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- PDB-3i7v: Crystal structure of AP4A hydrolase complexed with AP4A (ATP) (aq... -

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Basic information

Entry
Database: PDB / ID: 3i7v
TitleCrystal structure of AP4A hydrolase complexed with AP4A (ATP) (aq_158) from Aquifex aeolicus Vf5
ComponentsAP4A hydrolase
KeywordsHYDROLASE / NUDIX PROTEIN / DIADENOSINE POLYPHOSPHATE / AP4A / STRUCTURAL GENOMICS / NPPSFA / NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI
Function / homology
Function and homology information


AMP biosynthetic process / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / ATP biosynthetic process / ATP binding
Similarity search - Function
NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / BIS(ADENOSINE)-5'-TETRAPHOSPHATE / AP4A hydrolase
Similarity search - Component
Biological speciesAquifex aeolicus Vf5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsJeyakanthan, J. / Kanaujia, S.P. / Nakagawa, N. / Sekar, K. / Kuramitsu, S. / Shinkai, A. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Free and ATP-bound structures of Ap(4)A hydrolase from Aquifex aeolicus V5
Authors: Jeyakanthan, J. / Kanaujia, S.P. / Nishida, Y. / Nakagawa, N. / Praveen, S. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Sekar, K.
History
DepositionJul 9, 2009Deposition site: RCSB / Processing site: PDBJ
SupersessionJul 21, 2009ID: 2PQ1
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: AP4A hydrolase
B: AP4A hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,04014
Polymers31,5712
Non-polymers2,46912
Water6,215345
1
A: AP4A hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3156
Polymers15,7851
Non-polymers1,5305
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AP4A hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7258
Polymers15,7851
Non-polymers9407
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.301, 59.234, 67.419
Angle α, β, γ (deg.)90.00, 92.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein AP4A hydrolase


Mass: 15785.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus Vf5 (bacteria) / Strain: VF5 / Gene: apfA, aq_158 / Plasmid: pET21A / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA(DE3) / References: UniProt: O66548

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Non-polymers , 5 types, 357 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-B4P / BIS(ADENOSINE)-5'-TETRAPHOSPHATE / Ap4A


Mass: 836.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28N10O19P4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 0.1M Tris-Hcl, 25% PEG 3350, 0.2M NaCl, pH 8.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 12, 2007 / Details: Rh Coated Bent-Cyrindrical Mirror
RadiationMonochromator: Si (1 1 1) Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 20328 / % possible obs: 99.8 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.058 / Num. measured all: 107834
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.227 / Num. unique all: 1996 / Rsym value: 0.249 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3I7U

3i7u


Resolution: 1.95→35.27 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 158515.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1943 9.9 %RANDOM
Rwork0.194 ---
obs0.194 19707 96.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.7512 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1--4.92 Å20 Å24.91 Å2
2--0.89 Å20 Å2
3---4.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.95→35.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2232 0 155 345 2732
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d1.31
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.333 299 9.6 %
Rwork0.267 2800 -
obs--91.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramion.top
X-RAY DIFFRACTION3ion.paramwater_protin.top
X-RAY DIFFRACTION4ligand.paramligand.top

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