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- PDB-5a68: Crystal structure of the AtTTM3 product complex with two orthopho... -

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Basic information

Entry
Database: PDB / ID: 5a68
TitleCrystal structure of the AtTTM3 product complex with two orthophosphates and manganese ions (form B)
ComponentsTRIPHOSPHATE TUNEL METALLOENZYME 3
KeywordsHYDROLASE / INORGANIC POLYPHOSPHATE / TRIPOLYPHOSPHATE / TRIPHOSPHATE TUNNEL METALLOENZYME
Function / homology
Function and homology information


triphosphatase / inorganic triphosphate phosphatase activity / root development / anaphase-promoting complex / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
Hypothetical Protein Pfu-838710-001 / Hypothetical Protein Pfu-838710-001 / CYTH / CYTH domain / CYTH domain / CYTH domain profile. / CYTH-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Triphosphate tunnel metalloenzyme 3
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.67 Å
AuthorsMartinez, J. / Truffault, V. / Hothorn, M.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Determinants for Substrate Binding and Catalysis in Triphosphate Tunnel Metalloenzymes.
Authors: Martinez, J. / Truffault, V. / Hothorn, M.
History
DepositionJun 24, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Oct 7, 2015Group: Database references
Revision 1.3Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRIPHOSPHATE TUNEL METALLOENZYME 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6796
Polymers24,3241
Non-polymers3555
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.331, 33.811, 71.812
Angle α, β, γ (deg.)90.00, 94.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TRIPHOSPHATE TUNEL METALLOENZYME 3 / ADENOSINETRIPHOSPHATASE / ATPASE / TRIPHOSPHATASE / PPPASE / INORGANIC TRIPHOSPHATASE


Mass: 24323.764 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Strain: COL0 / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q9SIY3, EC: 3.6.1.3, triphosphatase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.16 Å3/Da / Density % sol: 42.96 % / Description: NONE
Crystal growpH: 7 / Details: 0.1 M BIS TRIS PH 7.0, 20 % PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 1.67→43.2 Å / Num. obs: 23035 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.5
Reflection shellResolution: 1.67→1.77 Å / Redundancy: 2.95 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.75 / % possible all: 76.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.67→43.2 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.345 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22223 1097 4.8 %RANDOM
Rwork0.17915 ---
obs0.18117 21931 94.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.197 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20 Å20.52 Å2
2---0.55 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.67→43.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1650 0 13 136 1799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191713
X-RAY DIFFRACTIONr_bond_other_d0.0020.021633
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.9762317
X-RAY DIFFRACTIONr_angle_other_deg0.87133775
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2845211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.59723.76585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73315317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0721515
X-RAY DIFFRACTIONr_chiral_restr0.0760.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021906
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02391
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_it0.861.431820
X-RAY DIFFRACTIONr_mcbond_other0.861.431819
X-RAY DIFFRACTIONr_mcangle_it1.1372.1421024
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.9471.593893
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr0.76533346
X-RAY DIFFRACTIONr_sphericity_free18.861538
X-RAY DIFFRACTIONr_sphericity_bonded3.98153413
LS refinement shellResolution: 1.671→1.715 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 48 -
Rwork0.277 835 -
obs--49.92 %
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)
12.9621.12620.46999.8454-0.0931.54960.003-0.01860.0489-0.0488-0.18070.45480.0236-0.10290.17760.1015-0.0034-0.01030.0109-0.02110.0446-10.677-2.892-28.187
21.9148-1.7965-2.99352.25852.44734.9822-0.1377-0.0937-0.00840.14850.08-0.06790.2850.11290.05770.1409-0.0212-0.02380.0303-0.00570.0205-5.107-5.445-19.861
313.2038-8.4571-0.897810.7920.29384.4691-0.14920.05870.48670.1620.0306-0.41940.19550.05170.11860.1724-0.0391-0.02880.01270.01010.0299-9.3112.322-10.045
41.6264-0.82722.6851.599-1.38158.1404-0.0725-0.00860.13760.158-0.0344-0.2216-0.10030.09280.10690.0908-0.0062-0.05350.01310.00070.0483-8.3657.376-14.709
52.0503-0.7551-2.33942.57252.07114.6626-0.0752-0.29220.08920.4986-0.05270.0580.12260.05530.1280.1959-0.0049-0.04320.0831-0.03860.046-10.4215.049-4.519
612.62475.8513-8.75656.7317-4.609810.1716-0.04310.0911-0.21730.1871-0.06860.0090.0908-0.28170.11170.14540.0078-0.02660.02-0.00790.0148-8.287-5.36-25.343
72.50211.14091.67279.85636.50027.6668-0.01290.26440.2101-0.650.0043-0.0189-0.407-0.01520.00860.12830.0082-0.00370.05660.03620.0264-6.6073.923-36.117
84.2628-2.2931-4.1024.97323.31613.6360.1180.0458-0.0061-0.0941-0.0580.1552-0.0432-0.5893-0.060.1145-0.0427-0.05370.05880.00840.0487-16.659-3.53-26.88
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 17
2X-RAY DIFFRACTION2A18 - 40
3X-RAY DIFFRACTION3A41 - 70
4X-RAY DIFFRACTION4A71 - 98
5X-RAY DIFFRACTION5A99 - 146
6X-RAY DIFFRACTION6A147 - 169
7X-RAY DIFFRACTION7A170 - 187
8X-RAY DIFFRACTION8A188 - 207

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