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- PDB-2j4r: Structural Study of the Aquifex aeolicus PPX-GPPA enzyme -

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Basic information

Entry
Database: PDB / ID: 2j4r
TitleStructural Study of the Aquifex aeolicus PPX-GPPA enzyme
ComponentsEXOPOLYPHOSPHATASE
KeywordsHYDROLASE / PPGPP / AQUIFEX AEOLICUS / STRINGENT RESPONSE / EXOPOLYPHOSPHATASE / GUANOSINE PENTAPHOSPHATE
Function / homology
Function and homology information


pyrophosphatase activity / 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
GUANOSINE-5',3'-TETRAPHOSPHATE / Exopolyphosphatase
Similarity search - Component
Biological speciesAQUIFEX AEOLICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsKristensen, O.
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: Structure of the Ppx/Gppa Phosphatase from Aquifex Aeolicus in Complex with the Alarmone Ppgpp
Authors: Kristensen, O. / Ross, B. / Gajhede, M.
#1: 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.
History
DepositionSep 5, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EXOPOLYPHOSPHATASE
B: EXOPOLYPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6003
Polymers69,9972
Non-polymers6031
Water3,045169
1
A: EXOPOLYPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6022
Polymers34,9981
Non-polymers6031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: EXOPOLYPHOSPHATASE


Theoretical massNumber of molelcules
Total (without water)34,9981
Polymers34,9981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)70.460, 70.460, 223.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.98603, 0.01721, 0.16569), (0.02173, 0.99944, 0.02548), (-0.16516, 0.02872, -0.98585)
Vector: -60.31409, -0.46948, -39.36101)

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Components

#1: Protein EXOPOLYPHOSPHATASE / GUANOSINE PENTAPHOSPHATE PHOSPHOHYDROLASE


Mass: 34998.434 Da / Num. of mol.: 2 / Fragment: RESIDUES 7-310 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AQUIFEX AEOLICUS (bacteria) / Plasmid: PET28-A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O67040
#2: Chemical ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N5O17P4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 19 TO ASN ENGINEERED RESIDUE IN CHAIN B, TYR 19 TO ASN

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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: 2.36 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growDetails: SODIUM ACETATE, MES, MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.085
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 28, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.085 Å / Relative weight: 1
ReflectionResolution: 2.71→74.54 Å / Num. obs: 85915 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 35.9 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.5
Reflection shellResolution: 2.71→2.86 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.2 / % possible all: 88.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T6C

1t6c


Resolution: 2.71→61.02 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 1874853.94 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.296 439 2.5 %RANDOM
Rwork0.212 ---
obs0.212 17621 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.7665 Å2 / ksol: 0.328112 e/Å3
Displacement parametersBiso mean: 43.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.224 Å2-5.98 Å20 Å2
2---0.224 Å20 Å2
3---0.449 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.71→61.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4792 0 36 169 4997
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.42
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it3.032.5
LS refinement shellResolution: 2.71→2.88 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.343 61 2.3 %
Rwork0.278 2571 -
obs--89.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3G4P_CNS_PRODRG.PARAMG4P_CNS_PRODRG.TOP

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