HEADER DE NOVO PROTEIN 28-JUL-23 8K83 TITLE DE NOVO DESIGN PROTEIN -N2 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 8K83 0 JRNL AUTH S.WANG,Y.LIU JRNL TITL DE NOVO DESIGN PROTEIN -N2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 34557 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1743 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 33.1300 - 4.1200 0.99 2878 121 0.1829 0.2066 REMARK 3 2 4.1200 - 3.2700 1.00 2782 137 0.1699 0.1880 REMARK 3 3 3.2700 - 2.8600 1.00 2786 132 0.1731 0.1978 REMARK 3 4 2.8600 - 2.6000 0.99 2710 170 0.1780 0.2344 REMARK 3 5 2.6000 - 2.4100 0.99 2720 182 0.1740 0.1984 REMARK 3 6 2.4100 - 2.2700 0.99 2750 116 0.1685 0.2222 REMARK 3 7 2.2700 - 2.1500 0.99 2721 139 0.1827 0.2073 REMARK 3 8 2.1500 - 2.0600 0.99 2722 139 0.1925 0.2530 REMARK 3 9 2.0600 - 1.9800 0.99 2722 148 0.1940 0.2549 REMARK 3 10 1.9800 - 1.9100 0.98 2668 162 0.2172 0.2813 REMARK 3 11 1.9100 - 1.8500 0.98 2660 150 0.2764 0.2664 REMARK 3 12 1.8500 - 1.8000 0.99 2695 147 0.3310 0.3632 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) : 0.223 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.170 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.57 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.18 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 2636 REMARK 3 ANGLE : 0.696 3602 REMARK 3 CHIRALITY : 0.040 447 REMARK 3 PLANARITY : 0.007 465 REMARK 3 DIHEDRAL : 10.202 383 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): 13.4255 -2.8204 46.2865 REMARK 3 T TENSOR REMARK 3 T11: 0.1622 T22: 0.1692 REMARK 3 T33: 0.1835 T12: -0.0108 REMARK 3 T13: -0.0095 T23: 0.0020 REMARK 3 L TENSOR REMARK 3 L11: 0.1952 L22: 0.2011 REMARK 3 L33: 0.5198 L12: -0.0737 REMARK 3 L13: -0.0283 L23: -0.0803 REMARK 3 S TENSOR REMARK 3 S11: -0.0023 S12: 0.0112 S13: 0.0014 REMARK 3 S21: 0.0059 S22: -0.0017 S23: 0.0126 REMARK 3 S31: 0.0301 S32: -0.1324 S33: 0.0000 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 8K83 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_1300039740. 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 : 34581 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 52.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 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 (%): 52.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M MES MONOHYDRATE PH5.3, 20% W/V REMARK 280 POLYETHYLENE GLYCOL 4,000, 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 19.67000 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 175 REMARK 465 HIS A 176 REMARK 465 HIS A 177 REMARK 465 HIS A 178 REMARK 465 HIS A 179 REMARK 465 HIS A 180 REMARK 465 GLY B 0 REMARK 465 HIS B 178 REMARK 465 HIS B 179 REMARK 465 HIS B 180 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 HIS B 177 CG ND1 CD2 CE1 NE2 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 B 84 27.85 49.99 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 B 426 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH B 427 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH B 428 DISTANCE = 6.74 ANGSTROMS DBREF 8K83 A 0 180 PDB 8K83 8K83 0 180 DBREF 8K83 