HEADER DE NOVO PROTEIN 05-AUG-23 8KC0 TITLE DE NOVO DESIGN PROTEIN -NB8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGN PROTEIN -NB8; 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 DE NOVO DESIGN PROTEIN, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.WANG,Y.LIU REVDAT 1 07-AUG-24 8KC0 0 JRNL AUTH S.WANG,Y.LIU JRNL TITL DE NOVO DESIGN PROTEIN -NB8 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 32.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 15117 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1496 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 32.6400 - 4.6700 1.00 1241 141 0.2215 0.2403 REMARK 3 2 4.6600 - 3.7100 0.99 1261 141 0.1804 0.1812 REMARK 3 3 3.7000 - 3.2400 1.00 1246 135 0.2020 0.3235 REMARK 3 4 3.2400 - 2.9400 1.00 1258 141 0.2600 0.2658 REMARK 3 5 2.9400 - 2.7300 1.00 1239 138 0.2824 0.3513 REMARK 3 6 2.7300 - 2.5700 1.00 1246 143 0.2910 0.3103 REMARK 3 7 2.5700 - 2.4400 0.99 1262 134 0.2591 0.3710 REMARK 3 8 2.4400 - 2.3400 0.96 1197 127 0.2652 0.3208 REMARK 3 9 2.3400 - 2.2500 0.98 1231 126 0.2678 0.3120 REMARK 3 10 2.2500 - 2.1700 0.97 1249 135 0.2847 0.3224 REMARK 3 11 2.1700 - 2.1000 0.98 1191 135 0.3095 0.3988 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) : 0.291 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.276 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.28 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.15 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 : 0.004 857 REMARK 3 ANGLE : 0.739 1157 REMARK 3 CHIRALITY : 0.051 142 REMARK 3 PLANARITY : 0.005 148 REMARK 3 DIHEDRAL : 4.435 118 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 29 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.9836 -26.4003 -9.0896 REMARK 3 T TENSOR REMARK 3 T11: 0.6197 T22: 0.5607 REMARK 3 T33: 0.2912 T12: 0.0996 REMARK 3 T13: 0.0996 T23: 0.1094 REMARK 3 L TENSOR REMARK 3 L11: 4.8531 L22: 6.3195 REMARK 3 L33: 9.4429 L12: 0.0145 REMARK 3 L13: 0.5490 L23: -1.7497 REMARK 3 S TENSOR REMARK 3 S11: -0.5094 S12: -1.1659 S13: -0.6407 REMARK 3 S21: 0.1290 S22: 0.1767 S23: 0.2984 REMARK 3 S31: 1.5469 S32: 0.6573 S33: 0.0505 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 30 THROUGH 77 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.4429 -23.0074 -24.0786 REMARK 3 T TENSOR REMARK 3 T11: 0.4529 T22: 0.3086 REMARK 3 T33: 0.2600 T12: -0.0799 REMARK 3 T13: -0.0211 T23: -0.0362 REMARK 3 L TENSOR REMARK 3 L11: 7.9822 L22: 5.8309 REMARK 3 L33: 6.7051 L12: 2.3921 REMARK 3 L13: -2.3406 L23: -3.8733 REMARK 3 S TENSOR REMARK 3 S11: -0.1186 S12: 0.3156 S13: -0.6556 REMARK 3 S21: -0.5315 S22: 0.0392 S23: 0.1467 REMARK 3 S31: 1.0431 S32: -0.2959 S33: 0.1086 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 78 THROUGH 95 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.2081 -18.0270 -16.7101 REMARK 3 T TENSOR REMARK 3 T11: 0.2958 T22: 0.5230 REMARK 3 T33: 0.3119 T12: 0.0121 REMARK 3 T13: 0.0284 T23: 0.0192 REMARK 3 L TENSOR REMARK 3 L11: 2.5105 L22: 4.7145 REMARK 3 L33: 5.3514 L12: 0.9473 REMARK 3 L13: -3.4393 L23: -0.2174 REMARK 3 S TENSOR REMARK 3 S11: 0.0452 S12: -0.2661 S13: 1.1199 REMARK 3 S21: 0.4199 S22: 0.1994 S23: 0.6738 REMARK 3 S31: -0.2555 S32: -1.0044 S33: -0.1696 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 96 THROUGH 116 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.1307 -18.8913 -8.2345 REMARK 3 T TENSOR REMARK 3 T11: 0.3874 T22: 0.7475 REMARK 3 T33: 0.3427 T12: 0.1243 REMARK 3 T13: 0.0049 T23: 0.1299 REMARK 3 L TENSOR REMARK 3 L11: 3.8948 L22: 7.5110 REMARK 3 L33: 4.8023 L12: -4.8953 REMARK 3 L13: -1.6725 L23: 1.3839 REMARK 3 S TENSOR REMARK 3 S11: -0.4116 S12: -0.8204 S13: 0.9776 REMARK 3 S21: 0.0809 S22: 0.6286 S23: 0.3817 REMARK 3 S31: -0.3690 S32: -0.4784 S33: -0.2866 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 8KC0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 08-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1300040042. