HEADER SUGAR BINDING PROTEIN 29-SEP-23 8UE1 TITLE CRYSTAL STRUCTURE OF HUMAN FRUCTOSAMINE-3-KINASE (FN3K) COMPND MOL_ID: 1; COMPND 2 MOLECULE: FRUCTOSAMINE-3-KINASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: FN3K; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FN3K, ATP-BINDING PROTEIN, KINASE, DEGLYCATION PROTEIN, SUGAR BINDING KEYWDS 2 PROTEIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.LOKHANDWALA,T.H.TRAN,J.M.BINNING REVDAT 4 16-OCT-24 8UE1 1 JRNL REVDAT 3 04-SEP-24 8UE1 1 JRNL REVDAT 2 21-AUG-24 8UE1 1 AUTHOR REVDAT 1 07-AUG-24 8UE1 0 JRNL AUTH J.LOKHANDWALA,J.K.MATLACK,T.B.SMALLEY,R.E.MINER 3RD, JRNL AUTH 2 T.H.TRAN,J.M.BINNING JRNL TITL STRUCTURAL BASIS FOR FN3K-MEDIATED PROTEIN DEGLYCATION. JRNL REF STRUCTURE V. 32 1711 2024 JRNL REFN ISSN 0969-2126 JRNL PMID 39173621 JRNL DOI 10.1016/J.STR.2024.07.018 REMARK 2 REMARK 2 RESOLUTION. 2.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.2 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 7721 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 3.0300 - 2.8500 0.98 752 0 0.3221 0.3491 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8UE1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1000277909. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7721 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.850 REMARK 200 RESOLUTION RANGE LOW (A) : 46.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : 3.410 REMARK 200 R MERGE (I) : 0.11300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.4100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.92 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.87000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES, PH 7.5, 300 MM NACL, 20% REMARK 280 PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 25.12050 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 129 REMARK 465 ARG A 130 REMARK 465 ARG A 131 REMARK 465 GLY A 132 REMARK 465 GLU A 133 REMARK 465 GLY A 134 REMARK 465 ALA A 135 REMARK 465 GLU A 136 REMARK 465 LYS A 309 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 ARG A 118 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 125 CG CD OE1 OE2 REMARK 470 ASP A 227 CG OD1 OD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 THR A 13 -72.90 -84.21 REMARK 500 LEU A 14 47.68 36.35 REMARK 500 ALA A 22 18.25 54.84 REMARK 500 CYS A 24 -53.36 -129.12 REMARK 500 MET A 74 -60.60 -130.29 REMARK 500 SER A 97 -75.14 -133.68 REMARK 500 GLN A 138 118.30 -162.38 REMARK 500 PRO A 155 109.87 -58.49 REMARK 500 ARG A 172 -64.52 -127.18 REMARK 500 ASP A 217 65.00 -152.02 REMARK 500 LEU A 218 70.87 -100.74 REMARK 500 ALA A 224 -158.72 -140.21 REMARK 500 ARG A 294 -9.80 -57.37 REMARK 500 REMARK 500 REMARK: NULL DBREF 8UE1 A 1 309 UNP Q9H479 FN3K_HUMAN 1 309 SEQADV 8UE1 GLY A -1 UNP Q9H479 EXPRESSION TAG SEQADV 8UE1 HIS A 0 UNP Q9H479 