HEADER DE NOVO PROTEIN 06-AUG-23 8KC4 TITLE DE NOVO DESIGN PROTEIN -NA05 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGN PROTEIN -NA05; 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 8KC4 0 JRNL AUTH S.WANG,Y.LIU JRNL TITL DE NOVO DESIGN PROTEIN -NA05 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 8701 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.254 REMARK 3 R VALUE (WORKING SET) : 0.253 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 427 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 30.0000 - 3.1700 1.00 2873 135 0.2295 0.2363 REMARK 3 2 3.1700 - 2.5200 1.00 2701 163 0.2994 0.3483 REMARK 3 3 2.5200 - 2.2000 1.00 2700 129 0.3092 0.4003 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) : 0.398 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 40.597 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.45 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 : 0.002 1130 REMARK 3 ANGLE : 0.367 1540 REMARK 3 CHIRALITY : 0.031 200 REMARK 3 PLANARITY : 0.002 197 REMARK 3 DIHEDRAL : 2.830 158 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 115 THROUGH 135 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.1313 12.6648 7.2472 REMARK 3 T TENSOR REMARK 3 T11: 0.5891 T22: 0.6263 REMARK 3 T33: 0.3934 T12: 0.0033 REMARK 3 T13: -0.0067 T23: -0.0150 REMARK 3 L TENSOR REMARK 3 L11: 7.2538 L22: 3.2908 REMARK 3 L33: 7.4519 L12: -3.4226 REMARK 3 L13: -1.5718 L23: 4.0061 REMARK 3 S TENSOR REMARK 3 S11: -0.5787 S12: -0.2437 S13: -0.0829 REMARK 3 S21: 0.9215 S22: 0.6070 S23: -0.5347 REMARK 3 S31: 0.4227 S32: 0.9942 S33: 0.0054 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 136 THROUGH 158 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.4822 13.6855 -3.0509 REMARK 3 T TENSOR REMARK 3 T11: 0.8794 T22: 0.5300 REMARK 3 T33: 0.3446 T12: 0.0237 REMARK 3 T13: 0.0126 T23: -0.0670 REMARK 3 L TENSOR REMARK 3 L11: 5.6290 L22: 9.2459 REMARK 3 L33: 9.2294 L12: 3.9225 REMARK 3 L13: -2.5930 L23: -7.8650 REMARK 3 S TENSOR REMARK 3 S11: 0.0890 S12: 0.1132 S13: -0.0287 REMARK 3 S21: -0.7026 S22: -0.1397 S23: -0.6642 REMARK 3 S31: 0.9554 S32: -0.2424 S33: -0.0901 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 8 THROUGH 40 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.1656 10.4848 23.6758 REMARK 3 T TENSOR REMARK 3 T11: 0.9136 T22: 0.8723 REMARK 3 T33: 0.6024 T12: -0.0185 REMARK 3 T13: 0.1573 T23: -0.0395 REMARK 3 L TENSOR REMARK 3 L11: 6.6489 L22: 9.4390 REMARK 3 L33: 7.1585 L12: 1.1670 REMARK 3 L13: 0.6067 L23: -1.4753 REMARK 3 S TENSOR REMARK 3 S11: 0.6874 S12: -1.3661 S13: -0.1819 REMARK 3 S21: 1.3716 S22: -0.4492 S23: 0.2842 REMARK 3 S31: -0.7844 S32: -1.1915 S33: -0.1782 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 41 THROUGH 74 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.8219 9.3168 18.8673 REMARK 3 T TENSOR REMARK 3 T11: 0.7065 T22: 0.4734 REMARK 3 T33: 0.3992 T12: -0.1259 REMARK 3 T13: -0.1666 T23: 0.0037 REMARK 3 L TENSOR REMARK 3 L11: 7.1849 L22: 0.6986 REMARK 3 L33: 3.9449 L12: 1.2963 REMARK 3 L13: 0.9012 L23: -1.1710 REMARK 3 S TENSOR REMARK 3 S11: 0.1426 S12: -0.3279 S13: -0.0635 REMARK 3 S21: 1.3257 S22: -0.4371 S23: -0.8951 REMARK 3 S31: -0.2400 S32: 0.2509 S33: -0.1012 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 75 THROUGH 114 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.7930 13.9782 9.4508 REMARK 3 T TENSOR REMARK 3 T11: 0.5100 T22: 0.4847 REMARK 3 T33: 0.2615 T12: -0.0523 REMARK 3 T13: 0.0028 T23: 0.0549 REMARK 3 L TENSOR REMARK 3 L11: 5.6589 L22: 5.8502 REMARK 3 L33: 6.4872 L12: 1.9820 REMARK 3 L13: -0.8824 L23: -1.8624 REMARK 3 S TENSOR REMARK 3 S11: 0.1478 S12: -0.3813 S13: 0.3456 REMARK 3 S21: 0.8746 S22: -0.1791 S23: 0.3030 REMARK 3 S31: -0.8306 S32: -0.0467 S33: -0.0094 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 8KC4 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_1300040056. 