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- PDB-1yxy: Crystal Structure of putative N-acetylmannosamine-6-P epimerase f... -

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Basic information

Entry
Database: PDB / ID: 1yxy
TitleCrystal Structure of putative N-acetylmannosamine-6-P epimerase from Streptococcus pyogenes (APC29713) Structural genomics, MCSG
ComponentsPutative N-acetylmannosamine-6-phosphate 2-epimerase
KeywordsISOMERASE / Structural genomics / epimerase / Streptococcus pyogenes / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


N-acylglucosamine-6-phosphate 2-epimerase / N-acetylmannosamine catabolic process / N-acylglucosamine-6-phosphate 2-epimerase activity / N-acetylneuraminate catabolic process / carbohydrate metabolic process / cytosol
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
Putative N-acetylmannosamine-6-phosphate 2-epimerase
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsRotella, F.J. / Zhang, R.G. / Lezondra, L.E.O. / Collart, F.R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The 1.6 A crystal structure of putative N-acetylmannosamine-6-P epimerase from Streptococcus pyogenes
Authors: Rotella, F.J. / Zhang, R.G. / Lezondra, L.E.O. / Collart, F.R. / Joachimiak, A.
History
DepositionFeb 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,1882
Polymers50,1882
Non-polymers00
Water12,232679
1
A: Putative N-acetylmannosamine-6-phosphate 2-epimerase


Theoretical massNumber of molelcules
Total (without water)25,0941
Polymers25,0941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative N-acetylmannosamine-6-phosphate 2-epimerase


Theoretical massNumber of molelcules
Total (without water)25,0941
Polymers25,0941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Putative N-acetylmannosamine-6-phosphate 2-epimerase

B: Putative N-acetylmannosamine-6-phosphate 2-epimerase


Theoretical massNumber of molelcules
Total (without water)50,1882
Polymers50,1882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_754-x+5/2,-y,z-1/21
Buried area3070 Å2
ΔGint-35 kcal/mol
Surface area18830 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)59.640, 83.521, 104.256
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsthe biological assembly is a dimer

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Components

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


Mass: 25094.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: nanE / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P65522, N-acylglucosamine-6-phosphate 2-epimerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 679 / 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: 2.69 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: ammonium sulfate, BIS-TRIS buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979484 Å
DetectorType: SBC-3 / Detector: CCD / Date: Nov 7, 2004
Details: horizontal-focussing Si-111 double-crystal monochromator and vertical-focusing mirror
RadiationMonochromator: sagitally focused Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979484 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 69461 / Num. obs: 68381 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 13 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 26
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.809 / Mean I/σ(I) obs: 2.4 / Num. unique all: 6793 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
Omodel building
Cootmodel building
CCP4phasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.531 / SU ML: 0.055 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.084
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20717 3508 5.1 %RANDOM
Rwork0.19337 ---
obs0.19407 65953 99.53 %-
all-69461 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.286 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.94 Å2
Refine analyzeLuzzati coordinate error obs: 0.182 Å
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3452 0 0 679 4131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223504
X-RAY DIFFRACTIONr_angle_refined_deg1.0261.9944736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7695458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39925.606132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.61615640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4911516
X-RAY DIFFRACTIONr_chiral_restr0.0660.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022562
X-RAY DIFFRACTIONr_nbd_refined0.190.21820
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22464
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1010.2510
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0930.232
X-RAY DIFFRACTIONr_mcbond_it0.4711.52362
X-RAY DIFFRACTIONr_mcangle_it0.78723680
X-RAY DIFFRACTIONr_scbond_it1.73431262
X-RAY DIFFRACTIONr_scangle_it2.544.51056
LS refinement shellResolution: 1.6→1.639 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 259 -
Rwork0.345 4615 -
obs--95.98 %

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