HEADER DE NOVO PROTEIN 10-OCT-24 9JWT TITLE DE NOVO DESIGNED D-ALLOSE BINDING PROTEIN BASED ON 1RPJ COMPND MOL_ID: 1; COMPND 2 MOLECULE: MSD3-HOLO; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI B; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 37762 KEYWDS DE NOVO DESIGNED D-ALLOSE BINDING PROTEIN BASED ON 1RPJ, DE NOVO KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.WANG,Y.LIU REVDAT 2 31-DEC-25 9JWT 1 JRNL REVDAT 1 15-OCT-25 9JWT 0 JRNL AUTH Y.LIU,R.WU,X.WANG,S.WANG,L.CHEN,F.LI,Q.CHEN,H.LIU JRNL TITL ENHANCING FUNCTIONAL PROTEINS THROUGH MULTIMODAL INVERSE JRNL TITL 2 FOLDING WITH ABACUS-T. JRNL REF NAT COMMUN V. 16 10177 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 41261139 JRNL DOI 10.1038/S41467-025-65175-3 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.1_5286 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 33382 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1694 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 38.9700 - 3.6600 0.98 2810 157 0.1625 0.1701 REMARK 3 2 3.6600 - 2.9100 0.99 2750 134 0.1657 0.1945 REMARK 3 3 2.9100 - 2.5400 0.99 2675 137 0.1860 0.2177 REMARK 3 4 2.5400 - 2.3100 0.99 2713 130 0.1874 0.2425 REMARK 3 5 2.3100 - 2.1400 0.98 2599 147 0.1803 0.2322 REMARK 3 6 2.1400 - 2.0200 0.98 2635 132 0.1867 0.2575 REMARK 3 7 2.0200 - 1.9100 0.98 2616 133 0.1865 0.2248 REMARK 3 8 1.9100 - 1.8300 0.98 2618 137 0.2153 0.2447 REMARK 3 9 1.8300 - 1.7600 0.98 2589 126 0.2283 0.2807 REMARK 3 10 1.7600 - 1.7000 0.98 2559 162 0.2375 0.2741 REMARK 3 11 1.7000 - 1.6500 0.98 2577 148 0.2551 0.2826 REMARK 3 12 1.6500 - 1.6000 0.97 2547 151 0.2677 0.2888 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.179 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.161 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.08 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.19 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 : 0.006 2169 REMARK 3 ANGLE : 0.802 2937 REMARK 3 CHIRALITY : 0.051 351 REMARK 3 PLANARITY : 0.007 376 REMARK 3 DIHEDRAL : 14.831 800 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 9JWT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 15-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1300052461. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUN-24 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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97923 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33452 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 71.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.86700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 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 (%): 39.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CONDITION:25% W/V POLYTHYLENE GLYCOL REMARK 280 1500, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 20.24800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 71.64550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.51900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 71.64550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.24800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.51900 REMARK 290 SMTRY3 4 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 ALA A 1 REMARK 465 HIS A 294 REMARK 465 HIS A 295 REMARK 465 HIS A 296 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 HIS A 293 CG ND1 CD2 CE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 637 O HOH A 660 2.14 REMARK 500 O HOH A 645 O HOH A 652 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 