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- PDB-2a3n: Crystal structure of a putative glucosamine-fructose-6-phosphate ... -

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Basic information

Entry
Database: PDB / ID: 2a3n
TitleCrystal structure of a putative glucosamine-fructose-6-phosphate aminotransferase (stm4540.s) from salmonella typhimurium lt2 at 1.35 A resolution
Componentsputative glucosamine-fructose-6-phosphate aminotransferase
KeywordsSUGAR BINDING PROTEIN / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


glutamine-fructose-6-phosphate transaminase (isomerizing) activity / UDP-N-acetylglucosamine metabolic process / carbohydrate derivative binding / protein N-linked glycosylation / fructose 6-phosphate metabolic process
Similarity search - Function
Fructosamine deglycase FrlB / Fructosamine deglycase FrlB, SIS domain 1 / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glucosamine-fructose-6-phosphate aminotransferase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.23 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative glucosamine-fructose-6-phosphate aminotransferase (16423107) from SALMONELLA TYPHIMURIUM LT2 at 1.35 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative glucosamine-fructose-6-phosphate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4002
Polymers41,3381
Non-polymers621
Water8,611478
1
A: putative glucosamine-fructose-6-phosphate aminotransferase
hetero molecules

A: putative glucosamine-fructose-6-phosphate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8004
Polymers82,6762
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6550 Å2
ΔGint-8 kcal/mol
Surface area23070 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)81.220, 102.610, 49.296
Angle α, β, γ (deg.)90.000, 123.210, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-391-

HOH

21A-535-

HOH

31A-812-

HOH

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Components

#1: Protein putative glucosamine-fructose-6-phosphate aminotransferase


Mass: 41338.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: 16423107 / Plasmid: HK100 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZJX7
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.83 Å3/Da / Density % sol: 32.4 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 8.2
Details: 0.2M Na3Citrate, 20.0% PEG-3350, No Buffer pH 8.2, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162, 0.97932, 0.97920
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 5, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979321
30.97921
ReflectionResolution: 1.23→28.33 Å / Num. obs: 74674 / % possible obs: 76.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value% possible all
1.23-1.2620.3861.912540.38617.3
1.26-1.32.20.3421.519350.34227.6
1.3-1.332.40.272.726430.2738.5
1.33-1.382.60.2433.132720.24349.5
1.38-1.422.70.2183.440030.21862.3
1.42-1.472.90.1933.847310.19376.3
1.47-1.533.40.1724.255810.17292.8
1.53-1.593.70.1554.657790.155100
1.59-1.663.70.1325.455190.132100
1.66-1.743.70.125.653050.12100
1.74-1.833.80.1056.550550.105100
1.83-1.943.80.091747620.091100
1.94-2.083.80.0768.344950.076100
2.08-2.253.80.0649.841960.064100
2.25-2.463.80.0639.938410.063100
2.46-2.753.80.0629.934870.062100
2.75-3.183.80.05212.230620.052100
3.18-3.893.80.04613.326050.046100
3.89-5.53.80.04611.420340.046100
5.5-28.333.70.0548.611150.05499.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.23→28.33 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.175 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.041
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS THE NOMINAL RESOLUTION IS 1.35 A WITH 7019 OBSERVED REFLECTIONS BETWEEN 1.35-1.23 (29.6% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.14 3724 5 %RANDOM
Rwork0.112 ---
all0.113 ---
obs0.113 70950 76.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.369 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å2-0.41 Å2
2---0.34 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.23→28.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2684 0 4 478 3166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222968
X-RAY DIFFRACTIONr_bond_other_d0.0020.022678
X-RAY DIFFRACTIONr_angle_refined_deg1.631.9474073
X-RAY DIFFRACTIONr_angle_other_deg0.89536257
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5075399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00623.836146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.37515523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7191521
X-RAY DIFFRACTIONr_chiral_restr0.1020.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023421
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02652
X-RAY DIFFRACTIONr_nbd_refined0.2460.2574
X-RAY DIFFRACTIONr_nbd_other0.1910.22667
X-RAY DIFFRACTIONr_nbtor_refined0.1920.21455
X-RAY DIFFRACTIONr_nbtor_other0.0890.21711
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2357
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3830.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.340.2109
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.255
X-RAY DIFFRACTIONr_mcbond_it2.52531906
X-RAY DIFFRACTIONr_mcbond_other1.443721
X-RAY DIFFRACTIONr_mcangle_it3.06752916
X-RAY DIFFRACTIONr_scbond_it4.29381320
X-RAY DIFFRACTIONr_scangle_it5.307111127
X-RAY DIFFRACTIONr_rigid_bond_restr2.59936441
X-RAY DIFFRACTIONr_sphericity_free9.1933481
X-RAY DIFFRACTIONr_sphericity_bonded3.55235544
LS refinement shellResolution: 1.23→1.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 62 -
Rwork0.218 1192 -
obs--17.36 %

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