HEADER SIGNALING PROTEIN 27-JUN-25 9VM0 TITLE CRYSTAL STRUCTURE OF COMPUTATIONAL DESIGNED PROTEIN CSD101 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CSD101; COMPND 3 CHAIN: A; 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; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KINASE, CELL SIGNALLING, MAP KINASE PATHWAY, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.S.SANDHOLU,A.SIBA,S.T.AROLD REVDAT 1 15-JUL-26 9VM0 0 JRNL AUTH A.S.SANDHOLU,A.SIBA,S.T.AROLD JRNL TITL CRYSTAL STRUCTURE OF COMPUTATIONAL DESIGNED PROTEIN CSD101 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.980 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 29654 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1462 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 41.3500 - 4.0900 0.99 2835 155 0.1741 0.2038 REMARK 3 2 4.0900 - 3.2400 0.99 2871 154 0.1785 0.2152 REMARK 3 3 3.2400 - 2.8300 0.98 2816 153 0.2110 0.3035 REMARK 3 4 2.8300 - 2.5800 0.98 2846 160 0.2294 0.2787 REMARK 3 5 2.5800 - 2.3900 0.98 2815 150 0.2287 0.2657 REMARK 3 6 2.3900 - 2.2500 0.98 2821 138 0.2468 0.2893 REMARK 3 7 2.2500 - 2.1400 0.97 2768 155 0.2691 0.3059 REMARK 3 8 2.1400 - 2.0400 0.97 2838 138 0.2643 0.3049 REMARK 3 9 2.0400 - 1.9700 0.96 2810 119 0.2864 0.3249 REMARK 3 10 1.9700 - 1.9000 0.96 2772 140 0.3567 0.3643 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 44.21 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 2904 REMARK 3 ANGLE : 0.819 3935 REMARK 3 CHIRALITY : 0.053 431 REMARK 3 PLANARITY : 0.007 508 REMARK 3 DIHEDRAL : 17.685 1109 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESSEQ 10:356) REMARK 3 ORIGIN FOR THE GROUP (A): -0.1391 -1.2691 0.9141 REMARK 3 T TENSOR REMARK 3 T11: 0.2909 T22: 0.3492 REMARK 3 T33: 0.3532 T12: 0.0077 REMARK 3 T13: 0.0425 T23: 0.0152 REMARK 3 L TENSOR REMARK 3 L11: 0.8879 L22: 1.5704 REMARK 3 L33: 3.3152 L12: 0.3742 REMARK 3 L13: 1.2223 L23: 1.0098 REMARK 3 S TENSOR REMARK 3 S11: -0.1157 S12: 0.0416 S13: -0.0147 REMARK 3 S21: -0.0542 S22: 0.1348 S23: -0.0216 REMARK 3 S31: -0.4018 S32: 0.3183 S33: 0.0011 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 9VM0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JUN-25. REMARK 100 THE DEPOSITION ID IS D_1300060991. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAR-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29683 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 41.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 1.05900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 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 (%): 50.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG200, 0.1 M BIS-TRIS PROPANE AT REMARK 280 PH 9.0, 18% W/V POLYETHYLENE GLYCOL 8,000, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 MET A -7 REMARK 465 GLY A -6 REMARK 465 SER A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 HIS A 1 REMARK 465 GLY A 2 REMARK 465 SER A 3 REMARK 465 GLY A 4 REMARK 465 GLY A 5 REMARK 465 SER A 6 REMARK 465 ALA A 7 REMARK 465 GLY A 8 REMARK 465 PRO A 9 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 PHE A 17 68.50 -153.24 REMARK 500 GLN A 60 19.39 55.57 REMARK 500 ALA A 90 151.63 -48.83 REMARK 500 LYS A 97 -63.19 -130.55 REMARK 500 ARG A 146 -9.55 79.43 REMARK 500 ASP A 147 40.33 -142.87 REMARK 500 ASP A 165 50.66 77.17 REMARK 500 LYS A 201 -143.11 -172.90 REMARK 500 SER A 221 -5.02 -141.94 REMARK 500 LEU A 292 54.65 -94.39 REMARK 500 ASP A 316 86.60 -157.54 REMARK 