HEADER DE NOVO PROTEIN 13-OCT-25 9YP0 TITLE CRYSTAL STRUCTURE OF DE NOVO CYSTEINE PROTEASE (HC34 WT APO) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HC34 WT APO; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: SEQUENCE STARTS AT S(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 9YP0 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. 1.77 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) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 16495 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1651 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 37.8800 - 4.0400 1.00 1346 150 0.1942 0.2230 REMARK 3 2 4.0400 - 3.2100 1.00 1270 142 0.1598 0.2096 REMARK 3 3 3.2100 - 2.8000 1.00 1251 139 0.1744 0.2185 REMARK 3 4 2.8000 - 2.5500 1.00 1235 137 0.1747 0.2304 REMARK 3 5 2.5500 - 2.3600 1.00 1220 136 0.1750 0.2205 REMARK 3 6 2.3600 - 2.2200 1.00 1233 137 0.1835 0.2518 REMARK 3 7 2.2200 - 2.1100 1.00 1230 136 0.1914 0.2626 REMARK 3 8 2.1100 - 2.0200 1.00 1224 137 0.2111 0.2488 REMARK 3 9 2.0200 - 1.9400 1.00 1214 134 0.2317 0.2911 REMARK 3 10 1.9400 - 1.8800 1.00 1215 135 0.2355 0.2789 REMARK 3 11 1.8800 - 1.8200 0.99 1214 135 0.2772 0.3619 REMARK 3 12 1.8200 - 1.7700 0.99 1192 133 0.3160 0.3386 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) : 0.187 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.134 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.39 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.30 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 : 0.012 1537 REMARK 3 ANGLE : 1.147 2088 REMARK 3 CHIRALITY : 0.073 230 REMARK 3 PLANARITY : 0.010 269 REMARK 3 DIHEDRAL : 18.672 589 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): 1.3801 -5.1583 7.6363 REMARK 3 T TENSOR REMARK 3 T11: 0.0400 T22: 0.0693 REMARK 3 T33: 0.1002 T12: 0.0111 REMARK 3 T13: 0.0031 T23: -0.0161 REMARK 3 L TENSOR REMARK 3 L11: 1.6113 L22: 1.5690 REMARK 3 L33: 1.1061 L12: -0.0154 REMARK 3 L13: 0.0282 L23: 0.1171 REMARK 3 S TENSOR REMARK 3 S11: 0.0314 S12: -0.1576 S13: 0.1694 REMARK 3 S21: 0.0388 S22: 0.0250 S23: 0.0528 REMARK 3 S31: -0.0742 S32: -0.0159 S33: -0.0392 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 9YP0 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_1000301020. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-AUG-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97931 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16545 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 37.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.900 REMARK 200 R MERGE (I) : 0.28400 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) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.80000 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 (%): 35.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M SODIUM CITRATE PH 6.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 18.72050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.87700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.51750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.87700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.72050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.51750 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 SER A 187 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 62 -164.33 -74.42 REMARK 500 GLN A 65 6.92 57.60 REMARK 500 ASP A 72 -101.87 57.48 REMARK 500 REMARK 500 REMARK: NULL DBREF 9YP0 A 1 187 PDB 9YP0 9YP0 1 187 SEQRES 1 A 187 SER GLU LYS ALA GLU TYR GLU LYS ARG ALA GLU GLY VAL SEQRES 2 A 187 LYS GLU ILE TYR GLU VAL TYR TYR GLU THR GLY LYS LYS SEQRES 3 A 187 LEU ALA GLU GLU TYR PRO ASP ALA THR VAL ASN LEU VAL SEQRES 4 A 187 ASN TYR ASP ASN SER HIS PHE TYR LEU GLU LEU GLU THR SEQRES 5 A 187 PRO GLU GLY THR VAL ILE VAL ASP GLY ASP GLU ASN GLN SEQRES 6 A 187 TYR PRO VAL VAL THR LYS ASP GLY LYS LYS THR VAL ASP SEQRES 7 A 187 GLU GLU ALA LYS GLU LYS LEU LYS GLU ILE ALA GLU LYS SEQRES 8 A 187 TYR ASP ILE ASP LEU SER THR THR OCS LEU ILE ARG SER SEQRES 9 A 187 LEU ALA ILE VAL GLN ALA TYR TRP GLU THR ARG ASN GLY SEQRES 10 A 187 LYS ALA PRO VAL ARG LEU TYR THR GLU GLY THR GLY VAL SEQRES 11 A 187 PRO ARG GLN GLU VAL ALA GLU ALA ASN LEU SER GLY LYS SEQRES 12 A 187 ILE TYR LYS LYS ASP ASP LYS SER LYS TYR LEU LYS VAL SEQRES 13 A 187 THR GLY ALA TRP ARG PRO ASP GLY VAL LEU THR LEU ASN SEQRES 14 A 187 LEU LEU ASP PRO GLU GLY ASN VAL LEU ALA SER TYR THR SEQRES 15 A 187 ILE ARG TYR GLY SER HET OCS A 100 9 HETNAM OCS CYSTEINESULFONIC ACID FORMUL 1 OCS C3 H7 N O5 S FORMUL 2 HOH *54(H2 O) HELIX 1 AA1 SER A 1 TYR A 31 1 31 HELIX 2 AA2 ASP A 78 ASP A 93 1 16 HELIX 3 AA3 ASP A 95 THR A 98 5 4 HELIX 4 AA4 THR A 99 ASN A 116 1 18 SHEET 1 AA1 7 LYS A 74 VAL A 77 0 SHEET 2 AA1 7 PRO A 67 LYS A 71 -1 N LYS A 71 O LYS A 74 SHEET 3 AA1 7 GLY A 55 GLY A 61 -1 N ILE A 58 O THR A 70 SHEET 4 AA1 7 HIS A 45 THR A 52 -1 N LEU A 50 O VAL A 57 SHEET 5 AA1 7 THR A 35 TYR A 41 -1 N ASN A 37 O GLU A 49 SHEET 6 AA1 7 VAL A 121 GLY A 127 1 O TYR A 124 N LEU A 38 SHEET 7 AA1 7 VAL A 130 GLU A 134 -1 O GLN A 133 N THR A 125 SHEET 1 AA2 4 ALA A 138 LYS A 146 0 SHEET 2 AA2 4 ASP A 149 TRP A 160 -1 O LEU A 154 N ILE A 144 SHEET 3 AA2 4 VAL A 165 LEU A 171 -1 O LEU A 171 N LYS A 155 SHEET 4 AA2 4 VAL A 177 ARG A 184 -1 O LEU A 178 N LEU A 170 LINK C THR A 99 N OCS A 100 1555 1555 1.33 LINK C OCS A 100 N LEU A 101 1555 1555 1.32 CRYST1 37.441 57.035 75.754 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 0.026709 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017533 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013201 0.00000 CONECT 805 810 CONECT 810 805 811 CONECT 811 810 812 814 CONECT 812 811 813 CONECT 813 812 816 817 818 CONECT 814 811 815 819 CONECT 815 814 CONECT 816 813 CONECT 817 813 CONECT 818 813 CONECT 819 814 MASTER 241 0 1 4 11 0 0 6 1544 1 11 15 END