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 : 8750 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 44.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 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 (%): 43.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M IMIDAZOLE MALATE PH7.0 20% W/V REMARK 280 PEG4000, VAPOR DIFFUSION, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 20.26750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.97800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.55050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.97800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.26750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.55050 REMARK 290 SMTRY3 4 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 GLY A 0 REMARK 465 LYS A 1 REMARK 465 LEU A 2 REMARK 465 PRO A 3 REMARK 465 GLU A 4 REMARK 465 GLU A 5 REMARK 465 GLU A 6 REMARK 465 LEU A 7 REMARK 465 HIS A 159 REMARK 465 HIS A 160 REMARK 465 HIS A 161 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 8 CG CD CE NZ REMARK 470 LYS A 9 CG CD CE NZ REMARK 470 LYS A 10 CG CD CE NZ REMARK 470 GLU A 12 CG CD OE1 OE2 REMARK 470 GLU A 13 CG CD OE1 OE2 REMARK 470 ASN A 16 CG OD1 ND2 REMARK 470 GLU A 20 CG CD OE1 OE2 REMARK 470 LYS A 32 CG CD CE NZ REMARK 470 GLU A 35 CG CD OE1 OE2 REMARK 470 GLU A 39 CG CD OE1 OE2 REMARK 470 ARG A 75 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 76 CG CD CE NZ REMARK 470 GLU A 77 CG CD OE1 OE2 REMARK 470 LYS A 113 CG CD CE NZ REMARK 470 LYS A 114 CG CD CE NZ REMARK 470 LYS A 115 CG CD CE NZ REMARK 470 LYS A 120 CG CD CE NZ REMARK 470 LYS A 123 CG CD CE NZ REMARK 470 GLU A 130 CG CD OE1 OE2 REMARK 470 LYS A 131 CG CD CE NZ REMARK 470 LYS A 136 CG CD CE NZ REMARK 470 LYS A 144 CG CD CE NZ REMARK 470 GLU A 147 CG CD OE1 OE2 DBREF 8KC4 A 0 161 PDB 8KC4 8KC4 0 161 SEQRES 1 A 162 GLY LYS LEU PRO GLU GLU GLU LEU LYS LYS LYS ILE GLU SEQRES 2 A 162 GLU PHE ALA ASN PHE PHE ILE GLU ASN LYS ASP VAL ASP SEQRES 3 A 162 LEU ASP GLU LEU ALA ASP LYS ILE LEU GLU ILE ALA GLU SEQRES 4 A 162 GLU THR GLY THR HIS ILE GLY ASP ILE TYR GLU GLN LEU SEQRES 5 A 162 VAL ALA LEU ALA PRO ASP GLU GLU THR LEU ARG THR LEU SEQRES 6 A 162 THR LEU ALA LEU VAL ARG LEU LEU GLY ARG ARG LYS GLU SEQRES 7 A 162 PRO LEU ASP LEU ASP LEU VAL ARG LEU LEU VAL GLU THR SEQRES 8 A 162 LEU VAL LEU ASP LEU GLY ALA THR ASP LEU ALA VAL GLU SEQRES 9 A 162 VAL VAL LYS LEU ALA PHE SER LEU ALA LYS LYS LYS GLU SEQRES 10 A 162 GLN LEU GLU LYS LEU LEU LYS ALA ILE ASP GLU VAL ILE SEQRES 11 A 162 GLU LYS ALA ARG LYS GLU LYS GLY MET ASP ALA ALA ALA SEQRES 12 A 162 GLU LYS LEU ARG GLU VAL LYS GLU LYS TYR LEU LEU GLU SEQRES 13 A 162 HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *21(H2 O) HELIX 1 AA1 LYS A 8 ASN A 21 1 14 HELIX 2 AA2 ASP A 25 GLY A 41 1 17 HELIX 3 AA3 HIS A 43 LEU A 54 1 12 HELIX 4 AA4 ASP A 57 ARG A 74 1 18 HELIX 5 AA5 ASP A 80 ASP A 94 1 15 HELIX 6 AA6 ALA A 97 ALA A 112 1 16 HELIX 7 AA7 LYS A 114 GLU A 135 1 22 HELIX 8 AA8 MET A 138 HIS A 158 1 21 CRYST1 40.535 59.101 67.956 90.00 90.00 90.00 P 21 21 21 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 0.024670 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016920 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014715 0.00000