HEADER DE NOVO PROTEIN 22-MAY-26 27AH TITLE CRYSTAL STRUCTURE OF THE DE NOVO DESIGNED MINIPROTEIN GPX15 IN THE TITLE 2 C121 SPACE GROUP. 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 DE NOVO DESIGNED MINIPROTEIN; RFDIFFUSION; TIM3, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.BARIK,S.GAYRI,A.KUMAR,S.S.GAIKWAD,R.D.MAKDE REVDAT 1 03-JUN-26 27AH 0 JRNL AUTH T.BARIK,S.GAYRI,A.KUMAR,S.S.GAIKWAD,R.D.MAKDE JRNL TITL CRYSTAL STRUCTURE OF THE DE NOVO DESIGNED MINIPROTEIN GPX15 JRNL TITL 2 IN THE C121 SPACE GROUP. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 33393 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1645 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 30.2200 - 3.2000 1.00 2771 137 0.1710 0.2010 REMARK 3 2 3.2000 - 2.5400 1.00 2723 134 0.1978 0.1996 REMARK 3 3 2.5400 - 2.2200 1.00 2661 146 0.1837 0.2002 REMARK 3 4 2.2200 - 2.0200 1.00 2657 140 0.1725 0.2207 REMARK 3 5 2.0200 - 1.8700 0.99 2641 142 0.1835 0.2316 REMARK 3 6 1.8700 - 1.7600 0.99 2673 112 0.1889 0.2017 REMARK 3 7 1.7600 - 1.6800 0.99 2628 147 0.1929 0.1934 REMARK 3 8 1.6800 - 1.6000 0.99 2620 121 0.1896 0.2401 REMARK 3 9 1.6000 - 1.5400 0.99 2618 138 0.1894 0.2845 REMARK 3 10 1.5400 - 1.4900 0.99 2633 133 0.2051 0.2300 REMARK 3 11 1.4900 - 1.4400 0.98 2569 149 0.2319 0.2567 REMARK 3 12 1.4400 - 1.4000 0.97 2554 146 0.2629 0.2984 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) : 0.171 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.767 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.46 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 : 0.015 1286 REMARK 3 ANGLE : 1.540 1721 REMARK 3 CHIRALITY : 0.085 191 REMARK 3 PLANARITY : 0.012 223 REMARK 3 DIHEDRAL : 17.830 497 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): 16.6101 0.4695 14.2120 REMARK 3 T TENSOR REMARK 3 T11: 0.1340 T22: 0.0938 REMARK 3 T33: 0.0931 T12: -0.0026 REMARK 3 T13: -0.0127 T23: 0.0249 REMARK 3 L TENSOR REMARK 3 L11: 0.6348 L22: 0.6410 REMARK 3 L33: 1.1259 L12: 0.0831 REMARK 3 L13: 0.0748 L23: 0.4827 REMARK 3 S TENSOR REMARK 3 S11: 0.0169 S12: -0.0437 S13: -0.0283 REMARK 3 S21: 0.0386 S22: -0.0032 S23: -0.0122 REMARK 3 S31: -0.0071 S32: -0.0606 S33: -0.0130 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 -1 through 28 or REMARK 3 resid 30 through 41 or resid 43 through REMARK 3 45 or resid 47 through 80)) 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 -1 through 28 or REMARK 3 resid 30 through 41 or resid 43 through REMARK 3 45 or resid 47 through 80)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 27AH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-MAY-26. REMARK 100 THE DEPOSITION ID IS D_1300074629. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-26 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4 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) : 0.978930 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS 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 : 33408 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 40.720 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.88200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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 (%): 49.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MIB BUFFER PH 4, 25% PEG 1500; REMARK 280 31MG/ML MINIPROTEIN, MICROBATCH, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 41.54900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.05950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 41.54900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.05950 REMARK 290 SMTRY3 4 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 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 212 DISTANCE = 6.08 ANGSTROMS DBREF 27AH A -1 80 PDB 27AH 27AH -1 80 DBREF 27AH B -1 80 PDB 27AH 27AH -1 80 SEQRES 1 A 82 GLY SER SER GLU LYS ALA LYS GLU ALA ILE LYS LEU ALA SEQRES 2 A 82 LYS GLU ALA ALA LYS LEU ALA LYS ASP ALA ALA LYS THR SEQRES 3 A 82 GLU THR THR ALA GLU ALA LEU ALA ALA ALA TYR ARG LYS SEQRES 4 A 82 ALA GLY ALA LEU TYR GLY GLU ALA ARG LYS LEU ARG ASP SEQRES 5 A 82 LYS TYR LYS ASP GLU PHE THR PRO GLU GLU LEU GLU GLU SEQRES 6 A 82 PHE ASP LYS ALA LEU ALA GLU ALA VAL LYS ALA MET GLN SEQRES 7 A 82 ALA LEU VAL ALA SEQRES 1 B 82 GLY SER SER GLU LYS ALA LYS GLU ALA ILE LYS LEU ALA SEQRES 2 B 82 LYS GLU ALA ALA LYS LEU ALA LYS ASP ALA ALA LYS THR SEQRES 3 B 82 GLU THR THR ALA GLU ALA LEU ALA ALA ALA TYR ARG LYS SEQRES 4 B 82 ALA GLY ALA LEU TYR GLY GLU ALA ARG LYS LEU ARG ASP SEQRES 5 B 82 LYS TYR LYS ASP GLU PHE THR PRO GLU GLU LEU GLU GLU SEQRES 6 B 82 PHE ASP LYS ALA LEU ALA GLU ALA VAL LYS ALA MET GLN SEQRES 7 B 82 ALA LEU VAL ALA FORMUL 3 HOH *233(H2 O) HELIX 1 AA1 SER A 1 GLU A 25 1 25 HELIX 2 AA2 THR A 27 LYS A 53 1 27 HELIX 3 AA3 ASP A 54 PHE A 56 5 3 HELIX 4 AA4 THR A 57 ALA A 80 1 24 HELIX 5 AA5 SER B 1 GLU B 25 1 25 HELIX 6 AA6 THR B 27 LYS B 53 1 27 HELIX 7 AA7 ASP B 54 PHE B 56 5 3 HELIX 8 AA8 THR B 57 ALA B 80 1 24 CRYST1 83.098 34.119 61.669 90.00 101.49 90.00 C 1 2 1 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 0.012034 0.000000 0.002447 0.00000 SCALE2 0.000000 0.029309 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016547 0.00000 MTRIX1 1 -0.999053 -0.033580 0.027670 32.74063 1 MTRIX2 1 -0.030569 0.089123 -0.995551 15.35906 1 MTRIX3 1 0.030965 -0.995454 -0.090065 15.83284 1 MASTER 248 0 0 8 0 0 0 9 1473 2 0 14 END