HEADER SUGAR BINDING PROTEIN 04-DEC-21 7QF7 TITLE ORTHORHOMBIC CRYSTAL STRUCTURE OF PTG CBM21 IN COMPLEX WITH BETA- TITLE 2 CYCLODEXTRIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 3C; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CBM21 DOMAIN (RESIDUES 132-264); COMPND 5 SYNONYM: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 5,PP1 SUBUNIT R5, COMPND 6 PROTEIN TARGETING TO GLYCOGEN,PTG; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PPP1R3C, PPP1R5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CARBOHYDRATE BINDING, IMMUNOGLOBULIN-LIKE FOLD, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.S.SEMRAU,P.STORICI,G.LOLLI REVDAT 2 31-JAN-24 7QF7 1 REMARK REVDAT 1 02-NOV-22 7QF7 0 JRNL AUTH M.S.SEMRAU,G.GIACHIN,S.COVACEUSZACH,A.CASSETTA,N.DEMITRI, JRNL AUTH 2 P.STORICI,G.LOLLI JRNL TITL MOLECULAR ARCHITECTURE OF THE GLYCOGEN- COMMITTED PP1/PTG JRNL TITL 2 HOLOENZYME. JRNL REF NAT COMMUN V. 13 6199 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 36261419 JRNL DOI 10.1038/S41467-022-33693-Z REMARK 2 REMARK 2 RESOLUTION. 1.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 26883 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 1320 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 44.0740 - 3.0575 1.00 3022 150 0.1716 0.1736 REMARK 3 2 3.0575 - 2.4268 1.00 2891 128 0.1938 0.2188 REMARK 3 3 2.4268 - 2.1201 1.00 2833 163 0.1658 0.1914 REMARK 3 4 2.1201 - 1.9262 1.00 2816 148 0.1536 0.1905 REMARK 3 5 1.9262 - 1.7882 1.00 2803 165 0.1579 0.2065 REMARK 3 6 1.7882 - 1.6827 1.00 2813 134 0.1670 0.2092 REMARK 3 7 1.6827 - 1.5985 1.00 2821 141 0.1875 0.2305 REMARK 3 8 1.5985 - 1.5289 1.00 2779 140 0.2119 0.2689 REMARK 3 9 1.5289 - 1.4700 1.00 2785 151 0.2395 0.2803 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.960 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.89 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 : 0.005 1179 REMARK 3 ANGLE : 0.935 1613 REMARK 3 CHIRALITY : 0.090 196 REMARK 3 PLANARITY : 0.004 193 REMARK 3 DIHEDRAL : 21.169 399 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 7QF7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-DEC-21. REMARK 100 THE DEPOSITION ID IS D_1292119547. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 11.2C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9718 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26941 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470 REMARK 200 RESOLUTION RANGE LOW (A) : 44.074 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.98100 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: 2EEF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3 M NACL, PH 5.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.22150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.27650 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.22150 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.27650 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 SER A 131 REMARK 465 TRP A 261 REMARK 465 LYS A 262 REMARK 465 PRO A 263 REMARK 465 ASP A 264 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 ILE A 226 CG1 CG2 CD1 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 ASP A 137 41.46 -86.79 REMARK 500 ASP A 191 45.53 -146.79 REMARK 500 ASN A 253 171.78 60.