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- PDB-3dhn: Crystal structure of the putative epimerase Q89Z24_BACTN from Bac... -

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Basic information

Entry
Database: PDB / ID: 3dhn
TitleCrystal structure of the putative epimerase Q89Z24_BACTN from Bacteroides thetaiotaomicron. Northeast Structural Genomics Consortium target BtR310.
ComponentsNAD-dependent epimerase/dehydratase
Keywordsisomerase / lyase / Epimerase / Reductase / Dehydratase / PF01370 / Q89Z24_BACTN / NESG / BTR310 / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyNAD(P)H-binding / NAD(P)-binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NAD-dependent epimerase/dehydratase
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsVorobiev, S.M. / Su, M. / Seetharaman, J. / Wang, D. / Ciccosanti, C. / Foote, L.E. / Janjua, H. / Xiao, R. / Acton, T. / Montelione, G.T. ...Vorobiev, S.M. / Su, M. / Seetharaman, J. / Wang, D. / Ciccosanti, C. / Foote, L.E. / Janjua, H. / Xiao, R. / Acton, T. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the putative epimerase Q89Z24_BACTN from Bacteroides thetaiotaomicron.
Authors: Vorobiev, S.M. / Su, M. / Seetharaman, J. / Wang, D. / Ciccosanti, C. / Foote, L.E. / Janjua, H. / Xiao, R. / Acton, T. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionJun 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD-dependent epimerase/dehydratase


Theoretical massNumber of molelcules
Total (without water)25,6371
Polymers25,6371
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.339, 54.007, 93.451
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsauthors state that the biological unit is Monomer according to gel filtration data.

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Components

#1: Protein NAD-dependent epimerase/dehydratase


Mass: 25637.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: ATCC 29148/DSM 2079/NCTC 10582/E50/VPI-5482 / Gene: BT_4553 / Plasmid: pET21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) + Magic / References: UniProt: Q89Z24
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.53 Å3/Da / Density % sol: 51.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 14% PEG 20000, 0.1M NH(4)H(2)PO(4), 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97922, 0.97938, 0.96785
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 11, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979221
20.979381
30.967851
ReflectionResolution: 2→50 Å / Num. all: 33932 / Num. obs: 32609 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 14.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2.17 / Num. unique all: 3417 / % possible all: 76.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→35.34 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 114055.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1453 5 %RANDOM
Rwork0.232 ---
obs0.232 28968 85.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.6321 Å2 / ksol: 0.314696 e/Å3
Displacement parametersBiso mean: 37.8 Å2
Baniso -1Baniso -2Baniso -3
1-12.13 Å20 Å20 Å2
2---9.63 Å20 Å2
3----2.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2→35.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1661 0 0 123 1784
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 171 5.7 %
Rwork0.286 2831 -
obs--53.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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