HEADER DE NOVO PROTEIN 28-AUG-23 8W6E TITLE DE NOVO DESIGN OF HBC599 BINDER COMPND MOL_ID: 1; COMPND 2 MOLECULE: HBC599 IN COMPLEX WITH WFAP1.1; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARTIFICIAL SEQUENCES; SOURCE 3 ORGANISM_TAXID: 81077; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DE NOVO PROTEIN DESIGN; LIGAND BINDING; FLUOROGENIC; FLUORESCENT KEYWDS 2 PROTEIN, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.F.LIANG,J.Y.ZHU,P.L.LU REVDAT 1 27-NOV-24 8W6E 0 JRNL AUTH M.F.LIANG,J.Y.ZHU,P.L.LU JRNL TITL DE NOVO DESIGN OF HBC599 BINDER JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 20877 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.740 REMARK 3 FREE R VALUE TEST SET COUNT : 989 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 29.5700 - 4.0200 1.00 2897 153 0.2174 0.2352 REMARK 3 2 4.0200 - 3.2000 1.00 2885 151 0.1931 0.2177 REMARK 3 3 3.1900 - 2.7900 1.00 2875 133 0.2200 0.2563 REMARK 3 4 2.7900 - 2.5400 1.00 2841 176 0.2288 0.2694 REMARK 3 5 2.5400 - 2.3500 1.00 2884 132 0.2282 0.2398 REMARK 3 6 2.3500 - 2.2200 0.99 2877 119 0.2439 0.2842 REMARK 3 7 2.2200 - 2.1000 0.91 2629 125 0.2746 0.3225 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) : 0.263 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.649 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.96 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 : 0.011 2821 REMARK 3 ANGLE : 1.485 3749 REMARK 3 CHIRALITY : 0.089 418 REMARK 3 PLANARITY : 0.005 480 REMARK 3 DIHEDRAL : 19.054 1222 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 8W6E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1300040628. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JAN-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL02U1 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20877 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.82400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.330 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 (%): 43.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M LITHIUM SULFATE, 20% W/V PEG1000, REMARK 280 0.1M SODIUM PHOSPHATE CITRATE PH4.2, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 45.95600 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 ASN A 37 REMARK 465 VAL A 38 REMARK 465 THR A 39 REMARK 465 THR A 122 REMARK 465 THR A 123 REMARK 465 HIS A 164 REMARK 465 HIS A 165 REMARK 465 HIS A 166 REMARK 465 HIS A 167 REMARK 465 HIS A 168 REMARK 465 HIS A 169 REMARK 465 ASN B 37 REMARK 465 VAL B 38 REMARK 465 THR B 39 REMARK 465 HIS B 164 REMARK 465 HIS B 165 REMARK 465 HIS B 166 REMARK 465 HIS B 167 REMARK 465 HIS B 168 REMARK 465 HIS B 169 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 PHE A 33 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP A 40 CG OD1 OD2 REMARK 470 PHE A 44 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 46 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 56 CG CD CE NZ REMARK 470 ARG A 57 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 84 CG CD OE1 OE2 REMARK 470 ARG A 129 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 