B 0 180 PDB 8K83 8K83 0 180 SEQRES 1 A 181 GLY SER ALA ALA ALA VAL GLU ALA GLN ILE ALA ALA LEU SEQRES 2 A 181 VAL ALA ALA ALA ASN ALA ALA LEU ALA ALA ASP ASP GLN SEQRES 3 A 181 ALA ALA VAL ARG ALA ALA LEU ALA PRO LEU ALA GLU LEU SEQRES 4 A 181 ALA LYS GLU HIS PRO GLU LEU VAL ALA ALA ASN PRO GLU SEQRES 5 A 181 VAL GLN ALA LEU LEU LYS ALA LEU ILE ALA LYS PHE GLU SEQRES 6 A 181 GLU PHE ASP LEU GLU VAL GLN ARG LEU VAL LEU ALA VAL SEQRES 7 A 181 VAL ALA GLU LEU THR LYS ASP ASN PRO GLU ALA VAL ALA SEQRES 8 A 181 PHE LEU LYS ALA ALA GLY PHE TRP PRO HIS LEU ALA ALA SEQRES 9 A 181 ALA LEU ARG HIS PRO ASP LEU GLU LEU VAL ARG LEU ALA SEQRES 10 A 181 LEU ALA ILE LEU SER SER SER LEU ALA ALA VAL GLU ALA SEQRES 11 A 181 PHE VAL ALA ALA LEU GLY LEU GLU GLY LEU GLU ALA ASP SEQRES 12 A 181 LEU ALA TYR LEU ARG ALA ALA PHE PRO ASP SER PRO ALA SEQRES 13 A 181 ALA GLU LEU ILE ALA LYS VAL GLU ALA LEU LEU ALA GLU SEQRES 14 A 181 LEU ARG ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 181 GLY SER ALA ALA ALA VAL GLU ALA GLN ILE ALA ALA LEU SEQRES 2 B 181 VAL ALA ALA ALA ASN ALA ALA LEU ALA ALA ASP ASP GLN SEQRES 3 B 181 ALA ALA VAL ARG ALA ALA LEU ALA PRO LEU ALA GLU LEU SEQRES 4 B 181 ALA LYS GLU HIS PRO GLU LEU VAL ALA ALA ASN PRO GLU SEQRES 5 B 181 VAL GLN ALA LEU LEU LYS ALA LEU ILE ALA LYS PHE GLU SEQRES 6 B 181 GLU PHE ASP LEU GLU VAL GLN ARG LEU VAL LEU ALA VAL SEQRES 7 B 181 VAL ALA GLU LEU THR LYS ASP ASN PRO GLU ALA VAL ALA SEQRES 8 B 181 PHE LEU LYS ALA ALA GLY PHE TRP PRO HIS LEU ALA ALA SEQRES 9 B 181 ALA LEU ARG HIS PRO ASP LEU GLU LEU VAL ARG LEU ALA SEQRES 10 B 181 LEU ALA ILE LEU SER SER SER LEU ALA ALA VAL GLU ALA SEQRES 11 B 181 PHE VAL ALA ALA LEU GLY LEU GLU GLY LEU GLU ALA ASP SEQRES 12 B 181 LEU ALA TYR LEU ARG ALA ALA PHE PRO ASP SER PRO ALA SEQRES 13 B 181 ALA GLU LEU ILE ALA LYS VAL GLU ALA LEU LEU ALA GLU SEQRES 14 B 181 LEU ARG ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS HET MES A 201 12 HET GOL B 201 6 HET MES B 202 12 HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 MES 2(C6 H13 N O4 S) FORMUL 4 GOL C3 H8 O3 FORMUL 6 HOH *243(H2 O) HELIX 1 AA1 SER A 1 ALA A 22 1 22 HELIX 2 AA2 ASP A 24 HIS A 42 1 19 HELIX 3 AA3 HIS A 42 ASN A 49 1 8 HELIX 4 AA4 ASN A 49 LYS A 62 1 14 HELIX 5 AA5 PHE A 63 PHE A 66 5 4 HELIX 6 AA6 ASP A 67 LYS A 83 1 17 HELIX 7 AA7 GLU A 87 ALA A 95 1 9 HELIX 8 AA8 GLY A 96 LEU A 105 1 10 HELIX 9 AA9 ASP A 109 SER A 121 1 13 HELIX 10 AB1 SER A 123 PHE A 150 1 28 HELIX 11 AB2 PRO A 154 GLU A 174 1 21 HELIX 12 AB3 ALA B 2 ALA B 22 1 21 HELIX 13 AB4 ASP B 24 HIS B 42 1 19 HELIX 14 AB5 HIS B 42 ASN B 49 1 8 HELIX 15 AB6 ASN B 49 LYS B 62 1 14 HELIX 16 AB7 PHE B 63 PHE B 66 5 4 HELIX 17 AB8 ASP B 67 LYS B 83 1 17 HELIX 18 AB9 GLU B 87 ALA B 95 1 9 HELIX 19 AC1 GLY B 96 LEU B 105 1 10 HELIX 20 AC2 ASP B 109 SER B 121 1 13 HELIX 21 AC3 SER B 123 PHE B 150 1 28 HELIX 22 AC4 ALA B 155 HIS B 177 1 23 CRYST1 68.550 39.340 70.549 90.00 98.81 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 0.014588 0.000000 0.002260 0.00000 SCALE2 0.000000 0.025419 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014344 0.00000