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- PDB-2v4m: The isomerase domain of human glutamine-fructose-6-phosphate tran... -

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Basic information

Entry
Database: PDB / ID: 2v4m
TitleThe isomerase domain of human glutamine-fructose-6-phosphate transaminase 1 (GFPT1) in complex with fructose 6-phosphate
ComponentsGLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMERIZING] 1
KeywordsTRANSFERASE / PHOSPHOPROTEIN / AMINOTRANSFERASE / FRUCTOSE 6-PHOSPHATE / ALTERNATIVE SPLICING / GLUTAMINE AMIDOTRANSFERASE / DIMER / ISOMERASE / SIS DOMAINS
Function / homology
Function and homology information


Defective GFPT1 causes CMSTA1 / Synthesis of UDP-N-acetyl-glucosamine / glutamine-fructose-6-phosphate transaminase (isomerizing) / glutamine-fructose-6-phosphate transaminase (isomerizing) activity / UDP-N-acetylglucosamine metabolic process / UDP-N-acetylglucosamine biosynthetic process / XBP1(S) activates chaperone genes / energy reserve metabolic process / carbohydrate derivative binding / fructose 6-phosphate metabolic process ...Defective GFPT1 causes CMSTA1 / Synthesis of UDP-N-acetyl-glucosamine / glutamine-fructose-6-phosphate transaminase (isomerizing) / glutamine-fructose-6-phosphate transaminase (isomerizing) activity / UDP-N-acetylglucosamine metabolic process / UDP-N-acetylglucosamine biosynthetic process / XBP1(S) activates chaperone genes / energy reserve metabolic process / carbohydrate derivative binding / fructose 6-phosphate metabolic process / protein N-linked glycosylation / glutamine metabolic process / circadian regulation of gene expression / extracellular exosome / cytosol
Similarity search - Function
Glucosamine-fructose-6-phosphate aminotransferase, isomerising / : / Glutamine amidotransferase domain / GlmS/FrlB, SIS domain 2 / GlmS/AgaS, SIS domain 1 / Glutamine amidotransferase type 2 domain profile. / SIS domain / Glutamine amidotransferase type 2 domain / SIS domain / SIS domain profile. ...Glucosamine-fructose-6-phosphate aminotransferase, isomerising / : / Glutamine amidotransferase domain / GlmS/FrlB, SIS domain 2 / GlmS/AgaS, SIS domain 1 / Glutamine amidotransferase type 2 domain profile. / SIS domain / Glutamine amidotransferase type 2 domain / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Nucleophile aminohydrolases, N-terminal / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FRUCTOSE -6-PHOSPHATE / Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsMoche, M. / Lehtio, L. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Moche, M. / Lehtio, L. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Nilsson, M.E. / Nyman, T. / Persson, C. / Sagemark, J. / Svensson, S. / Schueler, H. / Thorsell, A.G. / Tresaugues, L. / Uppenberg, J. / Van Den Berg, S. / Welin, M. / Wisniewska, M. / Weigelt, J. / Nordlund, P. / Wikstrom, M.
CitationJournal: To be Published
Title: The Isomerase Domain of Human Gfpt1 in Complex with Fructose 6-Phosphate
Authors: Moche, M. / Lehtio, L. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / ...Authors: Moche, M. / Lehtio, L. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Nilsson, M.E. / Nyman, T. / Persson, C. / Sagemark, J. / Svensson, S. / Schueler, H. / Thorsell, A.G. / Tresaugues, L. / Uppenberg, J. / Van Den Berg, S. / Welin, M. / Wisniewska, M. / Weigelt, J. / Nordlund, P. / Wikstrom, M.
History
DepositionSep 26, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMERIZING] 1
B: GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMERIZING] 1
C: GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMERIZING] 1
D: GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMERIZING] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,5819
Polymers169,5054
Non-polymers1,0765
Water2,954164
1
A: GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMERIZING] 1
B: GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMERIZING] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2734
Polymers84,7522
Non-polymers5202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-10.2 kcal/mol
Surface area31710 Å2
MethodPQS
2
C: GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMERIZING] 1
D: GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMERIZING] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3085
Polymers84,7522
Non-polymers5563
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-7.1 kcal/mol
Surface area31500 Å2
MethodPQS
Unit cell
Length a, b, c (Å)178.824, 178.824, 157.113
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMERIZING] 1 / ISOMERASE DOMAIN OF GLUTAMINE-FRUCTOSE-6-PHOSPHATE TRANSAMINASE 1 / D-FRUCTOSE-6-PHOSPHATE ...ISOMERASE DOMAIN OF GLUTAMINE-FRUCTOSE-6-PHOSPHATE TRANSAMINASE 1 / D-FRUCTOSE-6-PHOSPHATE AMIDOTRANSFERASE 1 / HEXOSEPHOSPHATE AMINOTRANSFERASE 1 / GFAT 1


Mass: 42376.184 Da / Num. of mol.: 4
Fragment: EACH SUBUNIT HAS TWO SIS DOMAINS, RESIDUES 332-699
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q06210, glutamine-fructose-6-phosphate transaminase (isomerizing)
#2: Chemical
ChemComp-F6R / FRUCTOSE -6-PHOSPHATE / Fructose 6-phosphate


Mass: 260.136 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13O9P
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsC, D AND A, B ARE TWO DIMERS IN THE ASYMMETRIC UNIT. WE WORKED ON C-TERMINAL ISOMERASE DOMAIN OF ...C, D AND A, B ARE TWO DIMERS IN THE ASYMMETRIC UNIT. WE WORKED ON C-TERMINAL ISOMERASE DOMAIN OF GFPT1_HUMAN. N-TERMINAL 6XHIS TAG MGHHHHHH.

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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: 3.05 Å3/Da / Density % sol: 59.32 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 27, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.679
11-H-K, K, -L20.321
ReflectionResolution: 2.29→55 Å / Num. obs: 282618 / % possible obs: 99.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.6
Reflection shellResolution: 2.29→2.39 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.1 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0035refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MOQ
Resolution: 2.29→54.89 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.38 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY THE DATASET WAS TWINNED AS DETECTED IN PHENIX XTRIAGE. STRUCTURE REFINED USING TWO TWIN DOMAINS (-H-K, K, -L) ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY THE DATASET WAS TWINNED AS DETECTED IN PHENIX XTRIAGE. STRUCTURE REFINED USING TWO TWIN DOMAINS (-H-K, K, -L) AND A TWIN FRACTION OF 0.321 AS IMPLEMENTED IN REFMAC5.5
RfactorNum. reflection% reflectionSelection details
Rfree0.185 1957 2.3 %RANDOM
Rwork0.167 ---
obs0.168 82104 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.27 Å2
Baniso -1Baniso -2Baniso -3
1--10.25 Å20 Å20 Å2
2---10.25 Å20 Å2
3---20.5 Å2
Refinement stepCycle: LAST / Resolution: 2.29→54.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11006 0 65 164 11235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02211340
X-RAY DIFFRACTIONr_bond_other_d0.0010.027753
X-RAY DIFFRACTIONr_angle_refined_deg1.0941.98115313
X-RAY DIFFRACTIONr_angle_other_deg0.852318980
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.56851427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73923.814485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.654152136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0941587
X-RAY DIFFRACTIONr_chiral_restr0.0630.21792
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212450
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022201
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4481.57046
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.842211436
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.21534294
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9914.53877
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.29→2.35 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.258 113
Rwork0.221 5593

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