HEADER DE NOVO PROTEIN 09-JUN-26 27RQ TITLE CRYSTAL STRUCTURE OF THE DE NOVO DESIGNED MINIPROTEIN BINDER AGAINST TITLE 2 PDL1, GPX41. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGNED MINIPROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: PLYSS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PET3A BASED; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PST50TRC2STRHISN KEYWDS MINIPROTEIN BINDER, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.BARIK,A.KUMAR,S.S.GAIKWAD,R.D.MAKDE REVDAT 1 24-JUN-26 27RQ 0 JRNL AUTH T.BARIK,A.KUMAR,S.S.GAIKWAD,R.D.MAKDE JRNL TITL CRYSTAL STRUCTURE OF THE DE NOVO DESIGNED MINIPROTEIN BINDER JRNL TITL 2 AGAINST PDL1, GPX41. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.75 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 17193 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.220 REMARK 3 FREE R VALUE TEST SET COUNT : 897 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 43.2500 - 3.1800 1.00 2910 160 0.1628 0.1683 REMARK 3 2 3.1800 - 2.5200 1.00 2733 146 0.1699 0.2203 REMARK 3 3 2.5200 - 2.2000 1.00 2714 142 0.1622 0.2394 REMARK 3 4 2.2000 - 2.0000 1.00 2659 149 0.1615 0.2261 REMARK 3 5 2.0000 - 1.8600 1.00 2652 145 0.1909 0.2496 REMARK 3 6 1.8600 - 1.7500 1.00 2628 155 0.2343 0.2756 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) : 0.169 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.898 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.73 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.02 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 : 0.016 1111 REMARK 3 ANGLE : 1.479 1505 REMARK 3 CHIRALITY : 0.079 176 REMARK 3 PLANARITY : 0.009 198 REMARK 3 DIHEDRAL : 16.954 417 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): 23.7059 -0.5467 1.5664 REMARK 3 T TENSOR REMARK 3 T11: 0.1072 T22: 0.1309 REMARK 3 T33: 0.1731 T12: -0.0081 REMARK 3 T13: -0.0151 T23: -0.0114 REMARK 3 L TENSOR REMARK 3 L11: 1.2193 L22: 1.4813 REMARK 3 L33: 4.0721 L12: 0.1205 REMARK 3 L13: -0.1994 L23: -1.1698 REMARK 3 S TENSOR REMARK 3 S11: -0.0024 S12: -0.0536 S13: -0.0218 REMARK 3 S21: 0.0834 S22: 0.0055 S23: -0.0753 REMARK 3 S31: -0.1605 S32: -0.0539 S33: -0.0145 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : ens_1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "A" and (resid 0 through 3 or REMARK 3 resid 5 through 33 or resid 35 through 39 REMARK 3 or resid 41 through 73)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "B" and (resid 0 through 3 or REMARK 3 resid 5 through 33 or resid 35 through 39 REMARK 3 or resid 41 through 73)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 27RQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-JUN-26. REMARK 100 THE DEPOSITION ID IS D_1300075434. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAY-26 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 : RRCAT INDUS-2 REMARK 200 BEAMLINE : PX-BL21 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.980090 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17283 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 44.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 24.70 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.40 REMARK 200 R MERGE FOR SHELL (I) : 1.34800 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM FLUORIDE, 0.1M BIS-TRIS REMARK 280 PROPANE PH-6.5, 20% W/V POLYETHYLENE GLYCOL 3350, PH 6.5, REMARK 280 MICROBATCH, TEMPERATURE 294K 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 78.73700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 22.48950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 22.48950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 118.10550 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 22.48950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 22.48950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.36850 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 22.48950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 22.48950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 118.10550 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 22.48950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 22.48950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 39.36850 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 78.73700 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 176 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU B 51 CG GLU B 51 CD 0.091 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 ASP A 28 79.83 -153.60 REMARK 500 ASP B 28 80.96 -154.91 REMARK 500 REMARK 500 REMARK: NULL DBREF 27RQ A 0 73 PDB 27RQ 27RQ 0 73 DBREF 27RQ B 0 73 PDB 27RQ 27RQ 0 73 SEQRES 1 A 74 SER GLY SER SER ASP GLU ARG ILE GLN LYS ALA VAL GLU SEQRES 2 A 74 LEU ILE ASN GLU ALA THR ALA ALA ALA LYS GLU LEU ALA SEQRES 3 A 74 LYS VAL ASP PRO ALA LYS ALA ALA GLU LEU LEU ALA GLU SEQRES 4 A 74 ALA SER THR LEU ALA ALA TYR ALA ALA ALA ILE PRO GLU SEQRES 5 A 74 LYS PHE GLU GLU TYR TYR GLY LYS ALA GLU ALA LYS VAL SEQRES 6 A 74 ALA GLU MET LYS ALA LEU ALA ALA SER SEQRES 1 B 74 SER GLY SER SER ASP GLU ARG ILE GLN LYS ALA VAL GLU SEQRES 2 B 74 LEU ILE ASN GLU ALA THR ALA ALA ALA LYS GLU LEU ALA SEQRES 3 B 74 LYS VAL ASP PRO ALA LYS ALA ALA GLU LEU LEU ALA GLU SEQRES 4 B 74 ALA SER THR LEU ALA ALA TYR ALA ALA ALA ILE PRO GLU SEQRES 5 B 74 LYS PHE GLU GLU TYR TYR GLY LYS ALA GLU ALA LYS VAL SEQRES 6 B 74 ALA GLU MET LYS ALA LEU ALA ALA SER HET NA B 101 1 HETNAM NA SODIUM ION FORMUL 3 NA NA 1+ FORMUL 4 HOH *148(H2 O) HELIX 1 AA1 SER A 2 LYS A 26 1 25 HELIX 2 AA2 ASP A 28 ILE A 49 1 22 HELIX 3 AA3 LYS A 52 SER A 73 1 22 HELIX 4 AA4 SER B 2 LYS B 26 1 25 HELIX 5 AA5 ASP B 28 ILE B 49 1 22 HELIX 6 AA6 LYS B 52 SER B 73 1 22 CRYST1 44.979 44.979 157.474 90.00 90.00 90.00 P 43 21 2 16 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 0.022233 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022233 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006350 0.00000 MTRIX1 1 0.508539 -0.860917 -0.014471 11.27175 1 MTRIX2 1 -0.860879 -0.508697 0.010740 19.67104 1 MTRIX3 1 -0.016608 0.006996 -0.999838 3.75988 1 MASTER 290 0 1 6 0 0 0 9 1229 2 0 12 END