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- PDB-1t6c: Structural characterization of the Ppx/GppA protein family: cryst... -

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Basic information

Entry
Database: PDB / ID: 1t6c
TitleStructural characterization of the Ppx/GppA protein family: crystal structure of the Aquifex aeolicus family member
Componentsexopolyphosphatase
KeywordsHYDROLASE / alpha/beta protein / Actin-like fold
Function / homology
Function and homology information


guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity / pyrophosphatase activity / nucleobase-containing small molecule interconversion / regulation of transcription by RNA polymerase II / metal ion binding
Similarity search - Function
Ppx/GppA phosphatase / Ppx/GppA phosphatase family / Exopolyphosphatase. Domain 2 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Exopolyphosphatase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Molecular replacement with partial model, followed by the Arp/Warp procedure. / Resolution: 1.53 Å
AuthorsKristensen, O. / Laurberg, M. / Liljas, A. / Kastrup, J.S. / Gajhede, M.
Citation
Journal: Biochemistry / Year: 2004
Title: Structural characterization of the stringent response related exopolyphosphatase/guanosine pentaphosphate phosphohydrolase protein family
Authors: Kristensen, O. / Laurberg, M. / Liljas, A. / Kastrup, J.S. / Gajhede, M.
#1: Journal: Science / Year: 2001
Title: Role of inorganic polyphosphate in promoting ribosomal protein degradation by the Lon protease in E. coli
Authors: Kuroda, A. / Nomura, K. / Ohtomo, R. / Kato, J. / Ikeda, T. / Takiguchi, N. / Ohtake, H. / Kornberg, A.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Guanosine pentaphosphate phosphohydrolase of Escherichia coli is a long-chain exopolyphosphatase
Authors: Keasling, J.D. / Bertsch, L. / Kornberg, A.
#3: Journal: Trends Biochem.Sci. / Year: 1993
Title: Exopolyphosphate phosphatase and guanosine pentaphosphate phosphatase belong to the sugar kinase/actin/hsp 70 superfamily
Authors: Reizer, J. / Reizer, A. / Saier Jr., M.H. / Bork, P. / Sander, C.
History
DepositionMay 6, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: exopolyphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,81412
Polymers35,8311
Non-polymers98211
Water7,026390
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.776, 70.287, 90.783
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological relevant unit is monomeric.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein exopolyphosphatase / Ppx/GppA phosphatase


Mass: 35831.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: ppx / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS
References: UniProt: O67040, exopolyphosphatase, guanosine-5'-triphosphate,3'-diphosphate phosphatase

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Non-polymers , 5 types, 401 molecules

#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.3 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: MPD, MES, TRIS, KCl, DTT, The crystal was soaked in K2HgI4/KI containing solution, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.993 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 13, 2000
RadiationMonochromator: BENDABLE ASYMMETRICALLY CUT SI(111) CRYSTAL IN COMBINATION WITH VERTICALLY FOCUSING MIRROR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.993 Å / Relative weight: 1
ReflectionResolution: 1.53→15 Å / Num. all: 47505 / Num. obs: 47505 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.061 / Net I/σ(I): 22.8
Reflection shellResolution: 1.53→1.61 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 2.2 / Num. unique all: 5936 / Rsym value: 0.24 / % possible all: 84.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
ARP/wARPmodel building
RefinementMethod to determine structure: Molecular replacement with partial model, followed by the Arp/Warp procedure.
Starting model: A very incomplete model was obtained through experimental phasing and Arp/Warp tracing of the Type II crystal form

Resolution: 1.53→15 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.934 / SU B: 1.703 / SU ML: 0.058 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.073 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.217 472 1 %RANDOM
Rwork0.162 ---
obs0.162 46991 95.6 %-
all-47463 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.249 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å20 Å2
2---1 Å20 Å2
3---1.88 Å2
Refinement stepCycle: LAST / Resolution: 1.53→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2456 0 53 390 2899
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222609
X-RAY DIFFRACTIONr_bond_other_d0.0020.022552
X-RAY DIFFRACTIONr_angle_refined_deg1.49423517
X-RAY DIFFRACTIONr_angle_other_deg0.8535955
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1885305
X-RAY DIFFRACTIONr_chiral_restr0.0870.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022728
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02503
X-RAY DIFFRACTIONr_nbd_refined0.2160.2549
X-RAY DIFFRACTIONr_nbd_other0.240.23004
X-RAY DIFFRACTIONr_nbtor_other0.0840.21677
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2280
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.290
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.245
X-RAY DIFFRACTIONr_mcbond_it0.8791.51533
X-RAY DIFFRACTIONr_mcangle_it1.69822519
X-RAY DIFFRACTIONr_scbond_it2.61731076
X-RAY DIFFRACTIONr_scangle_it4.4854.5998
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 30 -
Rwork0.247 2892 -
obs-2657 82 %

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