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- PDB-4ohq: Crystal structure of chloroplast triose phosphate isomerase from ... -

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Basic information

Entry
Database: PDB / ID: 4ohq
TitleCrystal structure of chloroplast triose phosphate isomerase from Arabidopsis thaliana
ComponentsTriosephosphate isomerase, chloroplastic
KeywordsISOMERASE / TIM Barrel / chloroplast
Function / homology
Function and homology information


primary root development / : / triglyceride mobilization / chloroplast organization / thylakoid / reductive pentose-phosphate cycle / apoplast / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / chloroplast envelope ...primary root development / : / triglyceride mobilization / chloroplast organization / thylakoid / reductive pentose-phosphate cycle / apoplast / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / chloroplast envelope / triose-phosphate isomerase / triose-phosphate isomerase activity / chloroplast stroma / chloroplast / gluconeogenesis / glycolytic process / mitochondrion / cytosol
Similarity search - Function
Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Triosephosphate isomerase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsLara-Gonzalez, S. / Lopez-Castillo, M. / Brieba, L.G.
CitationJournal: Front Plant Sci / Year: 2016
Title: Structural Basis for Redox Regulation of Cytoplasmic and Chloroplastic Triosephosphate Isomerases from Arabidopsis thaliana.
Authors: Lopez-Castillo, L.M. / Jimenez-Sandoval, P. / Baruch-Torres, N. / Trasvina-Arenas, C.H. / Diaz-Quezada, C. / Lara-Gonzalez, S. / Winkler, R. / Brieba, L.G.
History
DepositionJan 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Triosephosphate isomerase, chloroplastic
B: Triosephosphate isomerase, chloroplastic


Theoretical massNumber of molelcules
Total (without water)54,4242
Polymers54,4242
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-18 kcal/mol
Surface area18000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.920, 100.920, 221.820
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CHAIN A AND RESID 6:204
21CHAIN B AND RESID 6:204
12CHAIN A AND RESID 208:254
22CHAIN B AND RESID 208:254

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111CHAIN A AND RESID 6:204A0
211CHAIN B AND RESID 6:204B0
112CHAIN A AND RESID 208:254A0
212CHAIN B AND RESID 208:254B0

NCS ensembles :
ID
1
2

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Components

#1: Protein Triosephosphate isomerase, chloroplastic / / TIM / Triose-phosphate isomerase


Mass: 27211.787 Da / Num. of mol.: 2 / Fragment: UNP residues 60-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TIM, At2g21170, F26H11.7 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9SKP6, triose-phosphate isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 3 Å3/Da / Density % sol: 58.94 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES Sodium, 1.4 M Sodium citrate tribasic dihydrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9786
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2013
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.15→28.885 Å / Num. all: 37106 / Num. obs: 37207 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.9 % / Biso Wilson estimate: 37.56 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 17 / Scaling rejects: 101
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
2.15-2.2213.70.7964.6430713153100
8.86-28.88110.04431.4681661995

