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- PDB-1oc2: The structure of NADH in the dTDP-D-glucose dehydratase (RmlB) enzyme -

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Basic information

Entry
Database: PDB / ID: 1oc2
TitleThe structure of NADH in the dTDP-D-glucose dehydratase (RmlB) enzyme
ComponentsDTDP-GLUCOSE 4,6-DEHYDRATASE
KeywordsLYASE / DEHYDRATASE / NADH / RHAMNOSE
Function / homology
Function and homology information


dTDP-glucose 4,6-dehydratase / UDP-L-rhamnose synthase activity / UDP-glucose 4,6-dehydratase activity / UDP-rhamnose biosynthetic process / dTDP-glucose 4,6-dehydratase activity / flavonol biosynthetic process / nucleotide binding
Similarity search - Function
dTDP-glucose 4,6-dehydratase / GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / THYMIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE / dTDP-glucose 4,6-dehydratase
Similarity search - Component
Biological speciesSTREPTOCOCCUS SUIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBeis, K. / Naismith, J.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2003
Title: The Structure of Nadh in the Enzyme Dtdp-D-Glucose Dehydratase (Rmlb)
Authors: Beis, K. / Allard, S.T. / Hegeman, A.D. / Murshudov, G. / Philp, D. / Naismith, J.H.
History
DepositionFeb 4, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DTDP-GLUCOSE 4,6-DEHYDRATASE
B: DTDP-GLUCOSE 4,6-DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6489
Polymers77,9652
Non-polymers2,6847
Water13,637757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.410, 94.829, 183.543
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DTDP-GLUCOSE 4,6-DEHYDRATASE


Mass: 38982.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS SUIS (bacteria) / Strain: SEROTYPE 2 / Cell line: BL21DE3 / Plasmid: PET21(+) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: Q8GIP9, dTDP-glucose 4,6-dehydratase
#2: Chemical ChemComp-TDX / THYMIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE


Mass: 534.303 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O15P2
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 757 / 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: 3.5 Å3/Da / Density % sol: 64.7 %
Crystal growpH: 5.4
Details: 30% PEG 4K, 0.1M CITRIC ACID, PH5.4, 0.3M AMMONIUM SULPHATE,, pH 5.40
Crystal grow
*PLUS
pH: 5.4 / Method: vapor diffusion, sitting drop
Details: used microseeding, Allard, S.T., (2002) Structure, 10, 81.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13.6 mg/mlprotein1drop
22.5 mMdithiothreitol1drop
34 mMNAD+1drop
47 mMdTDP-xylose1drop
535 %(w/v)PEG40001reservoir
60.1 Mcitric acid1reservoirpH5.4
70.3 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2001 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.5→91.28 Å / Num. obs: 179804 / % possible obs: 98.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 4.3
Reflection shellResolution: 1.1→1.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.2 / % possible all: 98.6
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 34.7 Å / Num. obs: 168795 / Num. measured all: 2567266 / Rmerge(I) obs: 0.116
Reflection shell
*PLUS
Mean I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KEP

1kep


Resolution: 1.5→91.29 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.322 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MISSING RESIDUES FROM REFINEMENT MET A 1 SER A 2 MET B 1 LYS B 348
RfactorNum. reflection% reflectionSelection details
Rfree0.2 16689 9.9 %RANDOM
Rwork0.17 ---
obs0.173 152105 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--1.36 Å20 Å2
3----1.41 Å2
Refinement stepCycle: LAST / Resolution: 1.5→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5479 0 171 757 6407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0215857
X-RAY DIFFRACTIONr_bond_other_d0.0080.024944
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.8611.9697988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.8213.00411597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr6.065690
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026494
X-RAY DIFFRACTIONr_gen_planes_other0.020.021152
X-RAY DIFFRACTIONr_nbd_refined0.2570.21388
X-RAY DIFFRACTIONr_nbd_other0.270.26251
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.090.23090
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2647
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3550.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6480.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5651.53433
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.21225542
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.22532424
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6534.52446
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.309 1104
Rwork0.28 10239
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.40840.04560.06850.4087-0.03880.4695-0.00630.02330.0090.0417-0.00710.0132-0.0008-0.00020.01340.04450.0073-0.00190.0094-0.00260.075940.49220.4977.345
20.31890.0578-0.03980.38490.10130.89750.04150.0183-0.03650.0087-0.01450.05070.1029-0.0744-0.02690.0412-0.0082-0.01170.0118-0.0290.100216.492-1.18159.313
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 348
2X-RAY DIFFRACTION2B1 - 348
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 34.7 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.019
X-RAY DIFFRACTIONr_angle_d0.008

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