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 301 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 182 O REMARK 620 2 HOH A 442 O 93.3 REMARK 620 3 HOH A 481 O 85.8 175.6 REMARK 620 4 HOH A 496 O 92.1 84.0 100.3 REMARK 620 5 HOH A 521 O 173.4 90.8 90.4 83.2 REMARK 620 6 GLC C 5 O3 89.9 78.9 96.7 162.9 96.0 REMARK 620 N 1 2 3 4 5 DBREF 7QF7 A 132 264 UNP Q9UQK1 PPR3C_HUMAN 132 264 SEQADV 7QF7 SER A 131 UNP Q9UQK1 EXPRESSION TAG SEQRES 1 A 134 SER LYS ASN LEU ILE LEU ASP PHE PRO GLN PRO SER THR SEQRES 2 A 134 ASP TYR LEU SER PHE ARG SER HIS PHE GLN LYS ASN PHE SEQRES 3 A 134 VAL CYS LEU GLU ASN CYS SER LEU GLN GLU ARG THR VAL SEQRES 4 A 134 THR GLY THR VAL LYS VAL LYS ASN VAL SER PHE GLU LYS SEQRES 5 A 134 LYS VAL GLN ILE ARG ILE THR PHE ASP SER TRP LYS ASN SEQRES 6 A 134 TYR THR ASP VAL ASP CYS VAL TYR MET LYS ASN VAL TYR SEQRES 7 A 134 GLY GLY THR ASP SER ASP THR PHE SER PHE ALA ILE ASP SEQRES 8 A 134 LEU PRO PRO VAL ILE PRO THR GLU GLN LYS ILE GLU PHE SEQRES 9 A 134 CYS ILE SER TYR HIS ALA ASN GLY GLN VAL PHE TRP ASP SEQRES 10 A 134 ASN ASN ASP GLY GLN ASN TYR ARG ILE VAL HIS VAL GLN SEQRES 11 A 134 TRP LYS PRO ASP HET GLC C 1 11 HET GLC C 2 11 HET GLC C 3 11 HET GLC C 4 11 HET GLC C 5 11 HET GLC C 6 11 HET GLC C 7 11 HET NA A 301 1 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM NA SODIUM ION HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 2 GLC 7(C6 H12 O6) FORMUL 3 NA NA 1+ FORMUL 4 HOH *134(H2 O) HELIX 1 AA1 GLN A 140 THR A 143 5 4 HELIX 2 AA2 ASP A 144 PHE A 156 1 13 SHEET 1 AA1 5 LEU A 134 LEU A 136 0 SHEET 2 AA1 5 TYR A 254 HIS A 258 -1 O VAL A 257 N ILE A 135 SHEET 3 AA1 5 ILE A 232 ALA A 240 -1 N PHE A 234 O TYR A 254 SHEET 4 AA1 5 LYS A 183 THR A 189 -1 N LYS A 183 O HIS A 239 SHEET 5 AA1 5 THR A 197 ASP A 200 -1 O VAL A 199 N ILE A 186 SHEET 1 AA2 4 LEU A 134 LEU A 136 0 SHEET 2 AA2 4 TYR A 254 HIS A 258 -1 O VAL A 257 N ILE A 135 SHEET 3 AA2 4 ILE A 232 ALA A 240 -1 N PHE A 234 O TYR A 254 SHEET 4 AA2 4 GLN A 243 ASP A 247 -1 O PHE A 245 N TYR A 238 SHEET 1 AA3 4 VAL A 157 GLN A 165 0 SHEET 2 AA3 4 THR A 168 LYS A 176 -1 O THR A 172 N GLU A 160 SHEET 3 AA3 4 SER A 213 ASP A 221 -1 O ILE A 220 N VAL A 169 SHEET 4 AA3 4 VAL A 202 TYR A 203 -1 N VAL A 202 O SER A 217 LINK O4 GLC C 1 C1 GLC C 2 1555 1555 1.38 LINK C1 GLC C 1 O4 GLC C 7 1555 1555 1.40 LINK O4 GLC C 2 C1 GLC C 3 1555 1555 1.42 LINK O4 GLC C 3 C1 GLC C 4 1555 1555 1.38 LINK O4 GLC C 4 C1 GLC C 5 1555 1555 1.41 LINK O4 GLC C 5 C1 GLC C 6 1555 1555 1.43 LINK O4 GLC C 6 C1 GLC C 7 1555 1555 1.40 LINK O LYS A 182 NA NA A 301 1555 1555 2.27 LINK NA NA A 301 O HOH A 442 1555 1555 2.40 LINK NA NA A 301 O HOH A 481 1555 1555 2.40 LINK NA NA A 301 O HOH A 496 1555 1555 2.50 LINK NA NA A 301 O HOH A 521 1555 1555 2.42 LINK NA NA A 301 O3 GLC C 5 1555 1555 2.66 CRYST1 38.593 56.443 70.553 90.00 90.00 90.00 P 2 21 21 4 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 0.025911 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017717 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014174 0.00000