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- PDB-2pk3: Crystal Structure of a GDP-4-keto-6-deoxy-D-mannose reductase -

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Basic information

Entry
Database: PDB / ID: 2pk3
TitleCrystal Structure of a GDP-4-keto-6-deoxy-D-mannose reductase
ComponentsGDP-6-deoxy-D-lyxo-4-hexulose reductase
KeywordsOXIDOREDUCTASE / sdr / short-chain dehydrogenase/reductase / rossmann fold
Function / homology
Function and homology information


GDP-4-dehydro-6-deoxy-D-mannose reductase activity / GDP-4-dehydro-6-deoxy-D-mannose reductase / oxidoreductase activity
Similarity search - Function
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
Chem-A2R / GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE / GDP-6-deoxy-D-mannose reductase
Similarity search - Component
Biological speciesAneurinibacillus thermoaerophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsWebb, N.A. / Garavito, R.M.
CitationJournal: Febs J. / Year: 2009
Title: The structural basis for catalytic function of GMD and RMD, two closely related enzymes from the GDP-D-rhamnose biosynthesis pathway.
Authors: King, J.D. / Poon, K.K. / Webb, N.A. / Anderson, E.M. / McNally, D.J. / Brisson, J.R. / Messner, P. / Garavito, R.M. / Lam, J.S.
History
DepositionApr 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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: GDP-6-deoxy-D-lyxo-4-hexulose reductase
B: GDP-6-deoxy-D-lyxo-4-hexulose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4926
Polymers72,0022
Non-polymers2,4894
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-33.8 kcal/mol
Surface area23710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.882, 55.744, 79.244
Angle α, β, γ (deg.)72.54, 82.95, 75.61
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a homodimer, the contects of the asymmetric unit.

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Components

#1: Protein GDP-6-deoxy-D-lyxo-4-hexulose reductase


Mass: 36001.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aneurinibacillus thermoaerophilus (bacteria)
Strain: L420-91T / Gene: rmd / Plasmid: pQE80 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: Q6T1X6
#2: Chemical ChemComp-A2R / [(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE


Mass: 639.296 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N5O17P3
#3: Chemical ChemComp-GDD / GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE


Mass: 605.341 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N5O16P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 35% pentaerythritol propoxylate (5/4 PO/OH), 100 mM Tris, 200 mM NaCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 27, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→29.8 Å / Num. obs: 64129 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.4
Reflection shellResolution: 1.82→1.89 Å / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.7 / Num. unique all: 6792 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1rpn

1rpn


Resolution: 1.82→29.79 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.346 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1989 3207 5 %RANDOM
Rwork0.1648 ---
obs0.16649 60922 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.423 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.04 Å20.72 Å2
2--0.2 Å2-0.3 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.82→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4810 0 158 350 5318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225220
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4762.0047120
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8085643
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.50924.554224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67815899
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1391532
X-RAY DIFFRACTIONr_chiral_restr0.0960.2816
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023852
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.22516
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23590
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2363
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.215
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8771.53264
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3525137
X-RAY DIFFRACTIONr_scbond_it2.3132252
X-RAY DIFFRACTIONr_scangle_it3.5474.51983
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 235 -
Rwork0.215 4472 -
obs--100 %
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)
10.78880.0966-0.20941.29870.05181.4064-0.0474-0.2079-0.10230.3238-0.0262-0.07520.34690.2030.07360.04950.05450.0513-0.10040.0385-0.016435.11218.78629.059
21.31670.1118-0.28381.3148-0.04910.6118-0.02720.1085-0.2469-0.1058-0.0046-0.27370.11610.1170.0318-0.11420.03910.0538-0.1413-0.01060.035847.4651.056-0.678
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 30813 - 320
2X-RAY DIFFRACTION2BB1 - 30813 - 320

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