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAR-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15117 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 46.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 22.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.7000 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) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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 (%): 48.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8M SUCCINIC ACID PH7.0, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 289K 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 63.57850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 23.08000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 23.08000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 95.36775 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 23.08000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 23.08000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 31.78925 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 23.08000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 23.08000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 95.36775 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 23.08000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 23.08000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 31.78925 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 63.57850 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 GLY A 0 REMARK 465 GLU A 1 REMARK 465 GLU A 117 REMARK 465 HIS A 118 REMARK 465 HIS A 119 REMARK 465 HIS A 120 REMARK 465 HIS A 121 REMARK 465 HIS A 122 REMARK 465 HIS A 123 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 LYS A 4 CG CD CE NZ REMARK 470 ASP A 10 CG OD1 OD2 REMARK 470 ASP A 13 CG OD1 OD2 REMARK 470 GLU A 14 CG CD OE1 OE2 REMARK 470 ARG A 17 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 21 CG CD OE1 OE2 REMARK 470 TRP A 30 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 30 CZ3 CH2 REMARK 470 GLU A 34 CG CD OE1 OE2 REMARK 470 LYS A 51 CG CD CE NZ REMARK 470 GLU A 56 CG CD OE1 OE2 REMARK 470 LYS A 59 CG CD CE NZ REMARK 470 LYS A 60 CG CD CE NZ REMARK 470 LYS A 64 CG CD CE NZ REMARK 470 LYS A 66 CG CD CE NZ REMARK 470 LYS A 96 CG CD CE NZ REMARK 470 LYS A 115 CG CD CE NZ REMARK 470 LEU A 116 CG CD1 CD2 DBREF 8KC0 A 0 123 PDB 8KC0 8KC0 0 123 SEQRES 1 A 124 GLY GLU GLU ILE LYS GLU THR PHE GLU VAL ASP ASP LEU SEQRES 2 A 124 ASP GLU ALA LEU ARG LEU SER ALA GLU LYS ILE ILE GLU SEQRES 3 A 124 GLU MET LYS LYS TRP GLY VAL THR GLU PHE ASP LEU LYS SEQRES 4 A 124 PHE TYR GLY LYS ASP ASP GLU LEU ALA LYS LYS ALA LYS SEQRES 5 A 124 GLU VAL ILE GLU GLU ALA ALA LYS LYS ALA GLY VAL LYS SEQRES 6 A 124 VAL LYS SER GLU PHE LEU TYR ASP GLU ASN LYS ASP LYS SEQRES 7 A 124 ILE THR LEU GLU LEU THR GLY PRO ASN GLY VAL LYS VAL SEQRES 8 A 124 THR SER GLU ILE SER LYS ASP GLY ILE LYS SER THR VAL SEQRES 9 A 124 GLU ARG PRO ASP ARG LYS VAL THR LEU THR PHE LYS LEU SEQRES 10 A 124 GLU HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *61(H2 O) HELIX 1 AA1 ASP A 11 TRP A 30 1 20 HELIX 2 AA2 ASP A 44 ALA A 61 1 18 HELIX 3 AA3 PRO A 85 GLY A 87 5 3 SHEET 1 AA1 7 ILE A 3 GLU A 8 0 SHEET 2 AA1 7 ARG A 108 LYS A 115 1 O THR A 111 N GLU A 5 SHEET 3 AA1 7 GLY A 98 ARG A 105 -1 N SER A 101 O LEU A 112 SHEET 4 AA1 7 LYS A 89 SER A 95 -1 N LYS A 89 O GLU A 104 SHEET 5 AA1 7 ILE A 78 THR A 83 -1 N ILE A 78 O ILE A 94 SHEET 6 AA1 7 GLU A 34 GLY A 41 -1 N LYS A 38 O GLU A 81 SHEET 7 AA1 7 LYS A 64 TYR A 71 1 O LEU A 70 N PHE A 39 CRYST1 46.160 46.160 127.157 90.00 90.00 90.00 P 43 21 2 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 0.021664 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021664 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007864 0.00000