HEADER DE NOVO PROTEIN 11-DEC-25 21GI TITLE CRYSTAL STRUCTURE OF A DESIGNED PROTEIN THREE-TWIST KNOT COMPND MOL_ID: 1; COMPND 2 MOLECULE: A DESIGNED PROTEIN THREE-TWIST KNOT; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 210; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS THREE-TWIST KNOT, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.H.SONG,X.D.SU REVDAT 1 01-JUL-26 21GI 0 JRNL AUTH L.XU,X.SONG,H.XU,W.H.WU,X.D.SU,W.B.ZHANG JRNL TITL COMPUTATIONAL DESIGN AND CELLULAR SYNTHESIS OF TWO PROTEIN JRNL TITL 2 TOPOLOGICAL ISOMERS: SOLOMON LINK VS. THREE-TWIST KNOT. JRNL REF PROC.NATL.ACAD.SCI.USA V. 123 91123 2026 JRNL REFN ESSN 1091-6490 JRNL PMID 42301778 JRNL DOI 10.1073/PNAS.2537891123 REMARK 2 REMARK 2 RESOLUTION. 2.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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) : 2.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 12687 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850 REMARK 3 FREE R VALUE TEST SET COUNT : 615 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 47.0730 - 3.6138 0.90 2969 129 0.2152 0.2467 REMARK 3 2 3.6138 - 2.8685 0.95 2941 188 0.2319 0.3016 REMARK 3 3 2.8685 - 2.5059 1.00 3130 135 0.2440 0.2817 REMARK 3 4 2.5059 - 2.2770 0.98 3032 163 0.2677 0.3193 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.780 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 : 0.004 1909 REMARK 3 ANGLE : 0.520 2544 REMARK 3 CHIRALITY : 0.033 277 REMARK 3 PLANARITY : 0.002 330 REMARK 3 DIHEDRAL : 21.526 1200 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 21GI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 17-DEC-25. REMARK 100 THE DEPOSITION ID IS D_1300067154. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-25 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 : BL10U2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12791 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.277 REMARK 200 RESOLUTION RANGE LOW (A) : 47.073 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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 (%): 47.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS BASE/HYDROCHLORIC ACID, MAGNESIUM REMARK 280 CHLORIDE, PEG 400, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 291K 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 31.20200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.96900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.82450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.96900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.20200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.82450 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 GLY A 1 REMARK 465 GLY A 2 REMARK 465 GLY A 3 REMARK 465 GLY A 4 REMARK 465 GLN A 117 REMARK 465 ALA A 118 REMARK 465 GLY A 119 REMARK 465 GLY A 120 REMARK 465 GLU A 121 REMARK 465 THR A 122 REMARK 465 VAL A 123 REMARK 465 ARG A 124 REMARK 465 PHE A 125 REMARK 465 GLN A 126 