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- PDB-5a67: Crystal structure of AtTTM3 in complex with tripolyphosphate and ... -

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Basic information

Entry
Database: PDB / ID: 5a67
TitleCrystal structure of AtTTM3 in complex with tripolyphosphate and manganese ion (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
TRIPHOSPHATE / : / Triphosphate tunnel metalloenzyme 3
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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

Downloads & links

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Assembly

Deposited unit
A: TRIPHOSPHATE TUNEL METALLOENZYME 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6373
Polymers24,3241
Non-polymers3132
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.375, 33.868, 72.216
Angle α, β, γ (deg.)90.00, 94.97, 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.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-3PO / TRIPHOSPHATE


Mass: 257.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H5O10P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.22 Å3/Da / Density % sol: 44.66 % / Description: NONE
Crystal growpH: 7 / Details: 20 % PEG 3350,0.2M NACL, 0.1 M BISTRIS PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000020, 1.823310
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.000021
21.823311
ReflectionResolution: 1.3→19.6 Å / Num. obs: 52725 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 6.24 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.04
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 5.27 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.94 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5A5Y

5a5y


Resolution: 1.3→19.61 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.892 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.17542 2541 4.8 %RANDOM
Rwork0.14044 ---
obs0.14211 50172 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.715 Å2
Baniso -1Baniso -2Baniso -3
1--1.24 Å20 Å20 Å2
2--1.57 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.3→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1674 0 14 244 1932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191830
X-RAY DIFFRACTIONr_bond_other_d0.0020.021769
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.9872494
X-RAY DIFFRACTIONr_angle_other_deg0.91334105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1075237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.64623.58792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37715352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.181518
X-RAY DIFFRACTIONr_chiral_restr0.1030.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022050
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02418
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_it1.6281.238859
X-RAY DIFFRACTIONr_mcbond_other1.6181.236858
X-RAY DIFFRACTIONr_mcangle_it2.091.8661080
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4331.59971
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_restr1.81833599
X-RAY DIFFRACTIONr_sphericity_free44.158558
X-RAY DIFFRACTIONr_sphericity_bonded12.43853741
LS refinement shellResolution: 1.295→1.329 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 169 -
Rwork0.249 3302 -
obs--88.37 %
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)
10.65310.54540.45553.18541.49681.17480.0312-0.05910.05710.0442-0.02960.077-0.027-0.0563-0.00160.04560.0020.00740.0083-00.0235-10.33015.9402-25.7904
22.81540.1318-0.04150.50350.1360.3327-0.02560.1414-0.0618-0.02330.0085-0.00460.0052-0.00170.01710.0394-0.00060.00250.0072-0.00190.0165-6.4776-11.8002-32.3871
32.0956-1.1599-2.16050.73211.22862.3803-0.0367-0.0171-0.0310.02080.0120.0290.04660.02850.02480.0341-0.0017-0.0060.0013-0.00150.0211-6.2251-3.2099-14.9071
41.465-0.82240.06890.82120.06860.6144-0.00420.01710.01870.0436-0.02090.03940.0184-0.07750.02510.0408-0.00620.00280.0108-0.00350.0297-15.8416.3272-9.7047
511.59133.7085-1.45781.7872-0.76740.4089-0.10520.0234-0.5862-0.09230.0319-0.26590.01780.04260.07340.0517-0.01650.02740.0479-0.02650.10154.6828-5.7983-10.6455
60.7929-0.25850.85330.1668-0.15851.3729-0.02990.01180.0241-0.00980.0046-0.0058-0.07710.0120.02530.0412-0.0051-0.0030.00230.00380.0252-12.31119.374-19.7238
70.6179-0.36970.23452.0836-1.47051.6425-0.0031-0.02650.0034-0.0186-0.0339-0.03080.06530.03140.03690.03560.0058-0.00680.0034-0.00180.0154-4.14871.4093-3.2113
80.2784-0.0084-0.15580.23710.25870.39940.0103-0.02390.0169-0.0015-0.02270.0164-0.0075-0.00640.01240.0390-0.00580.00550.00030.0229-11.26326.3829-4.535
90.90620.1858-0.73230.4979-0.25480.8716-0.018-0.0374-0.0018-0.01120.01060.00260.02860.01920.00740.0320.0004-0.0060.0025-0.00050.0184-6.9537-4.5116-26.1253
100.4474-0.003-0.30050.2863-0.07070.4464-0.00460.062-0.0004-0.0459-0.00980.01820.0021-0.0660.01440.0409-0.0021-0.01050.0128-0.00060.0233-12.7739-0.6086-30.8354
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 8
2X-RAY DIFFRACTION2A9 - 24
3X-RAY DIFFRACTION3A25 - 40
4X-RAY DIFFRACTION4A41 - 56
5X-RAY DIFFRACTION5A57 - 70
6X-RAY DIFFRACTION6A71 - 89
7X-RAY DIFFRACTION7A90 - 105
8X-RAY DIFFRACTION8A106 - 145
9X-RAY DIFFRACTION9A146 - 171
10X-RAY DIFFRACTION10A172 - 210

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