HEADER DE NOVO PROTEIN 13-OCT-25 9YOY TITLE CRYSTAL STRUCTURE OF DE NOVO CYSTEINE PROTEASE (HC12 C103A COMPLEX) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HC12 C103A 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 9YOY 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. 1.96 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) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 62.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 22605 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) : 0.186 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1117 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 62.1700 - 3.9200 0.99 2944 156 0.1421 0.1701 REMARK 3 2 3.9200 - 3.1100 0.99 2785 147 0.1740 0.1986 REMARK 3 3 3.1100 - 2.7200 1.00 2800 137 0.2130 0.2415 REMARK 3 4 2.7200 - 2.4700 1.00 2731 154 0.2237 0.2909 REMARK 3 5 2.4700 - 2.2900 0.93 2564 123 0.2240 0.2596 REMARK 3 6 2.2900 - 2.1600 0.90 2479 123 0.2330 0.3279 REMARK 3 7 2.1600 - 2.0500 0.97 2620 143 0.2833 0.3203 REMARK 3 8 2.0500 - 1.9600 0.94 2565 134 0.3229 0.3577 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) : 0.264 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.39 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.69 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 : 0.013 1555 REMARK 3 ANGLE : 1.210 2117 REMARK 3 CHIRALITY : 0.071 245 REMARK 3 PLANARITY : 0.012 280 REMARK 3 DIHEDRAL : 15.006 572 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): 1.1815 -26.9735 -20.7450 REMARK 3 T TENSOR REMARK 3 T11: 0.2608 T22: 0.2758 REMARK 3 T33: 0.2755 T12: 0.0112 REMARK 3 T13: 0.0157 T23: 0.0166 REMARK 3 L TENSOR REMARK 3 L11: 3.6648 L22: 2.6832 REMARK 3 L33: 3.8891 L12: 1.0583 REMARK 3 L13: 0.3675 L23: -0.4104 REMARK 3 S TENSOR REMARK 3 S11: 0.0874 S12: -0.2427 S13: -0.2144 REMARK 3 S21: 0.1102 S22: -0.0238 S23: 0.1415 REMARK 3 S31: 0.2609 S32: -0.4784 S33: -0.0536 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 9YOY 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_1000301017. 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 : 23491 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 104.660 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) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 26.60 REMARK 200 R MERGE FOR SHELL (I) : 1.95600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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 (%): 65.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 60% (V/V) TASCIMATE PH 7.0, VAPOR REMARK 280 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 52.32900 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 38.64350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 38.64350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 78.49350 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 38.64350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 38.64350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.16450 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 38.64350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.64350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 78.49350 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 38.64350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.64350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.16450 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 52.32900 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 SER A 205 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 32.81 -89.44 REMARK 500 GLN A 132 -36.83 -131.40 REMARK 500 SER A 181 -141.62 -151.28 REMARK 500 SER A 190 172.36 80.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 101 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 9YOY A 1 205 PDB 9YOY 9YOY 1 205 SEQRES 1 A 205 ALA THR GLN THR LEU THR VAL LYS VAL ALA PRO GLY VAL SEQRES 2 A 205 GLU VAL GLU VAL SER PHE GLU GLY THR GLU GLU GLN ARG SEQRES 3 A 205 GLU LYS ALA GLN ALA ILE VAL ASP GLU GLY ASN LYS THR SEQRES 4 A 205 LEU ASP SER VAL ASP LEU GLY LYS GLY LYS LEU TYR LYS SEQRES 5 A 205 ASP LYS ASN GLY ASN ILE ILE VAL GLU ILE SER ARG GLU SEQRES 6 A 205 GLN LEU GLY LYS ALA ALA GLU LEU ALA LYS THR ARG LEU SEQRES 7 A 205 PRO TYR ILE ASP GLY VAL ALA ALA ALA GLY ALA PRO GLY SEQRES 8 A 205 GLY SER ALA LEU PRO LEU SER ILE ILE ARG ALA TYR GLU SEQRES 9 A 205 GLU TYR TYR LYS ALA GLU GLU LEU GLY LYS GLU LEU GLY SEQRES 10 A 205 VAL PRO VAL SER ASP LYS VAL LEU VAL VAL ASN PHE ASN SEQRES 11 A 205 ASN GLN HIS PHE VAL VAL GLN VAL PRO VAL GLY ASP LYS SEQRES 12 A 205 LEU TYR VAL PHE ASP VAL ASP GLU ASN ASN ASN PRO VAL SEQRES 13 A 205 TYR TYR THR GLU PRO LEU PRO GLU LEU THR TYR VAL ALA SEQRES 14 A 205 ASP VAL ASN VAL THR PHE TYR ALA SER GLY ILE SER GLY SEQRES 15 A 205 SER ILE GLU ALA ILE PRO GLY SER GLY SER GLY SER GLY SEQRES 16 A 205 SER SER ILE VAL LEU THR GLY SER GLY SER FORMUL 2 HOH *64(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 TYR A 106 GLY A 117 1 12 SHEET 1 AA1 2 GLN A 3 ALA A 10 0 SHEET 2 AA1 2 VAL A 13 PHE A 19 -1 O VAL A 17 N LEU A 5 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 136 O PHE A 147 SHEET 4 AA2 9 LYS A 123 PHE A 129 -1 N LEU A 125 O GLN A 137 SHEET 5 AA2 9 ILE A 58 SER A 63 -1 N ILE A 62 O VAL A 124 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 171 N GLY A 48 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 LEU A 200 -1 O LEU A 200 N ILE A 184 CRYST1 77.287 77.287 104.658 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 0.012939 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012939 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009555 0.00000 MASTER 271 0 0 5 11 0 0 6 1584 1 0 16 END