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- PDB-5a61: Crystal structure of full-length E. coli ygiF in complex with tri... -

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Basic information

Entry
Database: PDB / ID: 5a61
TitleCrystal structure of full-length E. coli ygiF in complex with tripolyphosphate and two manganese ions.
ComponentsINORGANIC TRIPHOSPHATASE
KeywordsHYDROLASE / TRIPOLYPHOSPHATE / TRIPHOSPHATE TUNNEL METALLOENZYME
Function / homology
Function and homology information


triphosphatase / inorganic triphosphate phosphatase activity / metal ion binding
Similarity search - Function
Inorganic triphosphatase YgiF / CHAD domain / CHAD domain profile. / CYTH / CYTH domain / CYTH domain / CYTH domain profile. / CYTH-like domain superfamily
Similarity search - Domain/homology
TRIPHOSPHATE / : / Inorganic triphosphatase / Uncharacterized protein
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.5 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 23, 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 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INORGANIC TRIPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1927
Polymers48,6381
Non-polymers5546
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.676, 89.676, 125.329
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein INORGANIC TRIPHOSPHATASE


Mass: 48638.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL
References: UniProt: V8FJJ2, UniProt: P30871*PLUS, triphosphatase
#2: Chemical ChemComp-3PO / TRIPHOSPHATE


Mass: 257.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H5O10P3
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.99 Å3/Da / Density % sol: 58.88 % / Description: NONE
Crystal growDetails: 20% PEG 3,350, 0.2 M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999990, 1.700020
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: May 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.999991
21.700021
ReflectionResolution: 1.5→48.77 Å / Num. obs: 91340 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 15.48 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.35
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 14.18 % / Rmerge(I) obs: 1.34 / Mean I/σ(I) obs: 2.03 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.5→48.77 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.979 / SU B: 2.375 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED THE SECOND DATA SET CONTAINS ANOMALOUS DATA COLLECTED CLOSE TO THE MN K EDGE, AT 1.7 A. THE DATA SET CAN BE USED TO ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED THE SECOND DATA SET CONTAINS ANOMALOUS DATA COLLECTED CLOSE TO THE MN K EDGE, AT 1.7 A. THE DATA SET CAN BE USED TO CONFIRM THE POSITIONS OF THE TWO METAL COFACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.17087 4513 5 %RANDOM
Rwork0.15145 ---
obs0.15242 86573 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.368 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20.19 Å20 Å2
2--0.38 Å20 Å2
3----1.24 Å2
Refinement stepCycle: LAST / Resolution: 1.5→48.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3381 0 27 295 3703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193492
X-RAY DIFFRACTIONr_bond_other_d0.0020.023329
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.9544747
X-RAY DIFFRACTIONr_angle_other_deg0.8737628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3845432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7324.024169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.83515578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3771526
X-RAY DIFFRACTIONr_chiral_restr0.0660.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213980
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02818
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_it2.3844.5851722
X-RAY DIFFRACTIONr_mcbond_other2.3824.5841721
X-RAY DIFFRACTIONr_mcangle_it3.1236.8872153
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0775.0791770
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_restr0.81436821
X-RAY DIFFRACTIONr_sphericity_free26.526582
X-RAY DIFFRACTIONr_sphericity_bonded14.41856963
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 336 -
Rwork0.256 6408 -
obs--100 %
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)
10.4059-0.0110.42540.71090.7661.2972-0.0046-0.01250.00450.0178-0.0240.01640.0139-0.04130.02860.0257-0.0031-0.0010.01670.00850.043920.703947.494375.2908
20.37880.41330.37630.48750.44990.4192-0.0890.12540.0067-0.04010.1263-0.0126-0.0320.1166-0.03730.076-0.019-0.00930.06380.02520.105732.453157.32164.9362
30.2196-0.04190.0290.14070.03220.1749-0.0262-0.01650.0940.00690.0424-0.0982-0.00650.0292-0.01610.01160.0024-0.0070.0252-0.01830.109238.016660.957770.5019
40.2445-0.0558-0.07090.04110.02630.03210.0010.00840.05310.01850.0238-0.01490.0132-0.0014-0.02480.02070.00760.00050.03270.00060.057127.63852.822672.0894
50.0575-0.02370.02120.0183-0.03060.06790.0031-0.0018-0.0015-0.0007-0.0002-0.00020.0033-0.006-0.00290.02160.0009-0.0010.0236-0.00030.045735.193432.985477.8843
60.01780.01370.02320.12610.05570.19210.003-0.00320.0012-0.0084-0.0013-0.00460.0280.013-0.00180.02880.00370.0010.01820.00050.044750.615316.665674.2899
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 28
2X-RAY DIFFRACTION2A29 - 51
3X-RAY DIFFRACTION3A52 - 108
4X-RAY DIFFRACTION4A109 - 176
5X-RAY DIFFRACTION5A177 - 337
6X-RAY DIFFRACTION6A338 - 428

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