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- PDB-4hwg: Structure of UDP-N-acetylglucosamine 2-epimerase from Rickettsia ... -

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Basic information

Entry
Database: PDB / ID: 4hwg
TitleStructure of UDP-N-acetylglucosamine 2-epimerase from Rickettsia bellii
ComponentsUDP-N-acetylglucosamine 2-epimerase
KeywordsISOMERASE / SSGCID / UDP-N-acetylglucosamine 2-epimerase / epimerase / UDP / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing) / UDP-N-acetylglucosamine 2-epimerase activity
Similarity search - Function
UDP-N-acetylglucosamine 2-epimerase WecB-like / UDP-N-acetylglucosamine 2-epimerase domain / UDP-N-acetylglucosamine 2-epimerase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / UDP-N-acetylglucosamine 2-epimerase
Similarity search - Component
Biological speciesRickettsia bellii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Structure of UDP-N-acetylglucosamine 2-epimerase from Rickettsia bellii
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Sankaran, B. / Davies, D.R. / Edwards, T.E. / Staker, B.L.
History
DepositionNov 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylglucosamine 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5152
Polymers44,4201
Non-polymers951
Water4,360242
1
A: UDP-N-acetylglucosamine 2-epimerase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)267,09112
Polymers266,5226
Non-polymers5706
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area24770 Å2
ΔGint-137 kcal/mol
Surface area75160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.710, 146.710, 106.250
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-554-

HOH

21A-601-

HOH

31A-642-

HOH

41A-669-

HOH

51A-671-

HOH

61A-739-

HOH

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Components

#1: Protein UDP-N-acetylglucosamine 2-epimerase


Mass: 44420.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia bellii (bacteria) / Strain: RML369-C / Gene: RBE_0708, rffE / Plasmid: RibeA.00061.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q1RIM5, UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.48 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Emerald Bio JCSG+ D5: 1.6M Na/K phosphate, 100mM HEPES pH 7.5, RibeA.00061.a.B1.PW36203 29.7mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2012
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 29717 / Num. obs: 29671 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 30.303 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 17.75
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.050.494.181659321891100
2.05-2.110.3935.211598021001100
2.11-2.170.326.31575320801100
2.17-2.240.2757.31533020141100
2.24-2.310.2288.671465719341100
2.31-2.390.2129.371441818921100
2.39-2.480.18510.341387418241100
2.48-2.580.1512.48133281750199.9
2.58-2.70.1314.341288316931100
2.7-2.830.10616.861213315981100
2.83-2.980.08720.121165215381100
2.98-3.160.07224.01109171447199.9
3.16-3.380.0627.871029513631100
3.38-3.650.04934.3195391272199.8
3.65-40.04636.6788311183199.8
4-4.470.04139.9578791064199.8
4.47-5.160.03842.616812942198.9
5.16-6.320.04139.896070798199.3
6.32-8.940.03644.744713628198.7
8.94-500.0352.392564362196.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å19.63 Å
Translation3.5 Å19.63 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
BOSdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3beo, modified with ccp4 program CHAINSAW

3beo


Resolution: 2→43.8 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.1693 / WRfactor Rwork: 0.1362 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9005 / SU B: 5.729 / SU ML: 0.086 / SU R Cruickshank DPI: 0.1357 / SU Rfree: 0.124 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1822 1505 5.1 %RANDOM
Rwork0.1482 ---
all0.1499 29717 --
obs0.1499 29671 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.09 Å2 / Biso mean: 33.1379 Å2 / Biso min: 8.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.15 Å20 Å2
2---0.15 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 2→43.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2871 0 5 242 3118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192962
X-RAY DIFFRACTIONr_bond_other_d0.0010.022861
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.9724018
X-RAY DIFFRACTIONr_angle_other_deg0.82336564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4375378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61724.062128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65415523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5881519
X-RAY DIFFRACTIONr_chiral_restr0.0820.2472
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213322
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02655
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 107 -
Rwork0.204 2068 -
all-2175 -
obs-2189 99.68 %
Refinement TLS params.Method: refined / Origin x: 15.705 Å / Origin y: 16.675 Å / Origin z: 33.583 Å
111213212223313233
T0.1025 Å2-0.0321 Å20.0438 Å2-0.1015 Å20.1137 Å2--0.2713 Å2
L1.0303 °2-0.2869 °2-0.1213 °2-0.7385 °20.1258 °2--0.4847 °2
S0.0105 Å °0.2449 Å °0.3039 Å °-0.2266 Å °-0.0577 Å °-0.2435 Å °-0.1256 Å °0.0852 Å °0.0471 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 376
2X-RAY DIFFRACTION1A400

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