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- PDB-3dbn: Crystal structure of the Streptoccocus suis serotype2 D-mannonate... -

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Basic information

Entry
Database: PDB / ID: 3dbn
TitleCrystal structure of the Streptoccocus suis serotype2 D-mannonate dehydratase in complex with its substrate
ComponentsMannonate dehydratase
KeywordsLYASE / TIM Barrel
Function / homology
Function and homology information


glucuronate catabolic process / mannonate dehydratase / mannonate dehydratase activity
Similarity search - Function
Mannonate dehydratase / D-mannonate dehydratase (UxuA) / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
D-MANNONIC ACID / : / Mannonate dehydratase
Similarity search - Component
Biological speciesStreptococcus suis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPeng, H. / Zhang, Q. / Gao, F. / Gao, G.F.
CitationJournal: J.Bacteriol. / Year: 2009
Title: Crystal structures of Streptococcus suis mannonate dehydratase (ManD) and its complex with substrate: genetic and biochemical evidence for a catalytic mechanism
Authors: Zhang, Q. / Gao, F. / Peng, H. / Cheng, H. / Liu, Y. / Tang, J. / Thompson, J. / Wei, G. / Zhang, J. / Du, Y. / Yan, J. / Gao, G.F.
History
DepositionJun 2, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_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_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: Mannonate dehydratase
B: Mannonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3555
Polymers86,0492
Non-polymers3063
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-41 kcal/mol
Surface area26160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.520, 105.520, 160.077
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Mannonate dehydratase / / D-mannonate hydrolase


Mass: 43024.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus suis (bacteria) / Strain: 05ZYH33 / Gene: uxuA, SSU05_1157 / Plasmid: pET28b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A4VVI4, mannonate dehydratase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CS2 / D-MANNONIC ACID / D-MANNONATE


Mass: 196.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O7

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.49 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→88.04 Å / Num. obs: 20245

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.818 / Cor.coef. Fo:Fc free: 0.737 / SU B: 17.125 / SU ML: 0.337 / Cross valid method: THROUGHOUT / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28031 981 4.9 %RANDOM
Rwork0.23132 ---
obs0.23373 18872 95.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.971 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å20 Å2
2---0.69 Å20 Å2
3---1.38 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5469 0 15 0 5484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225614
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.9557624
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3065694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.20724.397257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.00715925
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9071530
X-RAY DIFFRACTIONr_chiral_restr0.1070.2827
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024304
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2460.22962
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.23726
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2210
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2630.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5231.53565
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.95125581
X-RAY DIFFRACTIONr_scbond_it1.1632374
X-RAY DIFFRACTIONr_scangle_it1.8734.52043
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 68 -
Rwork0.25 1389 -
obs--98.18 %

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