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- PDB-1wa4: Crystal structure of the M131F L135A EvaD double mutant -

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Basic information

Entry
Database: PDB / ID: 1wa4
TitleCrystal structure of the M131F L135A EvaD double mutant
ComponentsPCZA361.16
KeywordsEPIMERASE / EVAD / AMYCOLATOPSIS ORIENTALIS / DOUBLE MUTANT / ORF24
Function / homology
Function and homology information


dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / polysaccharide biosynthetic process / cytosol
Similarity search - Function
dTDP-4-dehydrorhamnose 3,5-epimerase-related / dTDP-4-dehydrorhamnose 3,5-epimerase / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesAMYCOLATOPSIS ORIENTALIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMerkel, A.B. / Naismith, J.H.
Citation
Journal: To be Published
Title: Crystal Structure of the M131F L135A Evad Double Mutant
Authors: Merkel, A.B. / Naismith, J.H.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: The Position of a Key Tzrosine in Dtdp-4-Keto-6-Deoxy-D-Glucose-5-Epimerase (Evad) Alters the Substrate Profile for This Rmlc-Like Enzyme
Authors: Merkel, A.B. / Major, L.L. / Errey, J.C. / Burkart, M.D. / Field, R.A. / Walsh, C.T. / Naismith, J.H.
History
DepositionOct 22, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
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: PCZA361.16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7624
Polymers22,4861
Non-polymers2763
Water1,65792
1
A: PCZA361.16
hetero molecules

A: PCZA361.16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5248
Polymers44,9712
Non-polymers5536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)51.632, 79.101, 48.777
Angle α, β, γ (deg.)90.00, 98.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PCZA361.16 / DTDP-4-KETO-6-DEOXY-D-GLUCOSE-5-EPIMERASE EVAD


Mass: 22485.596 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AMYCOLATOPSIS ORIENTALIS (bacteria) / Strain: COSMID PCZA361 (AJ223998) / Plasmid: PET24 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O52806
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION IN CHAIN A, MET 131 TO PHE ENGINEERED MUTATION IN CHAIN A, LEU 135 TO ALA

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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: 2.2 Å3/Da / Density % sol: 43.6 %
Crystal growpH: 8
Details: 100MM TRIS, PH8, 150MM NACL, 25%W/V PEG8000, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Nov 14, 2003 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.08→48.22 Å / Num. obs: 9756 / % possible obs: 98.6 % / Observed criterion σ(I): 1.5 / Redundancy: 2.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.2
Reflection shellResolution: 2.08→2.16 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 5.1 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OFN

1ofn


Resolution: 2.1→48.22 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.904 / SU B: 9.575 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 536 4.8 %RANDOM
Rwork0.176 ---
obs0.18 10650 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20.43 Å2
2--0.42 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1581 0 18 92 1691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221629
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9971.9782214
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1395204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.48222.95871
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.01615257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9711515
X-RAY DIFFRACTIONr_chiral_restr0.1250.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021234
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2390.2722
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21066
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2103
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3530.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3760.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0221.51062
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57521657
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8773649
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2414.5557
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: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.229 44
Rwork0.168 765

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