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- PDB-1fp3: CRYSTAL STRUCTURE OF N-ACYL-D-GLUCOSAMINE 2-EPIMERASE FROM PORCIN... -

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Basic information

Entry
Database: PDB / ID: 1fp3
TitleCRYSTAL STRUCTURE OF N-ACYL-D-GLUCOSAMINE 2-EPIMERASE FROM PORCINE KIDNEY
ComponentsN-ACYL-D-GLUCOSAMINE 2-EPIMERASE
KeywordsISOMERASE / ALPHA/ALPHA-BARREL / N-acyl-D-glucosamine 2-epimerase
Function / homology
Function and homology information


N-acylglucosamine 2-epimerase / N-acylglucosamine 2-epimerase activity / N-acetylmannosamine metabolic process / peptidase inhibitor activity / N-acetylglucosamine metabolic process / N-acetylneuraminate catabolic process
Similarity search - Function
AGE domain / N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
N-acylglucosamine 2-epimerase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsItoh, T. / Mikami, B. / Maru, I. / Ohta, Y. / Hashimoto, W. / Murata, K.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of N-acyl-D-glucosamine 2-epimerase from porcine kidney at 2.0 A resolution.
Authors: Itoh, T. / Mikami, B. / Maru, I. / Ohta, Y. / Hashimoto, W. / Murata, K.
History
DepositionAug 30, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Mar 13, 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: N-ACYL-D-GLUCOSAMINE 2-EPIMERASE
B: N-ACYL-D-GLUCOSAMINE 2-EPIMERASE


Theoretical massNumber of molelcules
Total (without water)92,9302
Polymers92,9302
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: N-ACYL-D-GLUCOSAMINE 2-EPIMERASE

B: N-ACYL-D-GLUCOSAMINE 2-EPIMERASE


Theoretical massNumber of molelcules
Total (without water)92,9302
Polymers92,9302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2450 Å2
ΔGint-22 kcal/mol
Surface area31110 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.138, 97.193, 100.651
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 related by the two-fold axis.

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Components

#1: Protein N-ACYL-D-GLUCOSAMINE 2-EPIMERASE


Mass: 46465.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Tissue: KIDNEY / Plasmid: PEP114 / Production host: Escherichia coli (E. coli) / References: UniProt: P17560, N-acylglucosamine 2-epimerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O / References: N-acylglucosamine 2-epimerase

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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: 2.06 Å3/Da / Density % sol: 40.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 6000, sodium citrate, ammonium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal
*PLUS
Density % sol: 58 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Details: Maru, I., (1996) J. Biochem., 120, 481.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mMTris-HCl1droppH7.2
25 mg/mlprotein1drop
35.5 %(w/v)PEG60001drop
4100 mMammonium acetate1drop
550 mMsodium citrate1droppH5.0
611 %(w/v)PEG60001reservoir
7200 mMammonium acetate1reservoir
8100 mMsodium citrate1reservoirpH5.0

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Apr 19, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.92→25 Å / Num. all: 49059 / Num. obs: 39143 / % possible obs: 82.1 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.056
Reflection shellResolution: 1.92→1.98 Å / Redundancy: 2.54 % / Rmerge(I) obs: 0.056 / Num. unique all: 1270 / % possible all: 82.1
Reflection
*PLUS
Num. measured all: 124509

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.851refinement
FRAMBOdata collection
SADIEdata scaling
SAINTdata scaling
RefinementResolution: 2→14.97 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 667176.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 3926 10 %RANDOM
Rwork0.169 ---
obs0.169 39143 74.8 %-
all-124509 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.37 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso mean: 25.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20 Å20 Å2
2---1.97 Å20 Å2
3---3.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2→14.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6530 0 0 145 6675
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_d1.3
X-RAY DIFFRACTIONx_dihedral_angle_d24.5
X-RAY DIFFRACTIONx_improper_angle_d0.64
X-RAY DIFFRACTIONx_mcbond_it1.781.5
X-RAY DIFFRACTIONx_mcangle_it2.662
X-RAY DIFFRACTIONx_scbond_it3.042
X-RAY DIFFRACTIONx_scangle_it4.352.5
LS refinement shellResolution: 2→2.12 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 427 10 %
Rwork0.249 3839 -
obs--49.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.32
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.64
X-RAY DIFFRACTIONx_mcbond_it1.781.5
X-RAY DIFFRACTIONx_scbond_it3.042
X-RAY DIFFRACTIONx_mcangle_it2.662
X-RAY DIFFRACTIONx_scangle_it4.352.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.294 / % reflection Rfree: 10 % / Rfactor Rwork: 0.249

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