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- PDB-3fvm: Crystal structure of Steptococcus suis mannonate dehydratase with... -

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Basic information

Entry
Database: PDB / ID: 3fvm
TitleCrystal structure of Steptococcus suis mannonate dehydratase with metal Mn++
ComponentsMannonate dehydratase
KeywordsLYASE / Xylose isomerase-like superfamily / TIM barrel
Function / homology
Function and homology information


D-glucuronate catabolic process / mannonate dehydratase / mannonate dehydratase activity / ferrous iron binding / manganese ion binding
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
: / Mannonate dehydratase
Similarity search - Component
Biological speciesStreptococcus suis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPeng, H. / Zhang, Q.J. / Gao, F. / Liu, Y. / Gao, F.G.
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
DepositionJan 16, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

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Assembly

Deposited unit
A: Mannonate dehydratase
B: Mannonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1043
Polymers86,0492
Non-polymers551
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-35 kcal/mol
Surface area25940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.690, 105.690, 159.572
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 / ManD


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


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn

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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: 2.59 Å3/Da / Density % sol: 52.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M potassium/sodium tartrate, 0.1M sodium citrate, 1M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 25673 / % possible obs: 94 % / Net I/σ(I): 5
Reflection shellResolution: 2.8→2.9 Å / % possible all: 95

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOSFLMdata reduction
REFMAC5.2.0019refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1tz9

1tz9


Resolution: 2.9→44.06 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.854 / SU B: 18.594 / SU ML: 0.361 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R Free: 0.446 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28585 1064 5.1 %RANDOM
Rwork0.23401 ---
all0.28 ---
obs0.2368 19634 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.716 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å20 Å2
2---1.1 Å20 Å2
3---2.19 Å2
Refinement stepCycle: LAST / Resolution: 2.9→44.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5471 0 1 0 5472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225605
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.9547610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2935694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97324.397257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.86915927
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.231530
X-RAY DIFFRACTIONr_chiral_restr0.1130.2822
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024300
X-RAY DIFFRACTIONr_nbd_refined0.2470.22915
X-RAY DIFFRACTIONr_nbtor_refined0.3220.23805
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2223
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2890.21
X-RAY DIFFRACTIONr_mcbond_it0.6751.53544
X-RAY DIFFRACTIONr_mcangle_it1.20625582
X-RAY DIFFRACTIONr_scbond_it1.34132355
X-RAY DIFFRACTIONr_scangle_it2.24.52028
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 87 -
Rwork0.247 1393 -
obs--100 %

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