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- PDB-2yvt: Crystal structure of aq_1956 -

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Basic information

Entry
Database: PDB / ID: 2yvt
TitleCrystal structure of aq_1956
ComponentsHypothetical protein aq_1956
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyMetallophosphoesterase, TT1561-like / Metallophosphatase TT1561 / Metallophosphoesterase, calcineurin superfamily / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta / Metallophosphoesterase TT1561-like domain-containing protein
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsIshii, R. / Bessho, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of aq_1956
Authors: Ishii, R. / Bessho, Y. / Yokoyama, S.
History
DepositionApr 15, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 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 / pdbx_struct_special_symmetry / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein aq_1956


Theoretical massNumber of molelcules
Total (without water)30,0221
Polymers30,0221
Non-polymers00
Water5,999333
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.733, 72.733, 90.873
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-267-

HOH

21A-338-

HOH

31A-480-

HOH

41A-572-

HOH

51A-581-

HOH

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Components

#1: Protein Hypothetical protein aq_1956


Mass: 30022.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: UPF0047 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta834(DE3) / References: UniProt: O67769
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 293 K / Method: oil batch / pH: 4.5
Details: 30% (w/v) PEG 8000, 0.1M acetate, 0.2M Li Sulfate , pH 4.5, oil batch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97893 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 24, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 37608 / Num. obs: 37232 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 48
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 6 % / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 7.8 / Num. unique all: 3679 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1UF3

1uf3


Resolution: 1.6→19.27 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.658 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20189 1858 5 %RANDOM
Rwork0.16951 ---
obs0.17114 35321 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.818 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2103 0 0 333 2436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222157
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1531.9652918
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.815256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9323.645107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39615381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.5351515
X-RAY DIFFRACTIONr_chiral_restr0.0790.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021650
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.21087
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21498
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2254
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.252
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7121321
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.41132082
X-RAY DIFFRACTIONr_scbond_it2.0162937
X-RAY DIFFRACTIONr_scangle_it2.9173836
X-RAY DIFFRACTIONr_rigid_bond_restr1.5932258
X-RAY DIFFRACTIONr_sphericity_free4.5343333
X-RAY DIFFRACTIONr_sphericity_bonded3.06532103
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 137 -
Rwork0.167 2549 -
obs--99.44 %

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