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- PDB-2o2g: Crystal structure of Dienelactone hydrolase (YP_324580.1) from An... -

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Basic information

Entry
Database: PDB / ID: 2o2g
TitleCrystal structure of Dienelactone hydrolase (YP_324580.1) from Anabaena variabilis ATCC 29413 at 1.92 A resolution
ComponentsDienelactone hydrolase
KeywordsHYDROLASE / YP_324580.1 / Dienelactone hydrolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Dienelactone hydrolase / Dienelactone hydrolase family / : / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Dienelactone hydrolase
Similarity search - Component
Biological speciesAnabaena variabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.92 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Dienelactone hydrolase (YP_324580.1) from Anabaena variabilis ATCC 29413 at 1.92 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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
Revision 1.5Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dienelactone hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5305
Polymers24,2141
Non-polymers3164
Water3,027168
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.895, 62.465, 67.998
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dienelactone hydrolase


Mass: 24214.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena variabilis (bacteria) / Gene: YP_324580.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3M5Q1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.1 Å3/Da / Density % sol: 41.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 9.5
Details: 1.26M (NH4)2SO4, 0.2M NaCl, 0.1M CHES pH 9.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.94645, 0.97942, 0.97921
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 19, 2006 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.946451
20.979421
30.979211
ReflectionResolution: 1.92→39.163 Å / Num. obs: 14877 / % possible obs: 92 % / Redundancy: 3.9 % / Biso Wilson estimate: 20.056 Å2 / Rmerge(I) obs: 0.07 / Χ2: 1.068 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.92-1.992.60.2752.85712730.93681
1.99-2.073.20.23614540.93291.9
2.07-2.163.70.21515520.95798.1
2.16-2.283.90.18610421.12165.4
2.28-2.424.20.15716040.97699.9
2.42-2.614.20.11715971.03399.8
2.61-2.874.30.09416011.18699.8
2.87-3.284.20.0616281.1199.7
3.28-4.144.10.0514131.17486
4.14-5040.03517131.13997.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0005refinement
SCALEPACKdata scaling
PDB_EXTRACT2data extraction
DENZOdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.92→39.163 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.103 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.172
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.70 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. TWO SULFATE MOLECULES FROM CRYSTALLIZATION SOLUTION AND TWO ETHYLENE GLYCOL MOLECULES (CRYOPROTECTANT) ARE INCLUDED IN THE MODEL. 5. ELECTRON DENSITY CORRESPONDING TO RESIDUES 1-6 WAS DISORDERED AND THESE RESIDUES WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 740 5 %RANDOM
Rwork0.183 ---
obs0.186 14828 91.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.006 Å2
Baniso -1Baniso -2Baniso -3
1-2.74 Å20 Å20 Å2
2---1.24 Å20 Å2
3----1.5 Å2
Refinement stepCycle: LAST / Resolution: 1.92→39.163 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 18 168 1798
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221688
X-RAY DIFFRACTIONr_bond_other_d0.0020.021576
X-RAY DIFFRACTIONr_angle_refined_deg1.6881.9772308
X-RAY DIFFRACTIONr_angle_other_deg0.91733644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.665225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.82723.82468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.20115261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1581511
X-RAY DIFFRACTIONr_chiral_restr0.0920.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021904
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02325
X-RAY DIFFRACTIONr_nbd_refined0.2140.3343
X-RAY DIFFRACTIONr_nbd_other0.1670.31619
X-RAY DIFFRACTIONr_nbtor_refined0.1750.5808
X-RAY DIFFRACTIONr_nbtor_other0.0830.51012
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.5216
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1030.37
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2260.358
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.516
X-RAY DIFFRACTIONr_mcbond_it2.11531110
X-RAY DIFFRACTIONr_mcbond_other0.623446
X-RAY DIFFRACTIONr_mcangle_it2.97751745
X-RAY DIFFRACTIONr_scbond_it5.418640
X-RAY DIFFRACTIONr_scangle_it6.9911558
LS refinement shellResolution: 1.92→1.969 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 50 -
Rwork0.252 849 -
obs-899 77.63 %
Refinement TLS params.Method: refined / Origin x: 32.1491 Å / Origin y: 4.2548 Å / Origin z: 15.1916 Å
111213212223313233
T-0.1706 Å2-0.0084 Å20.0055 Å2--0.1423 Å20.0063 Å2---0.1384 Å2
L1.1062 °2-0.6773 °20.1588 °2-2.0487 °20.3537 °2--1.8003 °2
S-0.0565 Å °-0.0549 Å °-0.0105 Å °0.0035 Å °0.0985 Å °0.0002 Å °-0.0339 Å °0.0407 Å °-0.042 Å °
Refinement TLS groupSelection: ALL

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