SER A 56 -6.76 -59.58 REMARK 500 ASP A 91 -64.79 72.03 REMARK 500 ASP A 227 -42.34 129.06 REMARK 500 ASN A 248 76.08 -119.97 REMARK 500 REMARK 500 REMARK: NULL DBREF 9JWT A 1 296 PDB 9JWT 9JWT 1 296 SEQRES 1 A 296 ALA LYS LYS TYR ALA VAL VAL LEU LYS THR LEU THR ASP SEQRES 2 A 296 PRO PHE TRP GLN SER MET LYS ALA GLY ILE GLU ALA GLU SEQRES 3 A 296 ALA LYS GLU LEU GLY VAL THR VAL ASP ILE PHE ALA ALA SEQRES 4 A 296 ALA SER GLU GLY ASP ALA GLU ALA GLN LEU ALA LEU PHE SEQRES 5 A 296 GLU SER LEU SER ASN LYS ASN TYR LYS GLY ILE ALA PHE SEQRES 6 A 296 ALA PRO LEU THR ALA ASP ASN LEU VAL GLU PRO VAL ALA SEQRES 7 A 296 SER ALA TRP LYS LYS GLY THR TYR LEU VAL ASN LEU ASP SEQRES 8 A 296 ASP LYS ILE ASP MET LYS ALA LEU LYS ALA ALA GLY GLY SEQRES 9 A 296 ASN VAL GLU ALA PHE VAL THR THR ASP ASN VAL ALA VAL SEQRES 10 A 296 GLY ALA GLN GLY ALA GLY TYR ILE ILE GLU LYS LEU GLY SEQRES 11 A 296 ALA GLU GLY GLY GLU VAL ALA ILE ILE GLU GLY GLU ALA SEQRES 12 A 296 GLY ASN ALA ALA GLY GLU ALA ARG THR LYS GLY ALA THR SEQRES 13 A 296 ASP ALA PHE ASP LYS ALA SER ASN ILE LYS LEU VAL ALA SEQRES 14 A 296 SER GLN PRO ALA ASP TRP ASP ARG ALA LYS ALA LYS GLN SEQRES 15 A 296 VAL ALA THR ASP ILE LEU ALA LYS HIS PRO ASN ILE LYS SEQRES 16 A 296 ALA ILE TYR CYS ALA ASN ASP THR MET ALA LEU GLY VAL SEQRES 17 A 296 ALA GLN ALA VAL ALA ASP ALA GLY LYS THR GLY LYS VAL SEQRES 18 A 296 LEU VAL VAL GLY THR ASP GLY ILE PRO GLU ALA GLN GLN SEQRES 19 A 296 ALA VAL LYS ALA GLY LYS MET THR ALA THR VAL ALA GLN SEQRES 20 A 296 ASN PRO ALA ALA ILE GLY ALA THR GLY LEU LYS LEU MET SEQRES 21 A 296 VAL ASP ALA GLN LYS LYS GLY LYS VAL ILE PRO LEU ASP SEQRES 22 A 296 LYS LYS PRO GLN TYR VAL LEU VAL ALA SER LYS LEU VAL SEQRES 23 A 296 THR LYS LEU GLU HIS HIS HIS HIS HIS HIS HET ALL A 301 12 HETNAM ALL BETA-D-ALLOPYRANOSE HETSYN ALL BETA-D-ALLOSE; D-ALLOSE; ALLOSE; D-ALLOPYRANOSE FORMUL 2 ALL C6 H12 O6 FORMUL 3 HOH *288(H2 O) HELIX 1 AA1 ASP A 13 GLY A 31 1 19 HELIX 2 AA2 ASP A 44 SER A 56 1 13 HELIX 3 AA3 LEU A 73 LYS A 83 1 11 HELIX 4 AA4 ASP A 95 ALA A 102 1 8 HELIX 5 AA5 ASP A 113 GLY A 130 1 18 HELIX 6 AA6 ASN A 145 ALA A 162 1 18 HELIX 7 AA7 ASP A 176 HIS A 191 1 16 HELIX 8 AA8 ASN A 201 ALA A 215 1 15 HELIX 9 AA9 ILE A 229 ALA A 238 1 10 HELIX 10 AB1 ASN A 248 GLN A 264 1 17 HELIX 11 AB2 LYS A 265 GLY A 267 5 3 SHEET 1 AA1 6 VAL A 34 PHE A 37 0 SHEET 2 AA1 6 TYR A 4 VAL A 7 1 N VAL A 6 O PHE A 37 SHEET 3 AA1 6 GLY A 62 PHE A 65 1 O ALA A 64 N VAL A 7 SHEET 4 AA1 6 TYR A 86 LEU A 90 1 O LEU A 90 N PHE A 65 SHEET 5 AA1 6 ALA A 108 THR A 112 1 O ALA A 108 N ASN A 89 SHEET 6 AA1 6 GLN A 277 VAL A 281 1 O VAL A 279 N PHE A 109 SHEET 1 AA2 6 ILE A 165 PRO A 172 0 SHEET 2 AA2 6 GLY A 134 GLU A 140 1 N VAL A 136 O LYS A 166 SHEET 3 AA2 6 ILE A 194 CYS A 199 1 O LYS A 195 N GLU A 135 SHEET 4 AA2 6 LEU A 222 ASP A 227 1 O VAL A 224 N CYS A 199 SHEET 5 AA2 6 ALA A 243 ALA A 246 1 O VAL A 245 N ASP A 227 SHEET 6 AA2 6 LYS A 284 THR A 287 -1 O LYS A 284 N ALA A 246 CRYST1 40.496 43.038 143.291 90.00 90.00 90.00 P 21 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 0.024694 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023235 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006979 0.00000 CONECT 2130 2131 2136 2140 CONECT 2131 2130 2132 2137 CONECT 2132 2131 2133 2138 CONECT 2133 2132 2134 2139 CONECT 2134 2133 2135 2140 CONECT 2135 2134 2141 CONECT 2136 2130 CONECT 2137 2131 CONECT 2138 2132 CONECT 2139 2133 CONECT 2140 2130 2134 CONECT 2141 2135 MASTER 248 0 1 11 12 0 0 6 2428 1 12 23 END