09491.9188-0.38432.5517-0.0949-0.0663-0.1315-0.06550.022-0.02290.21630.22260.0730.22170.01770.02050.1740.01550.114168.6812-40.931420.6103
333.9058-0.59421.58123.1265-3.29775.1997-0.106-0.1921-0.12240.1603-0.1095-0.18560.2020.23780.21550.18360.0406-0.01240.1126-0.02310.113768.437-46.193520.5325
343.1667-0.2982-0.11411.2640.77792.25670.01650.00910.0215-0.1590.0418-0.0675-0.03830.1065-0.05830.17610.00920.0040.17050.00570.063177.3548-33.042511.4781
352.6664-1.11041.00181.65980.1653.6431-0.0641-0.2986-0.0071-0.10650.2308-0.265-0.32830.2273-0.16660.1602-0.09690.09360.2274-0.05570.110289.0216-18.48215.516
362.5016-0.82870.55273.07760.72561.43350.01430.07170.0509-0.67970.1719-0.3858-0.28910.4992-0.18620.2994-0.12270.15510.2793-0.05960.087388.6922-18.63032.6844
371.113-0.4065-0.33651.02370.31050.58270.03360.0694-0.0462-0.2016-0.023-0.0373-0.03140.0702-0.01050.20040.0059-0.00020.1827-0.01120.053773.3544-29.84049.9401
381.0557-0.0027-0.04781.60770.71671.58510.1020.06440.1846-0.3294-0.0366-0.1155-0.39430.1344-0.06540.2967-0.02260.01040.10240.02480.047968.1842-5.40578.143
393.0022-0.4032-1.81870.9555-1.01793.0590.35770.16140.7174-0.07240.06270.0227-0.3922-0.1644-0.42040.46870.0315-0.09940.05190.08790.347359.55473.520412.523
400.54940.2157-0.11133.0885-0.00680.5258-0.01960.03-0.063-0.0930.02690.3928-0.1156-0.2088-0.00720.14580.0451-0.07820.1591-0.02640.134649.6896-24.104814.3562
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 61
2X-RAY DIFFRACTION2ALLA62 - 89
3X-RAY DIFFRACTION3ALLA90 - 118
4X-RAY DIFFRACTION4ALLA119 - 138
5X-RAY DIFFRACTION5ALLA139 - 164
6X-RAY DIFFRACTION6ALLA165 - 187
7X-RAY DIFFRACTION7ALLA188 - 199
8X-RAY DIFFRACTION8ALLA200 - 308
9X-RAY DIFFRACTION9ALLA309 - 362
10X-RAY DIFFRACTION10ALLA363 - 440
11X-RAY DIFFRACTION11ALLB0 - 42
12X-RAY DIFFRACTION12ALLB43 - 60
13X-RAY DIFFRACTION13ALLB61 - 70
14X-RAY DIFFRACTION14ALLB71 - 93
15X-RAY DIFFRACTION15ALLB94 - 127
16X-RAY DIFFRACTION16ALLB128 - 145
17X-RAY DIFFRACTION17ALLB146 - 177
18X-RAY DIFFRACTION18ALLB178 - 285
19X-RAY DIFFRACTION19ALLB286 - 390
20X-RAY DIFFRACTION20ALLB391 - 440
21X-RAY DIFFRACTION21ALLC-1 - 30
22X-RAY DIFFRACTION22ALLC31 - 60
23X-RAY DIFFRACTION23ALLC61 - 70
24X-RAY DIFFRACTION24ALLC71 - 130
25X-RAY DIFFRACTION25ALLC131 - 143
26X-RAY DIFFRACTION26ALLC144 - 188
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