HEADER DE NOVO PROTEIN 29-JUL-23 8K8G TITLE DE NOVO DESIGN PROTEIN -N9 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGN PROTEIN; 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 8K8G 0 JRNL AUTH S.WANG,Y.LIU JRNL TITL DE NOVO DESIGN PROTEIN -N9 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.35 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 38477 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1939 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 25.6100 - 3.2500 1.00 2782 143 0.1886 0.2211 REMARK 3 2 3.2500 - 2.5800 1.00 2653 151 0.1967 0.2305 REMARK 3 3 2.5800 - 2.2600 1.00 2638 149 0.1966 0.2161 REMARK 3 4 2.2600 - 2.0500 1.00 2601 160 0.1872 0.2015 REMARK 3 5 2.0500 - 1.9000 1.00 2597 125 0.2094 0.2642 REMARK 3 6 1.9000 - 1.7900 1.00 2646 126 0.2142 0.2190 REMARK 3 7 1.7900 - 1.7000 1.00 2592 133 0.2036 0.2011 REMARK 3 8 1.7000 - 1.6300 1.00 2586 142 0.2115 0.2208 REMARK 3 9 1.6300 - 1.5600 1.00 2599 124 0.2208 0.2488 REMARK 3 10 1.5600 - 1.5100 1.00 2582 131 0.2218 0.2667 REMARK 3 11 1.5100 - 1.4600 1.00 2580 127 0.2286 0.2451 REMARK 3 12 1.4600 - 1.4200 1.00 2585 141 0.2333 0.2783 REMARK 3 13 1.4200 - 1.3800 1.00 2548 159 0.2503 0.2623 REMARK 3 14 1.3800 - 1.3500 1.00 2549 128 0.2753 0.2867 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) : 0.152 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.819 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.31 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 : 0.006 1461 REMARK 3 ANGLE : 0.842 2010 REMARK 3 CHIRALITY : 0.074 255 REMARK 3 PLANARITY : 0.010 267 REMARK 3 DIHEDRAL : 11.199 502 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 8K8G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 31-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1300039792. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAY-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 : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 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 : 38537 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 43.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 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 (%): 39.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% W/V PEG 10000 0.1M HEPES PH7.5, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 64.82000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.82000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 17.50550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.99850 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 17.50550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.99850 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 64.82000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 17.50550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.99850 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 64.82000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 17.50550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 37.99850 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 64.82000 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 311 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 372 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 417 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 425 LIES ON A SPECIAL POSITION. 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 HIS A 209 REMARK 465 HIS A 210 REMARK 465 HIS A 211 REMARK 465 HIS A 212 REMARK 465 HIS A 213 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 GLU A 48 CG CD OE1 OE2 REMARK 470 HIS A 208 CG ND1 CD2 CE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 307 O HOH A 308 2.00 REMARK 500 O HOH A 330 O HOH A 396 2.10 REMARK 500 O HOH A 315 O HOH A 408 2.13 REMARK 500 O HOH A 420 O HOH A 422 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 A 511 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH A 512 DISTANCE = 6.06 ANGSTROMS REMARK 525 HOH A 513 DISTANCE = 7.57 ANGSTROMS DBREF 8K8G A 0 213 PDB 8K8G 8K8G 0 213 SEQRES 1 A 214 GLY ALA GLU ALA ALA ALA ALA ALA ALA VAL THR ALA GLU SEQRES 2 A 214 LEU ARG ALA PHE ARG ALA ALA GLY GLY THR VAL GLU LEU SEQRES 3 A 214 GLU ASP LEU PRO VAL THR PRO GLU THR LEU ALA ARG ALA SEQRES 4 A 214 GLU ALA ALA LEU ALA ARG LEU PRO PRO GLU SER VAL ALA SEQRES 5 A 214 VAL GLU THR TYR THR VAL PRO ALA PRO THR PRO GLU ALA SEQRES 6 A 214 PHE LEU ALA ALA LEU GLU ALA ALA LEU ALA ARG LEU ALA SEQRES 7 A 214 ALA GLU GLY LEU PRO ALA ILE LEU LEU ARG VAL VAL ASP SEQRES 8 A 214 ALA ASP GLY ASN LEU VAL GLY SER ILE LEU VAL ALA ALA SEQRES 9 A 214 ALA GLY PRO PRO ALA GLU SER ALA ALA ALA THR GLY ARG SEQRES 10 A 214 VAL LEU THR ILE TYR VAL ALA SER SER PRO GLU GLY LEU SEQRES 11 A 214 LYS VAL ALA ARG GLY LEU ALA ILE GLU THR ARG ASP ALA SEQRES 12 A 214 GLY GLY LEU ALA LEU ALA ILE GLY ALA SER GLY ALA TRP SEQRES 13 A 214 ALA LEU ALA GLY LEU ALA GLY ALA LEU ALA LEU ALA ARG SEQRES 14 A 214 ARG LEU ALA GLU ALA HIS GLY ALA PRO VAL ARG VAL VAL SEQRES 15 A 214 THR ILE GLY ASP PRO ALA ASN PRO THR ASP ALA ALA LEU SEQRES 16 A 214 ALA ALA ALA ILE ARG ALA ALA TYR ALA ALA ALA LEU GLU SEQRES 17 A 214 HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *213(H2 O) HELIX 1 AA1 GLY A 0 ALA A 19 1 20 HELIX 2 AA2 THR A 31 LEU A 45 1 15 HELIX 3 AA3 PRO A 46 VAL A 50 5 5 HELIX 4 AA4 THR A 61 GLY A 80 1 20 HELIX 5 AA5 PRO A 106 GLY A 115 1 10 HELIX 6 AA6 SER A 125 ALA A 142 1 18 HELIX 7 AA7 SER A 152 GLU A 172 1 21 HELIX 8 AA8 ASN A 188 GLU A 207 1 20 SHEET 1 AA1 7 VAL A 23 PRO A 29 0 SHEET 2 AA1 7 VAL A 178 GLY A 184 1 O VAL A 180 N GLU A 24 SHEET 3 AA1 7 LEU A 118 ALA A 123 1 N ILE A 120 O VAL A 181 SHEET 4 AA1 7 ALA A 146 GLY A 150 1 O LEU A 147 N TYR A 121 SHEET 5 AA1 7 LEU A 95 ALA A 102 -1 N ALA A 102 O ALA A 146 SHEET 6 AA1 7 ALA A 83 VAL A 89 -1 N LEU A 86 O ILE A 99 SHEET 7 AA1 7 ALA A 51 THR A 56 1 N ALA A 51 O LEU A 85 CRYST1 35.011 75.997 129.640 90.00 90.00 90.00 C 2 2 21 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 0.028562 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013158 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007714 0.00000