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- PDB-3q58: Structure of N-acetylmannosamine-6-Phosphate Epimerase from Salmo... -

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Basic information

Entry
Database: PDB / ID: 3q58
TitleStructure of N-acetylmannosamine-6-Phosphate Epimerase from Salmonella enterica
ComponentsN-acetylmannosamine-6-phosphate 2-epimerase
KeywordsISOMERASE / TIM beta/alpha barrel / ribulose-phosphate binding barrel / carbohydrate metabolic process / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


N-acylglucosamine-6-phosphate 2-epimerase / N-acylmannosamine-6-phosphate 2-epimerase activity / N-acylglucosamine-6-phosphate 2-epimerase activity / N-acetylmannosamine metabolic process / N-acetylneuraminate catabolic process / carbohydrate metabolic process
Similarity search - Function
Putative N-acetylmannosamine-6-phosphate epimerase / Putative N-acetylmannosamine-6-phosphate epimerase / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Putative N-acetylmannosamine-6-phosphate 2-epimerase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAnderson, S.M. / Wawrzak, Z. / Kudritska, M. / Kwon, K. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetylmannosamine-6-phosphate 2-epimerase
B: N-acetylmannosamine-6-phosphate 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,16522
Polymers49,0112
Non-polymers2,15520
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7600 Å2
ΔGint-3 kcal/mol
Surface area18700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.153, 139.310, 38.423
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein N-acetylmannosamine-6-phosphate 2-epimerase / ManNAc-6-P epimerase


Mass: 24505.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Strain: LT2 / Gene: nanE, STY1166, t1791 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL
References: UniProt: P60668, N-acylglucosamine-6-phosphate 2-epimerase
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.22 Å3/Da / Density % sol: 44.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 200mM sodium chloride, 25% PEG3350, 100mM BisTris, 2% isopropanol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.77483 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 13, 2010 / Details: bimorph KB mirrors
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.77483 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 39170 / % possible obs: 92.5 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 3.5 / Redundancy: 7.6 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 23.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 3.5 / Num. unique all: 3404 / % possible all: 84.6

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→26.43 Å / Occupancy max: 1 / Occupancy min: 0.44 / SU ML: 0.21 / σ(F): 0 / σ(I): 3.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2045 1934 4.94 %random
Rwork0.1741 ---
obs0.1757 38139 94.57 %-
all-41419 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.232 Å2 / ksol: 0.413 e/Å3
Displacement parametersBiso max: 204.49 Å2 / Biso mean: 35.1732 Å2 / Biso min: 14.73 Å2
Baniso -1Baniso -2Baniso -3
1-12.1527 Å2-0 Å20 Å2
2---12.9103 Å2-0 Å2
3---0.7576 Å2
Refinement stepCycle: LAST / Resolution: 1.8→26.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3391 0 141 277 3809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093606
X-RAY DIFFRACTIONf_angle_d1.0264861
X-RAY DIFFRACTIONf_chiral_restr0.067569
X-RAY DIFFRACTIONf_plane_restr0.006622
X-RAY DIFFRACTIONf_dihedral_angle_d12.9141353
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.8-1.8640.3381720.26233233495349585.8
1.864-1.9380.2681740.22434063580358087.5
1.938-2.0260.2671880.20435493737373791.2
2.026-2.1330.2741890.19335843773377392.5
2.133-2.2670.2011890.17837173906390695.3
2.267-2.4420.1951990.16837653964396496.6
2.442-2.6870.1982000.16338364036403698.2
2.687-3.0750.1712010.15839194120412099.2
3.075-3.8730.1692060.14839834189418999.2
3.873-26.430.2062160.1841544370437099.5
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)
11.33551.09830.31143.73770.54610.1417-0.00820.4503-0.076-0.89560.05070.0771-0.1262-0.0811-0.02350.54310.07060.02480.2727-0.02080.161322.3081-15.3758-30.8552
20.3558-0.35980.04973.5706-0.16660.1074-0.04870.0165-0.01630.11820.0027-0.2743-0.0064-0.00890.04270.228700.01060.2088-0.00730.189429.96-20.9503-12.1217
30.79780.0835-0.07650.5619-0.29410.36940.02490.05710.16630.1405-0.05010.0051-0.15880.06560.01270.284-0.03080.04470.1918-0.01920.189325.1667-4.7583-13.9037
40.96010.20570.31621.34730.24890.83260.03340.06360.15560.0659-0.02630.4388-0.1066-0.0130.00310.2270.0020.02080.1891-0.02580.28899.6871-12.0148-16.2219
50.5344-0.0125-0.31250.6383-0.14230.2162-0.0935-0.2089-0.01220.175-0.01250.0523-0.0770.01230.07210.29580.02260.02030.1925-0.010.217214.3952-27.1448-9.9957
61.6969-0.2834-0.07931.02850.06950.00690.145-0.530.0621.06540.0596-0.109-0.41070.4048-0.15870.75310.0268-0.02310.34110.05120.213321.0487-44.98947.9954
70.52390.2547-0.35032.7303-0.49810.43860.12590.0049-0.10850.1722-0.129-0.5983-0.10470.0420.01320.22540.004-0.04350.15240.01010.260532.5244-37.3342-6.3421
80.91560.4980.28170.8779-0.28351.06620.1246-0.0278-0.34820.13780.0238-0.53540.19350.0868-0.10810.31330.0027-0.09080.19440.05180.356133.2894-54.0516-5.2784
90.3853-0.4755-0.28951.88210.49770.64760.04490.011-0.16310.17580.02070.23410.1601-0.1618-0.05470.2831-0.01490.00480.21490.0670.243916.0867-51.1897-6.8691
100.42870.6202-0.37391.66620.96153.26110.19870.0833-0.0492-0.458-0.1232-0.49230.3349-0.0801-0.0860.35820.010.00190.1672-0.01040.194918.5585-31.4148-21.3745
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID -2:18)A-2 - 18
2X-RAY DIFFRACTION2(CHAIN A AND RESID 19:60)A19 - 60
3X-RAY DIFFRACTION3(CHAIN A AND RESID 61:130)A61 - 130
4X-RAY DIFFRACTION4(CHAIN A AND RESID 131:194)A131 - 194
5X-RAY DIFFRACTION5(CHAIN A AND RESID 195:226)A195 - 226
6X-RAY DIFFRACTION6(CHAIN B AND RESID -1:20)B-1 - 20
7X-RAY DIFFRACTION7(CHAIN B AND RESID 21:60)B21 - 60
8X-RAY DIFFRACTION8(CHAIN B AND RESID 61:127)B61 - 127
9X-RAY DIFFRACTION9(CHAIN B AND RESID 128:211)B128 - 211
10X-RAY DIFFRACTION10(CHAIN B AND RESID 212:226)B212 - 226

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