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- PDB-3qdf: Crystal structure of 2-hydroxyhepta-2,4-diene-1,7-dioate isomeras... -

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Basic information

Entry
Database: PDB / ID: 3qdf
TitleCrystal structure of 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase from Mycobacterium marinum
Components2-hydroxyhepta-2,4-diene-1,7-dioate isomerase
KeywordsISOMERASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID / 2-hydroxyhepta-2 / 4-diene-1 / 7-dioate isomerase / Mycobacterium / tuberculosis / non-pathogenic species / Rv2993c ortholog / homoprotocatechuate degradative pathway / 4-dienedioate / 2-oxohept-3-enedioate
Function / homology
Function and homology information


acetylpyruvate hydrolase activity / isomerase activity / metal ion binding
Similarity search - Function
Rv2993c-like, N-terminal / Rv2993c-like, N-terminal / FAH / Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase C-terminal / SH3 type barrels. / Roll ...Rv2993c-like, N-terminal / Rv2993c-like, N-terminal / FAH / Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase C-terminal / SH3 type barrels. / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
2-hydroxyhepta-2,4-diene-1,7-dioate isomerase
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 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
DepositionJan 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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Assembly

Deposited unit
A: 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4156
Polymers28,0981
Non-polymers3175
Water3,441191
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.700, 104.930, 136.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase


Mass: 28097.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (bacteria) / Strain: M / Gene: MMAR_1718 / Production host: Escherichia coli (E. coli)
References: UniProt: B2HIH3, 5-carboxymethyl-2-hydroxymuconate Delta-isomerase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 3.05 Å3/Da / Density % sol: 59.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: MymaA.00471.a.A1 PW30262 at 26.1 mg/mL against PACT screen condition A12, 10 mM ZnCl2, 0.1 M NaOAc pH 5.0, 20% PEG 6000 and cryo-protected with 25% ethylene glycol, crystal tracking ID ...Details: MymaA.00471.a.A1 PW30262 at 26.1 mg/mL against PACT screen condition A12, 10 mM ZnCl2, 0.1 M NaOAc pH 5.0, 20% PEG 6000 and cryo-protected with 25% ethylene glycol, crystal tracking ID 218461a12, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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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: Jan 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 22070 / Num. obs: 21732 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 31.963 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 14.42
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.05-2.12.80.4612.941441597146791.9
2.1-2.160.3963.15053156498.6
2.16-2.220.3813.65028148298.1
2.22-2.290.30754740140594
2.29-2.370.2555.45585142699.7
2.37-2.450.24165902138299.9
2.45-2.540.2127.465231362100
2.54-2.650.2057.66197128699.8
2.65-2.760.172958591235100
2.76-2.90.12110.957961202100
2.9-3.060.09612.854281129100
3.06-3.240.07915.45228107699.9
3.24-3.470.06521.44871102899.8
3.47-3.740.04730.4439995099.5
3.74-4.10.04234.5384085899.1
4.1-4.580.02943.9386180499.9
4.58-5.290.02843.13467725100
5.29-6.480.03732.6282160299.8
6.48-9.170.02541.92253493100
9.170.01953.4106225686.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 54.02 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å19.24 Å
Translation3 Å19.24 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2dfu molecule A, protein only

2dfu


Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.1908 / WRfactor Rwork: 0.1502 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8478 / SU B: 8.637 / SU ML: 0.103 / SU R Cruickshank DPI: 0.1588 / SU Rfree: 0.1536 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 1119 5.2 %RANDOM
Rwork0.1826 ---
obs0.185 21644 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 55.22 Å2 / Biso mean: 26.6039 Å2 / Biso min: 6.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--1.14 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1862 0 14 191 2067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221935
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.972643
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6415256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9292475
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04615296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0911514
X-RAY DIFFRACTIONr_chiral_restr0.0870.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0221466
X-RAY DIFFRACTIONr_mcbond_it0.621.51263
X-RAY DIFFRACTIONr_mcangle_it1.07322050
X-RAY DIFFRACTIONr_scbond_it1.6683672
X-RAY DIFFRACTIONr_scangle_it2.7174.5590
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 78 -
Rwork0.312 1381 -
all-1459 -
obs--91.42 %
Refinement TLS params.Method: refined / Origin x: 7.9664 Å / Origin y: 0.5843 Å / Origin z: 53.6786 Å
111213212223313233
T0.0502 Å20.0315 Å2-0.0006 Å2-0.0524 Å2-0.0235 Å2--0.0409 Å2
L0.9107 °2-0.1842 °20.1073 °2-1.2503 °2-0.1899 °2--1.575 °2
S0.1154 Å °0.1135 Å °-0.0637 Å °-0.2182 Å °-0.0853 Å °-0.0003 Å °0.0153 Å °0.0335 Å °-0.0302 Å °

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