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- PDB-2pw6: Crystal structure of uncharacterized protein JW3007 from Escheric... -

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Basic information

Entry
Database: PDB / ID: 2pw6
TitleCrystal structure of uncharacterized protein JW3007 from Escherichia coli K12
ComponentsUncharacterized protein ygiD
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / JW3007 / Uncharacterized protein / ESCHERICHIA COLI STRUCTURAL GENOMICS / PROTEIN STRUCTURE / Riken and PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


stizolobate synthase / DOPA dioxygenase activity / stizolobate synthase activity / cellular aromatic compound metabolic process / ferrous iron binding / zinc ion binding / cytoplasm
Similarity search - Function
Extradiol aromatic ring-opening dioxygenase, DODA-type / Protocatechuate 4,5-dioxygenase; Chain B / LigB-like / Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B / Catalytic LigB subunit of aromatic ring-opening dioxygenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4,5-DOPA dioxygenase extradiol
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.27 Å
AuthorsNewton, M.G. / Takagi, Y. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokayama, S. / Li, Y. / Chen, L. / Zhu, J. / Ruble, J. ...Newton, M.G. / Takagi, Y. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokayama, S. / Li, Y. / Chen, L. / Zhu, J. / Ruble, J. / Liu, Z.J. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG) / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of uncharacterized protein JW3007 from Escherichia coli K12.
Authors: Newton, M.G. / Takagi, Y. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokayama, S. / Li, Y. / Chen, L. / Zhu, J. / Ruble, J. / Liu, Z.J. / Rose, J.P. / Wang, B.-C.
History
DepositionMay 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Sep 13, 2017Group: Refinement description / Category: refine / Item: _refine.pdbx_method_to_determine_struct
Revision 1.4Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein ygiD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6894
Polymers30,4931
Non-polymers1963
Water91951
1
A: Uncharacterized protein ygiD
hetero molecules

A: Uncharacterized protein ygiD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3788
Polymers60,9862
Non-polymers3926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2350 Å2
ΔGint-202 kcal/mol
Surface area18970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)83.940, 83.940, 85.509
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-273-

ZN

DetailsThe biological assembly is a homo-dimer generated by a diagonal two-fold rotation axis of the space group [x,y,z; y,x,-z]. The homo-dimer has a very high complexation significance score (CSS) of 0.967 [PISA web site results at EBI]. The other four components of the unit cell are generated by operation of the three-fold screw axis 3(1).

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Components

#1: Protein Uncharacterized protein ygiD


Mass: 30492.955 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ygiD, b3039, JW3007 / Plasmid: PCR2.1-TOPO / Production host: Escherichia coli (E. coli) / References: UniProt: P24197
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2 microliter drops containing equal volumes of protein concentrate (11.38 mg/ml) in 20mM Tris-HCl, 200mM NaCl, 1mM DTT and resevoir solution containing 0.1M Hepes, 0.8M Sodium acetate, and 0. ...Details: 2 microliter drops containing equal volumes of protein concentrate (11.38 mg/ml) in 20mM Tris-HCl, 200mM NaCl, 1mM DTT and resevoir solution containing 0.1M Hepes, 0.8M Sodium acetate, and 0.05M Cadmium sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97243 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 6, 2006 / Details: ROSENBAUM
RadiationMonochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97243 Å / Relative weight: 1
ReflectionResolution: 2.27→72.74 Å / Num. obs: 16342 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 20.7 % / Rsym value: 0.096 / Net I/σ(I): 18.1
Reflection shellResolution: 2.27→2.35 Å / Redundancy: 20.7 % / Mean I/σ(I) obs: 5.63 / Rsym value: 0.63 / % possible all: 100

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Processing

Software
NameVersionClassification
SCA2STRUCTUREmodel building
REFMAC5.2.0019refinement
SERGUIdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SCA2STRUCTUREphasing
RefinementMethod to determine structure: SAD / Resolution: 2.27→72.74 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.833 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2667 825 5.1 %RANDOM
Rwork0.23457 ---
obs0.23616 15481 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.677 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å2-0.49 Å20 Å2
2---0.98 Å20 Å2
3---1.47 Å2
Refinement stepCycle: LAST / Resolution: 2.27→72.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1869 0 3 51 1923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221928
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.952638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7725241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.49223.89677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.81415281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.464157
X-RAY DIFFRACTIONr_chiral_restr0.1220.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021484
X-RAY DIFFRACTIONr_nbd_refined0.2130.2895
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21264
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.269
X-RAY DIFFRACTIONr_metal_ion_refined0.0550.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.24
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.4820.21
X-RAY DIFFRACTIONr_mcbond_it1.0221.51236
X-RAY DIFFRACTIONr_mcangle_it1.55421942
X-RAY DIFFRACTIONr_scbond_it2.1973815
X-RAY DIFFRACTIONr_scangle_it3.0084.5696
LS refinement shellResolution: 2.27→2.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 61 -
Rwork0.348 1101 -
obs--97.24 %

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