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- PDB-3r6o: Crystal structure of a probable 2-hydroxyhepta-2,4-diene-1, 7-dio... -

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Basic information

Entry
Database: PDB / ID: 3r6o
TitleCrystal structure of a probable 2-hydroxyhepta-2,4-diene-1, 7-dioateisomerase from Mycobacterium abscessus
Components2-hydroxyhepta-2,4-diene-1, 7-dioateisomerase
KeywordsISOMERASE / SSGCID / 2-hydroxyhepta-2 / 4-diene-1 / 7-dioateisomerase / structural genomics / seattle structural genomics center for infectious disease
Function / homology
Function and homology information


SH3 type barrels. - #980 / Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase family / SH3 type barrels. / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Probable 2-hydroxyhepta-2,4-diene-1,7-dioateisomerase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionMar 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 13, 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_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_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-hydroxyhepta-2,4-diene-1, 7-dioateisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3685
Polymers35,2371
Non-polymers1314
Water2,522140
1
A: 2-hydroxyhepta-2,4-diene-1, 7-dioateisomerase
hetero molecules

A: 2-hydroxyhepta-2,4-diene-1, 7-dioateisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,73510
Polymers70,4742
Non-polymers2618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y,z1
Buried area3920 Å2
ΔGint-90 kcal/mol
Surface area20890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.680, 90.680, 76.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-418-

HOH

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Components

#1: Protein 2-hydroxyhepta-2,4-diene-1, 7-dioateisomerase


Mass: 35236.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: ATCC 19977 / DSM 44196 / Gene: MAB_0915c / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1MJ53
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.33 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: EBS JCSG+ SCREEN B8: 200MM MGCL2, 100MM TRIS PH 7.0, 10% PEG 8000, MYABA.00471.B.A1 PS00908 AT 38.0MG/ML, CRYO PROTECTION: 25% PEG 400, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 7, 2010 / Details: RIGAKU VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 22527 / Num. obs: 22511 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 29.55 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.09
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QDF

3qdf


Resolution: 1.95→35.79 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.834 / SU ML: 0.096 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.185 1159 5.2 %RANDOM
Rwork0.15 ---
obs0.152 22475 99.7 %-
all-22527 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.82 Å2
Baniso -1Baniso -2Baniso -3
1--17.38 Å20 Å20 Å2
2---17.38 Å20 Å2
3---34.77 Å2
Refinement stepCycle: LAST / Resolution: 1.95→35.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1932 0 4 140 2076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221993
X-RAY DIFFRACTIONr_bond_other_d0.0010.021331
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.982725
X-RAY DIFFRACTIONr_angle_other_deg0.93133245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6015263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.47222.60373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44615278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8361515
X-RAY DIFFRACTIONr_chiral_restr0.0880.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212238
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02395
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3361.51327
X-RAY DIFFRACTIONr_mcbond_other0.0611.5529
X-RAY DIFFRACTIONr_mcangle_it0.64922124
X-RAY DIFFRACTIONr_scbond_it1.553666
X-RAY DIFFRACTIONr_scangle_it2.5114.5599
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 82 -
Rwork0.178 1526 -
obs--97.69 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.8557-0.5189-0.24757.598-0.63632.95340.2980.5519-0.0938-1.7442-0.2815-0.61380.2876-0.0772-0.01640.60080.09590.14460.4032-0.04760.04464.2594-0.6034-18.8854
21.23620.309-0.13162.12790.17520.3526-0.01960.1162-0.03990.03770.0068-0.1764-0.05820.01120.01290.25670.0049-0.00360.30490.00530.100656.45013.53880.6385
31.82970.51640.11582.49780.68640.790.02390.0485-0.1210.1097-0.0391-0.11760.012-0.06130.01520.250.0033-0.01910.29390.00820.065255.4529-1.8323.1178
41.30190.46930.24461.15610.18110.3465-0.02230.0944-0.0730.0390.0206-0.2439-0.00190.05230.00170.2722-0.0003-0.0140.30350.00270.11762.32823.38844.0426
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 71
2X-RAY DIFFRACTION2A72 - 128
3X-RAY DIFFRACTION3A129 - 187
4X-RAY DIFFRACTION4A188 - 302

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