HEADER DE NOVO PROTEIN 13-OCT-25 9YOZ TITLE CRYSTAL STRUCTURE OF DE NOVO CYSTEINE PROTEASE (HC12 WT COMPLEX) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HC12 WT COMPLEX; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: SEQUENCE STARTS AT ALA(1) 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 DESIGN, CYSTEINE PROTEASES, ENZYME DESIGN, DEEP LEARNING KEYWDS 2 METHOD RFD2-MI, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,H.CHOI,A.KANG,H.NGUYEN,D.BAKER REVDAT 1 09-SEP-26 9YOZ 0 JRNL AUTH H.CHOI,A.K.BERA,D.BAKER JRNL TITL COMPUTATIONAL DESIGN OF CYSTEINE PROTEASES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 62.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 16675 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 822 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 62.2100 - 3.9800 0.95 2706 145 0.1546 0.1998 REMARK 3 2 3.9800 - 3.1600 0.99 2686 131 0.1685 0.2622 REMARK 3 3 3.1600 - 2.7600 1.00 2649 148 0.2166 0.2600 REMARK 3 4 2.7600 - 2.5100 0.99 2635 124 0.2544 0.3044 REMARK 3 5 2.5100 - 2.3300 0.98 2588 129 0.2791 0.3346 REMARK 3 6 2.3300 - 2.1900 0.99 2589 145 0.3072 0.3361 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) : 0.284 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.323 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.79 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.07 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 1542 REMARK 3 ANGLE : 0.690 2096 REMARK 3 CHIRALITY : 0.049 243 REMARK 3 PLANARITY : 0.004 276 REMARK 3 DIHEDRAL : 16.718 565 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -1.5004 27.2432 -21.1799 REMARK 3 T TENSOR REMARK 3 T11: 0.1834 T22: 0.2030 REMARK 3 T33: 0.1891 T12: -0.0131 REMARK 3 T13: -0.0019 T23: -0.0031 REMARK 3 L TENSOR REMARK 3 L11: 1.3233 L22: 0.7424 REMARK 3 L33: 1.4896 L12: 0.1528 REMARK 3 L13: -0.2803 L23: 0.0507 REMARK 3 S TENSOR REMARK 3 S11: 0.0034 S12: -0.0608 S13: 0.0465 REMARK 3 S21: 0.0448 S22: -0.0223 S23: 0.0186 REMARK 3 S31: -0.1256 S32: 0.2441 S33: 0.0003 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 9YOZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-OCT-25. REMARK 100 THE DEPOSITION ID IS D_1000301018. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUL-25 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 : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97920 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17005 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.190 REMARK 200 RESOLUTION RANGE LOW (A) : 104.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 25.90 REMARK 200 R MERGE (I) : 0.43700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 27.60 REMARK 200 R MERGE FOR SHELL (I) : 1.51800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 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 (%): 66.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.8M SODIUM ACETATE TRIHYDRATE PH 7.0, REMARK 280 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 52.48700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 38.61700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 38.61700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 78.73050 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 38.61700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 38.61700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.24350 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 38.61700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.61700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 78.73050 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 38.61700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.61700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.24350 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 52.48700 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 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 122 36.92 -88.36 REMARK 500 GLN A 132 -31.89 -138.17 REMARK 500 VAL A 168 -60.09 -106.11 REMARK 500 SER A 181 -144.67 -142.71 REMARK 500 REMARK 500 REMARK: NULL DBREF 9YOZ A 1 203 PDB 9YOZ 9YOZ 1 203 SEQRES 1 A 203 ALA THR GLN THR LEU THR VAL LYS VAL ALA PRO GLY VAL SEQRES 2 A 203 GLU VAL GLU VAL SER PHE GLU GLY THR GLU GLU GLN ARG SEQRES 3 A 203 GLU LYS ALA GLN ALA ILE VAL ASP GLU GLY ASN LYS THR SEQRES 4 A 203 LEU ASP SER VAL ASP LEU GLY LYS GLY LYS LEU TYR LYS SEQRES 5 A 203 ASP LYS ASN GLY ASN ILE ILE VAL GLU ILE SER ARG GLU SEQRES 6 A 203 GLN LEU GLY LYS ALA ALA GLU LEU ALA LYS THR ARG LEU SEQRES 7 A 203 PRO TYR ILE ASP GLY VAL ALA ALA ALA GLY ALA PRO GLY SEQRES 8 A 203 GLY SER CYS LEU PRO LEU SER ILE ILE ARG ALA TYR GLU SEQRES 9 A 203 GLU TYR TYR LYS ALA GLU GLU LEU GLY LYS GLU LEU GLY SEQRES 10 A 203 VAL PRO VAL SER ASP LYS VAL LEU VAL VAL ASN PHE ASN SEQRES 11 A 203 ASN GLN HIS PHE VAL VAL GLN VAL PRO VAL GLY ASP LYS SEQRES 12 A 203 LEU TYR VAL PHE ASP VAL ASP GLU ASN ASN ASN PRO VAL SEQRES 13 A 203 TYR TYR THR GLU PRO LEU PRO GLU LEU THR TYR VAL ALA SEQRES 14 A 203 ASP VAL ASN VAL THR PHE TYR ALA SER GLY ILE SER GLY SEQRES 15 A 203 SER ILE GLU ALA ILE PRO GLY SER GLY SER GLY SER GLY SEQRES 16 A 203 SER SER ILE VAL LEU THR GLY SER FORMUL 2 HOH *69(H2 O) HELIX 1 AA1 THR A 22 LYS A 38 1 17 HELIX 2 AA2 ARG A 64 LYS A 75 1 12 HELIX 3 AA3 ARG A 77 ALA A 87 1 11 HELIX 4 AA4 SER A 93 GLU A 105 1 13 HELIX 5 AA5 GLU A 105 GLY A 117 1 13 HELIX 6 AA6 SER A 190 GLY A 195 1 6 SHEET 1 AA1 2 GLN A 3 ALA A 10 0 SHEET 2 AA1 2 VAL A 13 PHE A 19 -1 O PHE A 19 N GLN A 3 SHEET 1 AA2 9 PRO A 155 PRO A 161 0 SHEET 2 AA2 9 LYS A 143 VAL A 149 -1 N VAL A 146 O TYR A 158 SHEET 3 AA2 9 HIS A 133 VAL A 140 -1 N VAL A 140 O LYS A 143 SHEET 4 AA2 9 LYS A 123 PHE A 129 -1 N VAL A 127 O VAL A 135 SHEET 5 AA2 9 ILE A 58 SER A 63 -1 N VAL A 60 O VAL A 126 SHEET 6 AA2 9 ASP A 41 ASP A 53 -1 N LYS A 49 O GLU A 61 SHEET 7 AA2 9 LEU A 165 SER A 178 -1 O VAL A 173 N GLY A 46 SHEET 8 AA2 9 SER A 181 PRO A 188 -1 O ILE A 187 N ASN A 172 SHEET 9 AA2 9 ILE A 198 THR A 201 -1 O LEU A 200 N ILE A 184 CRYST1 77.234 77.234 104.974 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 0.012948 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012948 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009526 0.00000 MASTER 252 0 0 6 11 0 0 6 1586 1 0 16 END