HEADER DE NOVO PROTEIN 28-JUL-23 8K84 TITLE DE NOVO DESIGN PROTEIN -N3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGN PROTEIN; 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; 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 31-JUL-24 8K84 0 JRNL AUTH S.WANG,Y.LIU JRNL TITL DE NOVO DESIGN PROTEIN -N3 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 21066 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.580 REMARK 3 FREE R VALUE TEST SET COUNT : 1175 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 25.0100 - 4.0000 0.97 2537 153 0.1863 0.2254 REMARK 3 2 3.9900 - 3.1700 0.99 2502 156 0.1665 0.2244 REMARK 3 3 3.1700 - 2.7700 0.99 2534 101 0.1864 0.2545 REMARK 3 4 2.7700 - 2.5200 0.99 2487 142 0.1862 0.2435 REMARK 3 5 2.5200 - 2.3400 0.99 2482 149 0.1885 0.2661 REMARK 3 6 2.3400 - 2.2000 0.99 2445 145 0.1887 0.2288 REMARK 3 7 2.2000 - 2.0900 0.99 2453 157 0.2100 0.2656 REMARK 3 8 2.0900 - 2.0000 1.00 2451 172 0.2488 0.3327 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) : 0.258 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.757 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.05 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.91 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 2655 REMARK 3 ANGLE : 0.734 3607 REMARK 3 CHIRALITY : 0.041 431 REMARK 3 PLANARITY : 0.006 475 REMARK 3 DIHEDRAL : 4.024 375 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 8K84 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_1300039748. 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 : 21086 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 59.820 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 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 (%): 39.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M IMIDAZOLE MALATE PH5.5 33% W/V REMARK 280 PEG600, VAPOR DIFFUSION, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 17.79950 REMARK 290 SMTRY3 2 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 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 HIS A 174 REMARK 465 HIS A 175 REMARK 465 HIS A 176 REMARK 465 GLY B 0 REMARK 465 HIS B 175 REMARK 465 HIS B 176 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 99 CG CD OE1 OE2 REMARK 470 LYS A 120 CG CD CE NZ REMARK 470 GLU A 133 CG CD OE1 OE2 REMARK 470 ARG A 164 CG CD NE CZ NH1 NH2 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 HIS A 173 O HOH A 301 2.05 REMARK 500 O HOH A 318 O HOH A 413 2.10 REMARK 500 OE1 GLU B 152 O HOH B 201 2.13 REMARK 500 NZ LYS A 160 O HOH A 302 2.14 REMARK 500 O HOH B 239 O HOH B 317 2.14 REMARK 500 O HOH A 339 O HOH A 358 2.15 REMARK 500 O HOH A 342 O HOH A 421 2.15 REMARK 500 O HOH A 352 O HOH A 401 2.16 REMARK 500 O HOH B 284 O HOH B 319 2.16 REMARK 500 O HOH B 304 O HOH B 306 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 422 O HOH B 288 2556 2.13 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 19 70.75 -154.59 REMARK 500 ASP A 33 70.49 -154.85 REMARK 500 ASP A 76 73.45 -152.03 REMARK 500 ARG A 96 70.72 -109.40 REMARK 500 ASP B 19 71.67 -153.36 REMARK 500 ASP B 33 72.94 -153.71 REMARK 500 ASP B 76 72.75 -151.37 