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- PDB-2ffi: Crystal Structure of Putative 2-Pyrone-4,6-Dicarboxylic Acid Hydr... -

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Basic information

Entry
Database: PDB / ID: 2ffi
TitleCrystal Structure of Putative 2-Pyrone-4,6-Dicarboxylic Acid Hydrolase from Pseudomonas putida, Northeast Structural Genomics Target PpR23.
Components2-pyrone-4,6-dicarboxylic acid hydrolase, putative
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / TIM-barrel protein. / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


2-pyrone-4,6-dicarboxylate lactonase / 2-pyrone-4,6-dicarboxylate lactonase activity
Similarity search - Function
: / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / 2-pyrone-4,6-dicarboxylic acid hydrolase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.61 Å
AuthorsForouhar, F. / Su, M. / Jayaraman, S. / Conover, K. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of Putative 2-Pyrone-4,6-Dicarboxylic Acid Hydrolase from Pseudomonas putida, Northeast Structural Genomics Target PpR23.
Authors: Forouhar, F. / Su, M. / Jayaraman, S. / Conover, K. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
History
DepositionDec 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: 2-pyrone-4,6-dicarboxylic acid hydrolase, putative
B: 2-pyrone-4,6-dicarboxylic acid hydrolase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0454
Polymers64,8552
Non-polymers1902
Water99155
1
A: 2-pyrone-4,6-dicarboxylic acid hydrolase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5232
Polymers32,4281
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2-pyrone-4,6-dicarboxylic acid hydrolase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5232
Polymers32,4281
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.392, 46.289, 64.078
Angle α, β, γ (deg.)80.86, 76.86, 80.61
Int Tables number1
Space group name H-MP1

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Components

#1: Protein 2-pyrone-4,6-dicarboxylic acid hydrolase, putative


Mass: 32427.701 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: KT2440 / Gene: PP1699 / Plasmid: pET2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q88M75
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 1.89 Å3/Da / Density % sol: 34.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 100mM Na Acetate, 22.1% PEG3350, 100 mM KH2PO4, and 5 mM DTT, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9790, 0.9795, 0.9670
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 4, 2005 / Details: Mirrors.
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97951
30.9671
ReflectionResolution: 2.6→28.91 Å / Num. all: 28897 / Num. obs: 28492 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.133 / Rsym value: 0.112 / Net I/σ(I): 8.95
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 3 / Num. unique all: 1403 / Rsym value: 0.364 / % possible all: 97.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
XTALVIEWrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.61→28.91 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 259422.81 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.287 2116 9.3 %RANDOM
Rwork0.228 ---
all0.23 28492 --
obs0.228 22655 78.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 16.5855 Å2 / ksol: 0.294793 e/Å3
Displacement parametersBiso mean: 25.9 Å2
Baniso -1Baniso -2Baniso -3
1--4.43 Å23.9 Å2-3.88 Å2
2---0.9 Å2-6.59 Å2
3---5.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.61→28.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4266 0 10 55 4331
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 223 9.3 %
Rwork0.277 2176 -
obs-2176 48.9 %

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