500 MET A 331 -156.72 -129.59 REMARK 500 REMARK 500 REMARK: NULL DBREF 9VM0 A -7 356 PDB 9VM0 9VM0 -7 356 SEQRES 1 A 364 MET GLY SER HIS HIS HIS HIS HIS HIS GLY SER GLY GLY SEQRES 2 A 364 SER ALA GLY PRO GLU MET VAL ARG GLY GLN VAL PHE ASP SEQRES 3 A 364 VAL GLY PRO ARG TYR THR ASN LEU SER TYR ILE GLY GLU SEQRES 4 A 364 GLY ALA TYR GLY MET VAL CYS SER ALA TYR ASP ASN LEU SEQRES 5 A 364 ASN LYS VAL ARG VAL ALA ILE LYS LYS ILE SER PRO PHE SEQRES 6 A 364 GLU HIS GLN THR TYR CYS GLN ARG THR LEU ARG GLU ILE SEQRES 7 A 364 LYS ILE LEU LEU ARG PHE ARG HIS GLU ASN ILE ILE GLY SEQRES 8 A 364 ILE ASN ASP ILE ILE ARG ALA PRO THR ILE GLU GLN MET SEQRES 9 A 364 LYS ASP VAL TYR ILE VAL GLN ASP LEU MET GLU THR ASP SEQRES 10 A 364 LEU TYR LYS LEU LEU LYS THR GLN HIS LEU SER ASN ASP SEQRES 11 A 364 HIS ILE CYS TYR PHE LEU TYR GLN ILE LEU ARG GLY LEU SEQRES 12 A 364 LYS TYR ILE HIS SER ALA ASN VAL LEU HIS ARG ASP LEU SEQRES 13 A 364 LYS PRO SER ASN LEU LEU LEU ASN THR THR CYS ASP LEU SEQRES 14 A 364 LYS ILE CYS ASP PHE GLY LEU THR ASP ASP GLY LEU ALA SEQRES 15 A 364 ARG THR MET ASN PRO GLU ASN ASP GLU VAL PRO TYR ALA SEQRES 16 A 364 THR ARG TRP TYR ARG ALA PRO GLU ILE MET LEU ASN SER SEQRES 17 A 364 LYS GLY TYR THR LYS SER ILE ASP ILE TRP SER VAL GLY SEQRES 18 A 364 CYS ILE LEU ALA GLU MET LEU SER ASN ARG PRO ILE PHE SEQRES 19 A 364 PRO GLY LYS HIS TYR LEU ASP GLN LEU ASN HIS ILE LEU SEQRES 20 A 364 GLY ILE LEU GLY SER PRO SER GLN GLU ASP LEU ASN CYS SEQRES 21 A 364 ILE ILE ASN LEU LYS ALA ARG ASN TYR LEU LEU SER LEU SEQRES 22 A 364 PRO HIS LYS ASN LYS VAL PRO TRP ASN ARG LEU PHE PRO SEQRES 23 A 364 ASN ALA ASP SER LYS ALA LEU ASP LEU LEU ASP LYS MET SEQRES 24 A 364 LEU THR PHE ASN PRO HIS LYS ARG ILE GLU VAL GLU GLN SEQRES 25 A 364 ALA LEU ALA HIS PRO TYR LEU GLU GLN TYR TYR ASP PRO SEQRES 26 A 364 SER ASP GLU PRO ILE ALA GLU ALA PRO PHE LYS PHE ASP SEQRES 27 A 364 MET GLU LEU ASP ASP LEU PRO LYS GLU LYS LEU LYS GLU SEQRES 28 A 364 LEU ILE PHE GLU GLU THR ALA ARG PHE GLN PRO GLY TYR FORMUL 2 HOH *115(H2 O) HELIX 1 AA1 CYS A 63 PHE A 76 1 14 HELIX 2 AA2 LEU A 110 GLN A 117 1 8 HELIX 3 AA3 SER A 120 ALA A 141 1 22 HELIX 4 AA4 LYS A 149 SER A 151 5 3 HELIX 5 AA5 THR A 169 MET A 177 1 9 HELIX 6 AA6 PRO A 185 TRP A 190 5 6 HELIX 7 AA7 ALA A 193 ASN A 199 1 7 HELIX 8 AA8 LYS A 205 ASN A 222 1 18 HELIX 9 AA9 HIS A 230 GLY A 243 1 14 HELIX 10 AB1 SER A 246 CYS A 252 1 7 HELIX 11 AB2 ASN A 255 LEU A 265 1 11 HELIX 12 AB3 PRO A 272 PHE A 277 1 6 HELIX 13 AB4 ASP A 281 LEU A 292 1 12 HELIX 14 AB5 GLU A 301 ALA A 307 1 7 HELIX 15 AB6 HIS A 308 GLU A 312 5 5 HELIX 16 AB7 ASP A 316 GLU A 320 5 5 HELIX 17 AB8 PRO A 337 THR A 349 1 13 HELIX 18 AB9 ALA A 350 GLN A 353 5 4 SHEET 1 AA1 2 MET A 11 VAL A 12 0 SHEET 2 AA1 2 GLN A 15 VAL A 16 -1 O GLN A 15 N VAL A 12 SHEET 1 AA2 5 TYR A 23 GLU A 31 0 SHEET 2 AA2 5 MET A 36 ASP A 42 -1 O TYR A 41 N THR A 24 SHEET 3 AA2 5 VAL A 47 ILE A 54 -1 O VAL A 49 N ALA A 40 SHEET 4 AA2 5 VAL A 99 ASP A 104 -1 O GLN A 103 N ALA A 50 SHEET 5 AA2 5 ASP A 86 ILE A 88 -1 N ASP A 86 O VAL A 102 SHEET 1 AA3 3 THR A 108 ASP A 109 0 SHEET 2 AA3 3 LEU A 153 LEU A 155 -1 O LEU A 155 N THR A 108 SHEET 3 AA3 3 LEU A 161 ILE A 163 -1 O LYS A 162 N LEU A 154 CRYST1 39.765 44.745 61.934 105.20 103.11 102.19 P 1 1 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 0.025148 0.005431 0.008067 0.00000 SCALE2 0.000000 0.022864 0.007878 0.00000 SCALE3 0.000000 0.000000 0.017535 0.00000 MASTER 253 0 0 18 10 0 0 6 2952 1 0 28 END