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- PDB-5a60: Crystal structure of full-length E. coli ygiF in complex with tri... -

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Basic information

Entry
Database: PDB / ID: 5a60
TitleCrystal structure of full-length E. coli ygiF in complex with tripolyphosphate and two magnesium ions
ComponentsINORGANIC TRIPHOSPHATASE
KeywordsHYDROLASE / INORGANIC POLYPHOSPHATE / TRIPOLYPHOSPHATE / TRIPHOSPHATE TUNNEL METALLOENZYMES
Function / homology
Function and homology information


triphosphatase / inorganic triphosphate phosphatase activity / metal ion binding
Similarity search - Function
Inorganic triphosphatase YgiF / CHAD domain / 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 / SAD / Resolution: 1.82 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 1.3Nov 6, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software / Item: _pdbx_database_status.status_code_sf
Revision 1.4May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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)49,0696
Polymers48,6381
Non-polymers4315
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.924, 89.924, 125.577
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-3PO / TRIPHOSPHATE


Mass: 257.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H5O10P3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 3.01 Å3/Da / Density % sol: 59.18 % / 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: 1.00001
DetectorType: DECTRIS HYBRID PHOTON / Date: Mar 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.82→48.88 Å / Num. obs: 50673 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.91
Reflection shellResolution: 1.82→1.93 Å / Redundancy: 9.06 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 2.18 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
XDSdata scaling
SHELXDphasing
SHARPphasing
RESOLVEphasing
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.82→48.88 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / SU B: 6.625 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.18948 2518 5 %RANDOM
Rwork0.15053 ---
obs0.15253 47520 97.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.658 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å2-0.28 Å20 Å2
2---0.56 Å20 Å2
3---1.82 Å2
Refinement stepCycle: LAST / Resolution: 1.82→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3385 0 23 289 3697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193496
X-RAY DIFFRACTIONr_bond_other_d0.0010.023334
X-RAY DIFFRACTIONr_angle_refined_deg1.1491.9544752
X-RAY DIFFRACTIONr_angle_other_deg0.8737640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.425432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3624.059170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3415580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4381526
X-RAY DIFFRACTIONr_chiral_restr0.0640.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213986
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02820
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_it3.0764.841722
X-RAY DIFFRACTIONr_mcbond_other3.0774.8381721
X-RAY DIFFRACTIONr_mcangle_it4.2487.2592153
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7925.3351774
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_restr1.19336830
X-RAY DIFFRACTIONr_sphericity_free34.338574
X-RAY DIFFRACTIONr_sphericity_bonded18.98356974
LS refinement shellResolution: 1.823→1.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 186 -
Rwork0.381 3314 -
obs--92.01 %
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)
10.7467-0.18850.5350.45040.1760.62360.055-0.0519-0.02880.0009-0.0158-0.01650.0517-0.0612-0.03920.0729-0.01280.00140.07250.01940.006820.677747.724575.4268
20.37020.0735-0.00720.04060.11360.5224-0.00450.05460.04130.00170.02280.00440.030.0173-0.01840.0692-0.00750.00720.06660.00330.0332.271659.943765.9808
30.41110.1809-0.17931.8476-0.7490.34120.0060.00480.01020.02-0.0243-0.07390.0059-0.00210.01820.0575-0.001-0.00070.0704-0.00080.017637.944351.50576.0587
41.34810.3256-0.58530.0836-0.11120.48330.0009-0.04150.1615-0.00080.01340.04170.0080.0896-0.01430.03820.0020.00070.0507-0.00880.041643.995165.903866.3039
50.1525-0.0426-0.0320.0987-0.03140.1519-0.0052-0.00310.02940.00780.00560.0143-0.0068-0.0051-0.00040.06550.0013-0.00080.0658-0.00110.019724.869351.646474.1479
60.05510.05060.02850.04660.02620.015-0.00340.00230.0076-0.00330.00010.00730.00230.00090.00330.06820.0010.00170.0680.00010.019736.490237.262171.2265
70.1080.01660.12910.05480.00690.196-0.0015-0.0154-0.00770.00160.0010.00360.0063-0.01620.00050.06670.00070.00160.0676-0.00010.018133.98429.542784.0136
80.0212-0.01290.04740.07250.01510.16180.0033-0.0039-0.0006-0.0083-0.0058-0.00770.00430.0050.00250.0689-0.0009-0.00020.0652-0.00030.018450.763616.765574.44
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 28
2X-RAY DIFFRACTION2A29 - 67
3X-RAY DIFFRACTION3A68 - 84
4X-RAY DIFFRACTION4A85 - 117
5X-RAY DIFFRACTION5A118 - 176
6X-RAY DIFFRACTION6A177 - 251
7X-RAY DIFFRACTION7A252 - 337
8X-RAY DIFFRACTION8A338 - 428

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