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- PDB-5olc: Crystal structure of the 3,6-anhydro-D-galactonate cycloisomerase... -

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Basic information

Entry
Database: PDB / ID: 5olc
TitleCrystal structure of the 3,6-anhydro-D-galactonate cycloisomerase from Zobellia galactanivorans
ComponentsGalactonate dehydratase
KeywordsISOMERASE / cycloisomerase / enolase superfamily / 3 / 6-anhydro-D-galactonate / carrageenan
Function / homology
Function and homology information


galactonate dehydratase / galactonate dehydratase activity / amino acid catabolic process
Similarity search - Function
Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain ...Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Galactonate dehydratase
Similarity search - Component
Biological speciesZobellia galactanivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsMichel, G. / Czjzek, M. / Jam, M.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-14-CE19-0020-01 France
French National Research AgencyANR-10-BTBR-04 France
CitationJournal: Nat Commun / Year: 2017
Title: Carrageenan catabolism is encoded by a complex regulon in marine heterotrophic bacteria.
Authors: Ficko-Blean, E. / Prechoux, A. / Thomas, F. / Rochat, T. / Larocque, R. / Zhu, Y. / Stam, M. / Genicot, S. / Jam, M. / Calteau, A. / Viart, B. / Ropartz, D. / Perez-Pascual, D. / Correc, G. ...Authors: Ficko-Blean, E. / Prechoux, A. / Thomas, F. / Rochat, T. / Larocque, R. / Zhu, Y. / Stam, M. / Genicot, S. / Jam, M. / Calteau, A. / Viart, B. / Ropartz, D. / Perez-Pascual, D. / Correc, G. / Matard-Mann, M. / Stubbs, K.A. / Rogniaux, H. / Jeudy, A. / Barbeyron, T. / Medigue, C. / Czjzek, M. / Vallenet, D. / McBride, M.J. / Duchaud, E. / Michel, G.
History
DepositionJul 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galactonate dehydratase
B: Galactonate dehydratase
C: Galactonate dehydratase
D: Galactonate dehydratase
E: Galactonate dehydratase
F: Galactonate dehydratase
G: Galactonate dehydratase
H: Galactonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,30113
Polymers359,1808
Non-polymers1225
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25700 Å2
ΔGint-145 kcal/mol
Surface area91290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.840, 154.070, 150.870
Angle α, β, γ (deg.)90.00, 104.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Galactonate dehydratase / / 3 / 6-anhydro-D-galactonate isomerase


Mass: 44897.438 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zobellia galactanivorans (bacteria) / Gene: dgoD, zobellia_3156 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0L7B8, galactonate dehydratase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.69 Å3/Da / Density % sol: 54.28 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: Optimized conditions were a 1:1 ratio of 0.2 M tri potassium citrate, 20% PEG 3350 to 25 mg/ml ZGAL_3156.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.79→49.17 Å / Num. obs: 93118 / % possible obs: 99 % / Redundancy: 3.6 % / Biso Wilson estimate: 79.39 Å2 / CC1/2: 0.978 / Net I/σ(I): 3.97
Reflection shellResolution: 2.79→2.87 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 0.87 / CC1/2: 0.473 / % possible all: 95.6

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HPN
Resolution: 2.79→49.17 Å / Cor.coef. Fo:Fc: 0.86 / Cor.coef. Fo:Fc free: 0.832 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.29 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.913 / SU Rfree Blow DPI: 0.345 / SU Rfree Cruickshank DPI: 0.361
RfactorNum. reflection% reflectionSelection details
Rfree0.266 4656 5 %RANDOM
Rwork0.231 ---
obs0.233 93114 98.6 %-
Displacement parametersBiso mean: 68.88 Å2
Baniso -1Baniso -2Baniso -3
1--25.4971 Å20 Å216.8867 Å2
2--13.7987 Å20 Å2
3---11.6984 Å2
Refine analyzeLuzzati coordinate error obs: 0 Å
Refinement stepCycle: 1 / Resolution: 2.79→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21809 0 5 92 21906
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0122257HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1930171HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7623SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes514HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3179HARMONIC5
X-RAY DIFFRACTIONt_it22257HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.58
X-RAY DIFFRACTIONt_other_torsion23.36
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2960SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact26040SEMIHARMONIC4
LS refinement shellResolution: 2.79→2.86 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 293 4.99 %
Rwork0.255 5573 -
all0.257 5866 -
obs--84.14 %

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