HEADER DE NOVO PROTEIN 06-AUG-24 9D01 TITLE CRYSTAL STRUCTURE OF A-ITHR-201 COMPND MOL_ID: 1; COMPND 2 MOLECULE: A-ITHR-201; 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; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DE NOVO PROTEIN, DESIGN MODEL, ML/AI EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,P.HARLEY,D.BAKER REVDAT 1 10-DEC-25 9D01 0 JRNL AUTH R.J.DE HAAS,H.PYLES,E.B.HUDDY,J.VAN OSSENBRUGGEN,C.ZHENG, JRNL AUTH 2 D.VAN DEN BROEK,S.N.GIEZEN,A.CARR,A.K.BERA,A.KANG, JRNL AUTH 3 E.BRACKENBROUGH,E.JOYCE,B.SANKARAN,D.BAKER,I.K.VOETS, JRNL AUTH 4 R.DE VRIES JRNL TITL INHIBITION OF ICE RECRYSTALLIZATION WITH DESIGNED TWISTLESS JRNL TITL 2 HELICAL REPEAT PROTEINS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 122 71122 2025 JRNL REFN ESSN 1091-6490 JRNL PMID 41289379 JRNL DOI 10.1073/PNAS.2514871122 REMARK 2 REMARK 2 RESOLUTION. 2.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_5288 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) : 2.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 21415 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.264 REMARK 3 R VALUE (WORKING SET) : 0.259 REMARK 3 FREE R VALUE : 0.312 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.330 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 44.9000 - 5.2500 0.99 1524 159 0.2384 0.2976 REMARK 3 2 5.2500 - 4.1700 1.00 1440 148 0.2288 0.2838 REMARK 3 3 4.1700 - 3.6400 0.99 1396 145 0.2260 0.2605 REMARK 3 4 3.6400 - 3.3100 1.00 1407 145 0.2437 0.3402 REMARK 3 5 3.3100 - 3.0700 1.00 1376 141 0.2743 0.2888 REMARK 3 6 3.0700 - 2.8900 1.00 1386 142 0.2712 0.3158 REMARK 3 7 2.8900 - 2.7500 1.00 1376 142 0.2942 0.3363 REMARK 3 8 2.7500 - 2.6300 1.00 1378 141 0.3224 0.3795 REMARK 3 9 2.6300 - 2.5300 1.00 1347 138 0.3036 0.3615 REMARK 3 10 2.5300 - 2.4400 1.00 1372 142 0.3133 0.3553 REMARK 3 11 2.4400 - 2.3600 1.00 1358 138 0.3345 0.3891 REMARK 3 12 2.3600 - 2.3000 1.00 1340 138 0.3914 0.4373 REMARK 3 13 2.2900 - 2.2300 1.00 1359 140 0.4137 0.5177 REMARK 3 14 2.2300 - 2.1800 0.99 1357 140 0.4555 0.5245 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) : 0.427 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.885 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 58.48 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 81.89 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 : 0.003 3013 REMARK 3 ANGLE : 0.461 4074 REMARK 3 CHIRALITY : 0.025 461 REMARK 3 PLANARITY : 0.005 538 REMARK 3 DIHEDRAL : 23.087 1152 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 9D01 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1000287075. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-APR-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00008 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21533 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.180 REMARK 200 RESOLUTION RANGE LOW (A) : 47.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 19.50 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 19.90 REMARK 200 R MERGE FOR SHELL (I) : 1.76400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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 (%): 46.