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Basic information

Entry
Database: PDB / ID: 4dbf
TitleCrystal structures of Cg1458
Components2-HYDROXYHEPTA-2,4-DIENE-1,7-DIOATE ISOMERASE
KeywordsISOMERASE / oxaloacetate decarboxylase
Function / homology
Function and homology information


Lyases; Carbon-carbon lyases; Carboxy-lyases / Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / isomerase activity / lyase 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 family / SH3 type barrels. ...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 family / SH3 type barrels. / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (Catechol pathway)
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRan, T.T. / Xu, D.Q. / Wang, W.W. / Gao, Y.Y. / Wang, M.T.
CitationJournal: Biochem.J. / Year: 2013
Title: Crystal structures of Cg1458 reveal a catalytic lid domain and a common catalytic mechanism for FAH family.
Authors: Ran, T. / Gao, Y. / Marsh, M. / Zhu, W. / Wang, M. / Mao, X. / Xu, L. / Xu, D. / Wang, W.
History
DepositionJan 15, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Data collection / Database references / Category: reflns_shell / struct_ref_seq_dif
Item: _reflns_shell.d_res_high / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 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_ncs_dom_lim / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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-DIOATE ISOMERASE
B: 2-HYDROXYHEPTA-2,4-DIENE-1,7-DIOATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4745
Polymers62,4012
Non-polymers733
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-34 kcal/mol
Surface area20150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.120, 124.120, 73.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4 / Auth seq-ID: 1 - 268 / Label seq-ID: 21 - 288

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein 2-HYDROXYHEPTA-2,4-DIENE-1,7-DIOATE ISOMERASE / 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1 / 7-dioic acid hydratase (Catechol pathway)


Mass: 31200.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q8NQY2, Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds, Lyases; Carbon-carbon lyases; Carboxy-lyases
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M MgCl2, 0.1M Bis-Tris pH 6.0, 25% w/v Polyethylene Glycol 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 26, 2010
RadiationMonochromator: SSRF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→87.77 Å / Num. obs: 45001 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.9-2197.6
2-20198.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0110refinement
XDSpackagedata reduction
XDSpackagedata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DFU

2dfu


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.489 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.15 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24365 2288 5.1 %RANDOM
Rwork0.19395 ---
obs0.19645 42829 98.47 %-
all-45001 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.704 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3903 0 3 222 4128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224007
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.011.9855451
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0745517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.17425.063158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23615677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6431521
X-RAY DIFFRACTIONr_chiral_restr0.1460.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0223023
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.2591.52579
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.08324193
X-RAY DIFFRACTIONr_scbond_it3.12231428
X-RAY DIFFRACTIONr_scangle_it4.9914.51256
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1922 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.510.5
Bmedium thermal2.052
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 162 -
Rwork0.234 3115 -
obs--97.7 %

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