21 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 31 CG CD NE CZ NH1 NH2 REMARK 470 PHE B 33 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG B 45 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 63 CG CD CE NZ REMARK 470 LYS B 109 CG CD CE NZ REMARK 470 THR B 122 OG1 CG2 REMARK 470 THR B 123 OG1 CG2 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 PRO B 80 60.69 -65.67 REMARK 500 THR B 123 -127.98 -120.75 REMARK 500 REMARK 500 REMARK: NULL DBREF 8W6E A 0 169 PDB 8W6E 8W6E 0 169 DBREF 8W6E B 0 169 PDB 8W6E 8W6E 0 169 SEQRES 1 A 170 MET ASP GLU GLU ARG LEU LYS GLU ILE LEU GLU GLU LEU SEQRES 2 A 170 GLU ARG ILE ILE GLU GLU VAL LYS ARG LEU LEU GLU LYS SEQRES 3 A 170 ASP GLU ARG LEU LEU ARG GLU PHE TYR ARG ARG ASN VAL SEQRES 4 A 170 THR ASP LYS GLU GLU PHE ARG ARG VAL ILE LYS LEU ASP SEQRES 5 A 170 GLU GLU VAL MET LYS ARG SER GLU GLU LEU LEU LYS ARG SEQRES 6 A 170 ALA GLU GLU LEU LEU ARG GLU LEU GLU GLU LEU ILE ARG SEQRES 7 A 170 ARG ILE PRO PHE SER GLU GLU ILE ARG ARG GLU LEU GLU SEQRES 8 A 170 GLU ILE LEU ARG ARG LEU LYS GLU LEU TYR GLU GLU ALA SEQRES 9 A 170 LYS ARG LEU MET GLU LYS ALA LYS GLU LEU THR LYS ARG SEQRES 10 A 170 ILE LYS LYS ILE ASP THR THR ASP GLU LYS THR LEU ARG SEQRES 11 A 170 GLU TRP TYR GLU ILE VAL ARG GLU LEU LEU GLU ARG ALA SEQRES 12 A 170 LYS GLU ILE ILE GLU GLU ILE GLU ARG LEU LEU ARG ARG SEQRES 13 A 170 LEU LEU GLU ILE LEU GLY LEU GLU HIS HIS HIS HIS HIS SEQRES 14 A 170 HIS SEQRES 1 B 170 MET ASP GLU GLU ARG LEU LYS GLU ILE LEU GLU GLU LEU SEQRES 2 B 170 GLU ARG ILE ILE GLU GLU VAL LYS ARG LEU LEU GLU LYS SEQRES 3 B 170 ASP GLU ARG LEU LEU ARG GLU PHE TYR ARG ARG ASN VAL SEQRES 4 B 170 THR ASP LYS GLU GLU PHE ARG ARG VAL ILE LYS LEU ASP SEQRES 5 B 170 GLU GLU VAL MET LYS ARG SER GLU GLU LEU LEU LYS ARG SEQRES 6 B 170 ALA GLU GLU LEU LEU ARG GLU LEU GLU GLU LEU ILE ARG SEQRES 7 B 170 ARG ILE PRO PHE SER GLU GLU ILE ARG ARG GLU LEU GLU SEQRES 8 B 170 GLU ILE LEU ARG ARG LEU LYS GLU LEU TYR GLU GLU ALA SEQRES 9 B 170 LYS ARG LEU MET GLU LYS ALA LYS GLU LEU THR LYS ARG SEQRES 10 B 170 ILE LYS LYS ILE ASP THR THR ASP GLU LYS THR LEU ARG SEQRES 11 B 170 GLU TRP TYR GLU ILE VAL ARG GLU LEU LEU GLU ARG ALA SEQRES 12 B 170 LYS GLU ILE ILE GLU GLU ILE GLU ARG LEU LEU ARG ARG SEQRES 13 B 170 LEU LEU GLU ILE LEU GLY LEU GLU HIS HIS HIS HIS HIS SEQRES 14 B 170 HIS HET KY6 A 201 43 HET KY6 B 201 43 HETNAM KY6 4-[(Z)-1-CYANO-2-{6-[(2-HYDROXYETHYL)(METHYL)AMINO]-1- HETNAM 2 KY6 BENZOTHIOPHEN-2-YL}ETHENYL]BENZONITRILE FORMUL 3 KY6 2(C21 H17 N3 O S) FORMUL 5 HOH *31(H2 O) HELIX 1 AA1 ASP A 1 ARG A 36 1 36 HELIX 2 AA2 LYS A 41 ILE A 79 1 39 HELIX 3 AA3 SER A 82 LYS A 118 1 37 HELIX 4 AA4 GLU A 125 GLY A 161 1 37 HELIX 5 AA5 ASP B 1 ARG B 36 1 36 HELIX 6 AA6 LYS B 41 ILE B 79 1 39 HELIX 7 AA7 SER B 82 LYS B 119 1 38 HELIX 8 AA8 ASP B 124 LEU B 160 1 37 CRYST1 40.557 91.912 52.198 90.00 107.79 90.00 P 1 21 1 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 0.024657 0.000000 0.007912 0.00000 SCALE2 0.000000 0.010880 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020120 0.00000