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.8 M SODIUM ACETATE TRIHYDRATE, PH REMARK 280 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 94.16250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 32.12050 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 32.12050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 141.24375 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 32.12050 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 32.12050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 47.08125 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 32.12050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.12050 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 141.24375 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 32.12050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.12050 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 47.08125 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 94.16250 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 GLY A 371 REMARK 465 GLN A 372 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 OE1 GLN A 128 O HOH A 401 1.88 REMARK 500 OE2 GLU A 77 O HOH A 402 2.16 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 LYS A 44 -49.90 64.04 REMARK 500 ALA A 91 14.27 59.39 REMARK 500 ALA A 277 -78.43 -65.65 REMARK 500 PRO A 281 109.10 -46.30 REMARK 500 REMARK 500 REMARK: NULL DBREF 9D01 A 1 372 PDB 9D01 9D01 1 372 SEQRES 1 A 372 ALA PRO SER PRO GLU SER ALA ARG ARG GLN LEU ALA GLU SEQRES 2 A 372 LEU GLU GLU THR GLN GLU ARG GLY GLU ALA GLU ILE ALA SEQRES 3 A 372 ARG ALA VAL GLU GLU GLY GLU ARG GLU LEU GLU ARG LEU SEQRES 4 A 372 GLU GLU GLU GLN LYS ALA GLY LEU PRO ALA THR GLU PHE SEQRES 5 A 372 HIS ALA ARG ALA ILE ALA ALA LEU THR GLU TRP ILE ALA SEQRES 6 A 372 ARG GLN GLU ALA LEU LEU THR ARG LEU GLN ALA GLU LEU SEQRES 7 A 372 GLU ALA GLN PHE THR ARG LEU LEU ALA GLU LEU LYS ALA SEQRES 8 A 372 GLY LEU GLU PRO SER ARG GLU THR LEU GLU GLN PHE LEU SEQRES 9 A 372 GLU LEU ARG GLU PHE TRP GLN GLU GLN GLY GLU ARG GLN SEQRES 10 A 372 LEU ALA LEU ALA ARG GLU LEU THR ASP ARG GLN LEU GLU SEQRES 11 A 372 TRP VAL LYS ARG LEU LYS GLU TRP GLY LEU PRO GLN THR SEQRES 12 A 372 GLU ALA ASN ALA LEU ALA ILE ALA THR LEU THR ARG GLY SEQRES 13 A 372 ALA ALA LEU LEU GLU ALA LEU LEU THR ARG THR VAL ALA SEQRES 14 A 372 GLY VAL GLU ALA ILE PHE THR GLU ALA LEU ALA ALA LEU SEQRES 15 A 372 ARG ALA GLY LEU GLU PRO SER ARG GLU THR LEU GLU GLN SEQRES 16 A 372 PHE LEU GLU LEU ARG GLU PHE TRP GLN GLU GLN GLY GLU SEQRES 17 A 372 ARG GLN LEU ALA LEU ALA ARG GLU LEU THR ASP ARG GLN SEQRES 18 A 372 LEU GLU TRP VAL LYS ARG LEU LYS GLU TRP GLY LEU PRO SEQRES 19 A 372 GLN THR GLU ALA ASN ALA LEU ALA ILE ALA THR LEU THR SEQRES 20 A 372 ARG GLY ALA ALA LEU LEU GLU ALA LEU LEU THR ARG THR SEQRES 21 A 372 VAL ALA GLY VAL GLU ALA ILE PHE THR GLU ALA LEU ALA SEQRES 22 A 372 ALA LEU ARG ALA GLY LEU GLU PRO SER GLU GLU PHE THR SEQRES 23 A 372 GLU LEU LEU GLU GLU LEU ARG GLU ARG PHE VAL GLU ALA SEQRES 24 A 372 TYR GLU ARG LEU LYS GLU ILE ALA ARG GLU LEU THR GLU SEQRES 25 A 372 TRP LEU LEU ARG TRP VAL GLU GLU PHE ARG GLU TRP GLY SEQRES 26 A 372 LEU PRO GLU THR GLU ALA GLU ALA LEU ARG GLU ALA VAL SEQRES 27 A 372 GLU THR ARG GLY ARG ALA LEU LEU GLU ALA ILE GLU THR SEQRES 28 A 372 ARG GLY GLU ALA ALA VAL GLU ALA ILE ARG THR GLU ARG SEQRES 29 A 372 GLU ALA ALA ARG ARG ALA GLY GLN FORMUL 2 HOH *12(H2 O) HELIX 1 AA1 SER A 3 GLN A 43 1 41 HELIX 2 AA2 PRO A 48 LYS A 90 1 43 HELIX 3 AA3 SER A 96 GLY A 139 1 44 HELIX 4 AA4 PRO A 141 GLY A 185 1 45 HELIX 5 AA5 ARG A 190 GLY A 232 1 43 HELIX 6 AA6 PRO A 234 LEU A 279 1 46 HELIX 7 AA7 SER A 282 TRP A 324 1 43 HELIX 8 AA8 PRO A 327 ARG A 369 1 43 CRYST1 64.241 64.241 188.325 90.00 90.00 90.00 P 43 21 2 8 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 0.015566 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015566 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005310 0.00000 MASTER 258 0 0 8 0 0 0 6 2984 1 0 29 END