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- PDB-3r6d: Crystal structure of NAD-dependent epimerase/dehydratase from Vei... -

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Basic information

Entry
Database: PDB / ID: 3r6d
TitleCrystal structure of NAD-dependent epimerase/dehydratase from Veillonella parvula DSM 2008 with Cz-methylated lysine
ComponentsNAD-dependent epimerase/dehydratase
KeywordsLYASE / ISOMERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / NAD-dependent epimerase/dehydratase / Veillonella parvula / reductive methylation
Function / homologyNAD(P)H-binding / NAD(P)-binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / nucleotide binding / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NAD-dependent epimerase/dehydratase
Function and homology information
Biological speciesVeillonella parvula DSM 2008 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.25 Å
AuthorsChang, C. / Hatzos-Skintges, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of NAD-dependent epimerase/dehydratase from Veillonella parvula DSM 2008 with Cz-methylated lysine
Authors: Chang, C. / Hatzos-Skintges, C. / Clancy, S. / Joachimiak, A.
History
DepositionMar 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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)24,9971
Polymers24,9971
Non-polymers00
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.446, 60.721, 69.612
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NAD-dependent epimerase/dehydratase


Mass: 24996.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Veillonella parvula DSM 2008 (bacteria)
Strain: ATCC 10790 / DSM 2008 / JCM 12972 / Te3 / Gene: Vpar_0111 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D1BQI7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Ammonium cetate, 0.1 M Bis-Tris pH 5.5, 17% PEG 10,000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2010
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. all: 61111 / Num. obs: 60921 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 37.8
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.68 / Num. unique all: 2901 / % possible all: 95.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDEphasing
RESOLVEphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.25→45.76 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 1.383 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.045
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1789 3087 5.1 %RANDOM
Rwork0.1484 ---
all0.1499 60848 --
obs0.1499 60848 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 91.6 Å2 / Biso mean: 18.0427 Å2 / Biso min: 7.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2---0.12 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.25→45.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1745 0 0 401 2146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211941
X-RAY DIFFRACTIONr_angle_refined_deg1.561.9832650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1745252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.01224.13887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75515298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6921513
X-RAY DIFFRACTIONr_chiral_restr0.0980.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211505
X-RAY DIFFRACTIONr_mcbond_it1.5211.51200
X-RAY DIFFRACTIONr_mcangle_it2.30321968
X-RAY DIFFRACTIONr_scbond_it3.1443741
X-RAY DIFFRACTIONr_scangle_it4.5574.5682
X-RAY DIFFRACTIONr_rigid_bond_restr1.58131941
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 246 -
Rwork0.294 4043 -
all-4289 -
obs-4289 96.27 %
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)
10.07540.0271-0.01420.10380.04690.02950.0001-0.0002-0.00220.01230.0029-0.01060.00150.0016-0.0030.01020.0009-0.00250.00730.00030.012550.334452.197520.1478
20.215-0.09110.06390.0834-0.01730.0572-0.00590.02460.0117-0.00270.0018-0.0132-0.00630.00480.00410.0068-0.0022-0.00040.0080.0010.01238.259154.28254.0435
30.1528-0.1310.03490.1886-0.0230.0143-0.0133-0.0121-0.01270.01850.01140.017-0.0019-0.00910.00190.00690.00040.00210.00970.00080.011528.398550.618115.5516
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 72
2X-RAY DIFFRACTION2A73 - 152
3X-RAY DIFFRACTION3A153 - 217

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