EXPRESSION TAG SEQRES 1 A 311 GLY HIS MET GLU GLN LEU LEU ARG ALA GLU LEU ARG THR SEQRES 2 A 311 ALA THR LEU ARG ALA PHE GLY GLY PRO GLY ALA GLY CYS SEQRES 3 A 311 ILE SER GLU GLY ARG ALA TYR ASP THR ASP ALA GLY PRO SEQRES 4 A 311 VAL PHE VAL LYS VAL ASN ARG ARG THR GLN ALA ARG GLN SEQRES 5 A 311 MET PHE GLU GLY GLU VAL ALA SER LEU GLU ALA LEU ARG SEQRES 6 A 311 SER THR GLY LEU VAL ARG VAL PRO ARG PRO MET LYS VAL SEQRES 7 A 311 ILE ASP LEU PRO GLY GLY GLY ALA ALA PHE VAL MET GLU SEQRES 8 A 311 HIS LEU LYS MET LYS SER LEU SER SER GLN ALA SER LYS SEQRES 9 A 311 LEU GLY GLU GLN MET ALA ASP LEU HIS LEU TYR ASN GLN SEQRES 10 A 311 LYS LEU ARG GLU LYS LEU LYS GLU GLU GLU ASN THR VAL SEQRES 11 A 311 GLY ARG ARG GLY GLU GLY ALA GLU PRO GLN TYR VAL ASP SEQRES 12 A 311 LYS PHE GLY PHE HIS THR VAL THR CYS CYS GLY PHE ILE SEQRES 13 A 311 PRO GLN VAL ASN GLU TRP GLN ASP ASP TRP PRO THR PHE SEQRES 14 A 311 PHE ALA ARG HIS ARG LEU GLN ALA GLN LEU ASP LEU ILE SEQRES 15 A 311 GLU LYS ASP TYR ALA ASP ARG GLU ALA ARG GLU LEU TRP SEQRES 16 A 311 SER ARG LEU GLN VAL LYS ILE PRO ASP LEU PHE CYS GLY SEQRES 17 A 311 LEU GLU ILE VAL PRO ALA LEU LEU HIS GLY ASP LEU TRP SEQRES 18 A 311 SER GLY ASN VAL ALA GLU ASP ASP VAL GLY PRO ILE ILE SEQRES 19 A 311 TYR ASP PRO ALA SER PHE TYR GLY HIS SER GLU PHE GLU SEQRES 20 A 311 LEU ALA ILE ALA LEU MET PHE GLY GLY PHE PRO ARG SER SEQRES 21 A 311 PHE PHE THR ALA TYR HIS ARG LYS ILE PRO LYS ALA PRO SEQRES 22 A 311 GLY PHE ASP GLN ARG LEU LEU LEU TYR GLN LEU PHE ASN SEQRES 23 A 311 TYR LEU ASN HIS TRP ASN HIS PHE GLY ARG GLU TYR ARG SEQRES 24 A 311 SER PRO SER LEU GLY THR MET ARG ARG LEU LEU LYS HET EPE A 401 15 HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 2 EPE C8 H18 N2 O4 S HELIX 1 AA1 HIS A 0 ARG A 10 1 11 HELIX 2 AA3 GLN A 47 SER A 64 1 18 HELIX 3 AA4 GLN A 99 THR A 127 1 29 HELIX 4 AA5 ASP A 163 ARG A 172 1 10 HELIX 5 AA6 ARG A 172 ALA A 185 1 14 HELIX 6 AA7 ASP A 186 ILE A 200 1 15 HELIX 7 AA8 PRO A 201 PHE A 204 5 4 HELIX 8 AA9 TRP A 219 GLY A 221 5 3 HELIX 9 AB1 HIS A 241 PHE A 252 1 12 HELIX 10 AB2 PRO A 256 ILE A 267 1 12 HELIX 11 AB3 GLY A 272 GLY A 293 1 22 HELIX 12 AB4 TYR A 296 LEU A 308 1 13 SHEET 1 AA1 5 ARG A 15 PHE A 17 0 SHEET 2 AA1 5 ARG A 29 THR A 33 -1 O ASP A 32 N ARG A 15 SHEET 3 AA1 5 GLY A 36 ASN A 43 -1 O VAL A 40 N ARG A 29 SHEET 4 AA1 5 ALA A 84 GLU A 89 -1 O PHE A 86 N LYS A 41 SHEET 5 AA1 5 PRO A 73 ASP A 78 -1 N ILE A 77 O ALA A 85 SHEET 1 AA2 2 VAL A 223 GLU A 225 0 SHEET 2 AA2 2 PRO A 230 ILE A 232 -1 O ILE A 231 N ALA A 224 SHEET 1 AA3 2 ALA A 212 LEU A 214 0 SHEET 2 AA3 2 PHE A 238 GLY A 240 -1 O GLY A 240 N ALA A 212 CRYST1 52.484 50.241 65.651 90.00 106.33 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.019053 0.000000 0.005582 0.00000 SCALE2 0.000000 0.019904 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015872 0.00000