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.05 Å28.89 Å
Translation5.05 Å28.89 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.1.29data scaling
PHASER2.5.2phasing
PHENIXdev_1593refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→28.88 Å / FOM work R set: 0.8512 / SU ML: 0.2 / σ(F): 1.33 / Phase error: 20.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2117 1998 5.38 %RANDOM
Rwork0.17 ---
obs0.1722 37106 99.88 %-
all-37106 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.43 Å2 / Biso mean: 43.4 Å2 / Biso min: 24.83 Å2
Refinement stepCycle: LAST / Resolution: 2.15→28.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3618 0 0 131 3749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013696
X-RAY DIFFRACTIONf_angle_d1.1455028
X-RAY DIFFRACTIONf_chiral_restr0.051574
X-RAY DIFFRACTIONf_plane_restr0.005657
X-RAY DIFFRACTIONf_dihedral_angle_d11.2281246
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1742X-RAY DIFFRACTION0.809TORSIONAL
12B1742X-RAY DIFFRACTION0.809TORSIONAL
21A394X-RAY DIFFRACTION0.809TORSIONAL
22B394X-RAY DIFFRACTION0.809TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.20380.23041390.196824482587100
2.2038-2.26330.23841390.195424452584100
2.2633-2.32990.27221400.185324612601100
2.3299-2.40510.25151390.187524652604100
2.4051-2.4910.23961400.18624522592100
2.491-2.59070.24351420.190724852627100
2.5907-2.70850.22891410.195724722613100
2.7085-2.85120.22551410.192224702611100
2.8512-3.02960.24991410.202624962637100
3.0296-3.26330.21951440.190825202664100
3.2633-3.59110.22941430.182425152658100
3.5911-4.10950.20811460.150125472693100
4.1095-5.17270.18721470.133425922739100
5.1727-28.88760.16611560.15712740289699
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6189-0.7218-0.62141.48790.37960.59340.0433-0.25440.01770.08190.07010.0136-0.07950.0976-0.00020.3291-0.0036-0.0240.4027-0.02340.3712-2.842443.55568.7509
21.5068-1.3762-0.15241.292-0.15752.1791-0.0564-0.3329-0.5960.21550.17460.38540.40060.04640.01710.3450.0075-0.03710.42070.09160.5013-1.666727.780714.1473
31.08090.0867-0.60550.051-0.01360.3672-0.3315-0.7856-0.51650.42280.4880.24770.3924-0.29430.02630.55970.06430.05540.68720.35980.9555-2.416321.61321.4935
41.4467-0.5692-1.25840.8963-0.00291.4581-0.3494-0.0951-0.82620.26180.38420.28350.25350.04890.00010.44770.0260.00470.64190.23260.6811-8.485127.87719.7287
50.7191-0.5135-0.35340.66480.2960.3097-0.1415-0.5759-0.57560.39330.11950.38960.02110.0003-0.03120.43320.04320.03350.64230.2270.5075-11.881532.410424.1399
60.3696-0.07350.05530.40220.07320.02680.0262-0.2973-0.10780.32050.0840.20760.1745-0.837-0.00310.411-0.00180.04170.59550.04850.462-18.304144.87919.2474
71.6104-0.0003-0.41071.4224-0.45370.8087-0.00610.16950.2283-0.1458-0.00960.0507-0.0885-0.024-0.00010.3062-0.0003-0.04530.3657-0.00590.3829.403141.7932-8.5026
80.0668-0.00150.01410.22940.15070.11970.22350.3154-0.0849-0.3789-0.24240.3926-0.21980.07380.00220.3240.0422-0.05090.5256-0.05840.4238-1.486340.2373-10.1549
90.4822-0.2338-0.79680.71260.44021.3144-0.1114-0.0248-0.239-0.0190.05650.35810.1288-0.27330.00010.3179-0.0242-0.0450.4036-0.05980.42326.603923.8031-9.5914
101.3325-0.0867-1.4611.93740.4481.9698-0.13710.1453-0.179-0.21890.04460.13920.24380.11160.00010.30610.0008-0.0510.3865-0.12020.339612.303521.1143-15.9875
110.95510.1425-0.19390.9605-0.51210.6444-0.0760.44210.007-0.24510.1392-0.19210.00510.2499-00.3240.0111-0.04220.475-0.06670.281517.951829.418-20.2677
120.13450.04980.07270.04860.03940.0444-0.46140.41120.1765-0.26430.3752-0.13310.12170.4161-0.00040.56030.0338-0.04080.77090.00450.397224.692137.5417-26.7034
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 6:85)A6 - 85
2X-RAY DIFFRACTION2(CHAIN A AND RESID 86:142)A86 - 142
3X-RAY DIFFRACTION3(CHAIN A AND RESID 143:151)A143 - 151
4X-RAY DIFFRACTION4(CHAIN A AND RESID 152:181)A152 - 181
5X-RAY DIFFRACTION5(CHAIN A AND RESID 182:237)A182 - 237
6X-RAY DIFFRACTION6(CHAIN A AND RESID 238:254)A238 - 254
7X-RAY DIFFRACTION7(CHAIN B AND RESID 6:79)B6 - 79
8X-RAY DIFFRACTION8(CHAIN B AND RESID 80:91)B80 - 91
9X-RAY DIFFRACTION9(CHAIN B AND RESID 92:138)B92 - 138
10X-RAY DIFFRACTION10(CHAIN B AND RESID 139:181)B139 - 181
11X-RAY DIFFRACTION11(CHAIN B AND RESID 182:247)B182 - 247
12X-RAY DIFFRACTION12(CHAIN B AND RESID 248:254)B248 - 254

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