REMARK 500 ARG B 96 68.81 -110.90 REMARK 500 REMARK 500 REMARK: NULL DBREF 8K84 A 0 176 PDB 8K84 8K84 0 176 DBREF 8K84 B 0 176 PDB 8K84 8K84 0 176 SEQRES 1 A 177 GLY SER LEU ALA GLU VAL LEU ALA GLU THR VAL ARG TRP SEQRES 2 A 177 LEU ARG LEU ALA ARG GLU ASP PRO GLU ALA PHE ALA ALA SEQRES 3 A 177 ARG VAL ALA ALA LEU LEU ALA ASP PRO ASP ALA PHE SER SEQRES 4 A 177 PRO THR GLU VAL ALA ALA ALA TYR VAL ALA LEU ALA VAL SEQRES 5 A 177 LEU ALA ARG GLU ARG GLY ASP ALA GLU ALA ALA ALA ALA SEQRES 6 A 177 ALA GLU ARG LEU GLY ALA HIS LEU LEU ALA THR ASP PRO SEQRES 7 A 177 GLU THR TYR LEU GLU ALA GLN VAL VAL LEU ALA ALA ILE SEQRES 8 A 177 GLU ALA LEU LEU GLY ARG GLU GLU GLU ALA GLU ALA VAL SEQRES 9 A 177 LEU GLU GLU ALA LEU SER ARG LEU THR ALA ALA ASN LYS SEQRES 10 A 177 GLY ASP LYS LYS ASP LEU LEU LYS ALA ILE LYS LYS LEU SEQRES 11 A 177 PHE GLU PRO GLU ALA ARG ALA GLN LEU ALA ALA ILE ALA SEQRES 12 A 177 ALA VAL LEU ASP ALA ALA ASP ASN VAL GLU ALA ALA LEU SEQRES 13 A 177 ALA ARG LEU GLU LYS TRP ALA GLU ARG LEU GLU LYS GLU SEQRES 14 A 177 LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 177 GLY SER LEU ALA GLU VAL LEU ALA GLU THR VAL ARG TRP SEQRES 2 B 177 LEU ARG LEU ALA ARG GLU ASP PRO GLU ALA PHE ALA ALA SEQRES 3 B 177 ARG VAL ALA ALA LEU LEU ALA ASP PRO ASP ALA PHE SER SEQRES 4 B 177 PRO THR GLU VAL ALA ALA ALA TYR VAL ALA LEU ALA VAL SEQRES 5 B 177 LEU ALA ARG GLU ARG GLY ASP ALA GLU ALA ALA ALA ALA SEQRES 6 B 177 ALA GLU ARG LEU GLY ALA HIS LEU LEU ALA THR ASP PRO SEQRES 7 B 177 GLU THR TYR LEU GLU ALA GLN VAL VAL LEU ALA ALA ILE SEQRES 8 B 177 GLU ALA LEU LEU GLY ARG GLU GLU GLU ALA GLU ALA VAL SEQRES 9 B 177 LEU GLU GLU ALA LEU SER ARG LEU THR ALA ALA ASN LYS SEQRES 10 B 177 GLY ASP LYS LYS ASP LEU LEU LYS ALA ILE LYS LYS LEU SEQRES 11 B 177 PHE GLU PRO GLU ALA ARG ALA GLN LEU ALA ALA ILE ALA SEQRES 12 B 177 ALA VAL LEU ASP ALA ALA ASP ASN VAL GLU ALA ALA LEU SEQRES 13 B 177 ALA ARG LEU GLU LYS TRP ALA GLU ARG LEU GLU LYS GLU SEQRES 14 B 177 LEU GLU HIS HIS HIS HIS HIS HIS HET PEG A 201 7 HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 3 PEG C4 H10 O3 FORMUL 4 HOH *257(H2 O) HELIX 1 AA1 SER A 1 ASP A 19 1 19 HELIX 2 AA2 ASP A 19 ASP A 33 1 15 HELIX 3 AA3 PRO A 34 PHE A 37 5 4 HELIX 4 AA4 SER A 38 GLY A 57 1 20 HELIX 5 AA5 ASP A 58 ASP A 76 1 19 HELIX 6 AA6 ASP A 76 LEU A 94 1 19 HELIX 7 AA7 ARG A 96 ALA A 114 1 19 HELIX 8 AA8 ASP A 118 LEU A 129 1 12 HELIX 9 AA9 GLU A 131 ASP A 146 1 16 HELIX 10 AB1 ALA A 147 ASP A 149 5 3 HELIX 11 AB2 ASN A 150 HIS A 173 1 24 HELIX 12 AB3 LEU B 2 ASP B 19 1 18 HELIX 13 AB4 ASP B 19 ASP B 33 1 15 HELIX 14 AB5 PRO B 34 PHE B 37 5 4 HELIX 15 AB6 SER B 38 GLY B 57 1 20 HELIX 16 AB7 ASP B 58 ASP B 76 1 19 HELIX 17 AB8 ASP B 76 LEU B 94 1 19 HELIX 18 AB9 ARG B 96 ALA B 114 1 19 HELIX 19 AC1 ASP B 118 LEU B 129 1 12 HELIX 20 AC2 GLU B 131 LEU B 145 1 15 HELIX 21 AC3 ALA B 147 ASP B 149 5 3 HELIX 22 AC4 ASN B 150 HIS B 174 1 25 CRYST1 69.899 35.599 70.422 90.00 117.01 90.00 P 1 21 1 4 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 0.014306 0.000000 0.007293 0.00000 SCALE2 0.000000 0.028091 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015939 0.00000