REMARK 465 PRO A 210 REMARK 465 GLY A 211 REMARK 465 GLY A 244 REMARK 465 GLU A 245 REMARK 465 THR A 246 REMARK 465 VAL A 247 REMARK 465 ARG A 248 REMARK 465 PHE A 249 REMARK 465 GLN A 250 REMARK 465 GLY A 251 REMARK 465 GLY A 252 REMARK 465 LEU A 253 REMARK 465 PRO A 254 REMARK 465 GLU A 255 REMARK 465 THR A 256 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 356 O HOH A 368 1.86 REMARK 500 O HOH A 333 O HOH A 373 1.96 REMARK 500 OE1 GLU A 155 O HOH A 301 2.08 REMARK 500 O HOH A 325 O HOH A 356 2.10 REMARK 500 OE1 GLU A 191 O HOH A 302 2.11 REMARK 500 OD2 ASP A 72 O HOH A 303 2.15 REMARK 500 N ASN A 5 O HOH A 304 2.19 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 ILE A 58 -62.92 -103.06 REMARK 500 GLU A 85 74.81 -150.37 REMARK 500 ALA A 240 -1.29 77.83 REMARK 500 REMARK 500 REMARK: NULL DBREF 21GI A 1 256 PDB 21GI 21GI 1 256 SEQRES 1 A 256 GLY GLY GLY GLY ASN PRO LEU ASP LYS TRP ASN ASP ILE SEQRES 2 A 256 ILE PHE HIS ALA SER LYS LYS LEU SER LYS LYS GLU LEU SEQRES 3 A 256 GLU ARG LEU LEU GLU LEU LEU ALA LEU LEU GLU THR PHE SEQRES 4 A 256 ILE GLU LYS GLU ASP LEU GLU GLU LYS PHE GLU SER PHE SEQRES 5 A 256 ALA LYS ALA LEU ARG ILE ASP GLU GLU LEU GLN GLN LYS SEQRES 6 A 256 ILE GLU SER ARG LYS THR ASP ILE VAL ILE GLN SER MET SEQRES 7 A 256 ALA ASN ILE LEU SER LYS GLU PRO GLY GLY GLU TYR PHE SEQRES 8 A 256 THR LEU GLN ILE ARG GLY ARG GLU ARG PHE GLU GLU PHE SEQRES 9 A 256 ARG GLU LYS ASN GLU ALA LEU GLU LEU LYS ASP ALA GLN SEQRES 10 A 256 ALA GLY GLY GLU THR VAL ARG PHE GLN GLY GLY ASN PRO SEQRES 11 A 256 LEU ASP LYS TRP ASN ASP ILE ILE PHE HIS ALA SER LYS SEQRES 12 A 256 LYS LEU SER LYS LYS GLU LEU GLU ARG LEU LEU GLU LEU SEQRES 13 A 256 LEU ALA LEU LEU GLU THR PHE ILE GLU LYS GLU ASP LEU SEQRES 14 A 256 GLU GLU LYS PHE GLU SER PHE ALA LYS ALA LEU ARG ILE SEQRES 15 A 256 ASP GLU GLU LEU GLN GLN LYS ILE GLU SER ARG LYS THR SEQRES 16 A 256 ASP ILE VAL ILE GLN SER MET ALA ASN ILE LEU SER LYS SEQRES 17 A 256 GLU PRO GLY GLY GLU TYR PHE THR LEU GLN ILE ARG GLY SEQRES 18 A 256 ARG GLU ARG PHE GLU GLU PHE ARG GLU LYS ASN GLU ALA SEQRES 19 A 256 LEU GLU LEU LYS ASP ALA GLN ALA GLY GLY GLU THR VAL SEQRES 20 A 256 ARG PHE GLN GLY GLY LEU PRO GLU THR FORMUL 2 HOH *76(H2 O) HELIX 1 AA1 ASN A 5 ALA A 17 1 13 HELIX 2 AA2 SER A 18 GLU A 43 1 26 HELIX 3 AA3 LEU A 45 ALA A 55 1 11 HELIX 4 AA4 LEU A 56 ILE A 58 5 3 HELIX 5 AA5 ASP A 59 GLU A 85 1 27 HELIX 6 AA6 GLY A 97 ALA A 116 1 20 HELIX 7 AA7 ASN A 129 ALA A 141 1 13 HELIX 8 AA8 SER A 142 GLU A 167 1 26 HELIX 9 AA9 LEU A 169 ARG A 181 1 13 HELIX 10 AB1 ASP A 183 LYS A 208 1 26 HELIX 11 AB2 GLY A 221 ASP A 239 1 19 SHEET 1 AA1 2 PHE A 91 ARG A 96 0 SHEET 2 AA1 2 TYR A 214 ILE A 219 -1 O ILE A 219 N PHE A 91 CRYST1 62.404 63.649 69.938 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 0.016025 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015711 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014298 0.00000 MASTER 263 0 0 11 2 0 0 6 1963 1 0 20 END