HEADER DE NOVO PROTEIN 27-AUG-25 9XZP TITLE CRYSTAL STRUCTURE OF AI-DESIGNED HOMODIMER MIYEI COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO 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 PROTEIN MIYEI, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.Y.WEI REVDAT 1 22-OCT-25 9XZP 0 JRNL AUTH T.P.RILEY,M.S.PARSA,P.KALANTARI,I.NADERI,K.AZIMIAN,N.BEGLOO, JRNL AUTH 2 O.MATUSOVSKY,K.AZIMIAN,K.Y.WEI JRNL TITL AN ARTIFICIAL INTELLIGENCE MODEL FOR TRANSLATING NATURAL JRNL TITL 2 LANGUAGE INTO FUNCTIONAL DE NOVO PROTEINS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0430 (REFMACAT 0.4.105) REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 14102 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.964 REMARK 3 FREE R VALUE TEST SET COUNT : 700 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.77 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.82 REMARK 3 REFLECTION IN BIN (WORKING SET) : 977 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.61 REMARK 3 BIN R VALUE (WORKING SET) : 0.3140 REMARK 3 BIN FREE R VALUE SET COUNT : 50 REMARK 3 BIN FREE R VALUE : 0.3210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1120 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 113 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.01 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.15700 REMARK 3 B22 (A**2) : -1.83200 REMARK 3 B33 (A**2) : 1.03100 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.94400 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.134 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.136 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.117 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.861 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1178 ; 0.005 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 1201 ; 0.002 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1607 ; 1.355 ; 1.803 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2750 ; 0.496 ; 1.735 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 172 ; 6.194 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 5 ; 0.565 ; 1.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 208 ;11.372 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 199 ; 0.058 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1406 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 226 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 188 ; 0.201 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 53 ; 0.146 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 566 ; 0.151 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 85 ; 0.118 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 647 ; 2.572 ; 3.547 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 646 ; 2.568 ; 3.539 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 813 ; 3.832 ; 6.350 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 814 ; 3.832 ; 6.356 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 531 ; 3.197 ; 3.950 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 531 ; 3.194 ; 3.949 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 787 ; 4.906 ; 7.092 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 788 ; 4.903 ; 7.097 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 9XZP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-AUG-25. REMARK 100 THE DEPOSITION ID IS D_1000299239. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUL-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8856 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X CDTE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.8.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14102 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.773 REMARK 200 RESOLUTION RANGE LOW (A) : 36.155 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.920 REMARK 200 R MERGE (I) : 0.09870 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.4600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 4.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 36.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.75 REMARK 200 R MERGE FOR SHELL (I) : 0.08260 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 21.23 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MORPHEUS G9: 30.0% W/V 550M_20K; 0.1 M REMARK 280 MB3 PH 8.5; 0.1 M MCA, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 26.54650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.73650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 26.54650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.73650 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 SER A 2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 5 NZ REMARK 480 GLN A 14 CD OE1 NE2 REMARK 480 LYS A 38 NZ REMARK 480 GLU A 49 CD OE1 OE2 REMARK 480 LYS B 5 NZ REMARK 480 LYS B 21 NZ REMARK 480 GLU B 29 CD OE1 OE2 REMARK 480 LYS B 45 CE NZ REMARK 480 ILE B 48 CD1 REMARK 480 GLU B 49 CD OE1 OE2 REMARK 480 LYS B 61 CE NZ REMARK 480 LYS B 68 CD CE NZ 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 ALA B 11 44.34 -86.52 REMARK 500 VAL B 57 -70.23 -87.78 REMARK 500 REMARK 500 REMARK: NULL DBREF 9XZP A 2 79 PDB 9XZP 9XZP 2 79 DBREF 9XZP B 2 79 PDB 9XZP 9XZP 2 79 SEQRES 1 A 78 SER GLY MET LYS ILE ALA VAL ILE GLY ALA THR GLY GLN SEQRES 2 A 78 VAL GLY ARG GLU ILE ALA LYS LEU LEU ALA GLU LYS GLY SEQRES 3 A 78 HIS GLU VAL THR ALA ILE ALA SER ARG SER LYS ASN PRO SEQRES 4 A 78 GLU GLU VAL ALA LYS LEU GLY ILE GLU ALA VAL TYR VAL SEQRES 5 A 78 ASP GLY GLU VAL LEU ASP PHE LYS SER VAL GLU GLU ALA SEQRES 6 A 78 VAL LYS ASN ALA ASP VAL VAL ILE SER VAL ALA GLY GLY SEQRES 1 B 78 SER GLY MET LYS ILE ALA VAL ILE GLY ALA THR GLY GLN SEQRES 2 B 78 VAL GLY ARG GLU ILE ALA LYS LEU LEU ALA GLU LYS GLY SEQRES 3 B 78 HIS GLU VAL THR ALA ILE ALA SER ARG SER LYS ASN PRO SEQRES 4 B 78 GLU GLU VAL ALA LYS LEU GLY ILE GLU ALA VAL TYR VAL SEQRES 5 B 78 ASP GLY GLU VAL LEU ASP PHE LYS SER VAL GLU GLU ALA SEQRES 6 B 78 VAL LYS ASN ALA ASP VAL VAL ILE SER VAL ALA GLY GLY FORMUL 3 HOH *113(H2 O) HELIX 1 AA1 GLY A 13 LYS A 26 1 14 HELIX 2 AA2 ASN A 39 LYS A 45 1 7 HELIX 3 AA3 ASP A 59 ASN A 69 1 11 HELIX 4 AA4 GLY B 13 LYS B 26 1 14 HELIX 5 AA5 ASN B 39 VAL B 43 5 5 HELIX 6 AA6 ASP B 59 ASN B 69 1 11 SHEET 1 AA1 6 GLU A 29 ALA A 34 0 SHEET 2 AA1 6 LYS A 5 GLY A 10 1 N ILE A 6 O GLU A 29 SHEET 3 AA1 6 VAL B 72 ALA B 77 1 O ILE B 74 N ALA A 7 SHEET 4 AA1 6 VAL A 72 GLY A 78 -1 N ALA A 77 O VAL B 73 SHEET 5 AA1 6 LYS B 5 ILE B 9 1 O ALA B 7 N ILE A 74 SHEET 6 AA1 6 GLU B 29 ALA B 32 1 O THR B 31 N ILE B 6 SHEET 1 AA2 2 ILE A 48 GLU A 49 0 SHEET 2 AA2 2 ARG B 36 SER B 37 -1 O ARG B 36 N GLU A 49 CRYST1 53.093 53.473 55.786 90.00 112.44 90.00 C 1 2 1 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 0.018835 0.000000 0.007780 0.00000 SCALE2 0.000000 0.018701 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019395 0.00000 MASTER 285 0 0 6 8 0 0 6 1233 2 0 12 END