HEADER DE NOVO PROTEIN 23-MAY-22 8CYK TITLE CRYSTAL STRUCTURE OF HALLUCINATED PROTEIN HALC1_878 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HALC1_878; COMPND 3 CHAIN: B, 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, HALLUCINATION PROTEIN MPNN, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.J.RAGOTTE,A.K.BERA,L.F.MILLES,B.I.M.WICKY,D.BAKER REVDAT 3 03-APR-24 8CYK 1 REMARK REVDAT 2 19-OCT-22 8CYK 1 JRNL REVDAT 1 28-SEP-22 8CYK 0 JRNL AUTH J.DAUPARAS,I.ANISHCHENKO,N.BENNETT,H.BAI,R.J.RAGOTTE, JRNL AUTH 2 L.F.MILLES,B.I.M.WICKY,A.COURBET,R.J.DE HAAS,N.BETHEL, JRNL AUTH 3 P.J.Y.LEUNG,T.F.HUDDY,S.PELLOCK,D.TISCHER,F.CHAN,B.KOEPNICK, JRNL AUTH 4 H.NGUYEN,A.KANG,B.SANKARAN,A.K.BERA,N.P.KING,D.BAKER JRNL TITL ROBUST DEEP LEARNING-BASED PROTEIN SEQUENCE DESIGN USING JRNL TITL 2 PROTEINMPNN. JRNL REF SCIENCE V. 378 49 2022 JRNL REFN ESSN 1095-9203 JRNL PMID 36108050 JRNL DOI 10.1126/SCIENCE.ADD2187 REMARK 2 REMARK 2 RESOLUTION. 1.65 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 33923 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 (%) : 3.450 REMARK 3 FREE R VALUE TEST SET COUNT : 1171 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 48.9800 - 3.3000 0.96 4174 148 0.1779 0.1981 REMARK 3 2 3.3000 - 2.6200 0.98 4155 152 0.1849 0.2010 REMARK 3 3 2.6200 - 2.2900 0.98 4148 144 0.1812 0.2238 REMARK 3 4 2.2900 - 2.0800 0.97 4110 147 0.1736 0.2148 REMARK 3 5 2.0800 - 1.9300 0.97 4077 142 0.1844 0.2543 REMARK 3 6 1.9300 - 1.8200 0.97 4065 144 0.2055 0.2513 REMARK 3 7 1.8200 - 1.7300 0.96 4034 145 0.2303 0.2650 REMARK 3 8 1.7300 - 1.6500 0.96 3989 149 0.2373 0.2772 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) : 0.161 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.908 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.35 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.35 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 : 0.011 2179 REMARK 3 ANGLE : 1.124 2930 REMARK 3 CHIRALITY : 0.068 355 REMARK 3 PLANARITY : 0.007 358 REMARK 3 DIHEDRAL : 16.611 866 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 8CYK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1000265632. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-APR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00003 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34565 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 48.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.960 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: DESIGN MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CITRIC ACID 3M NACL, PH 3.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-Z+1/2 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 29.19884 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.72650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 41.30264 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 29.19884 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.72650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 41.30264 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 MET B 1 REMARK 465 SER B 2 REMARK 465 GLY B 3 REMARK 465 MET B 4 REMARK 465 GLY B 134 REMARK 465 SER B 135 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 GLY A 134 REMARK 465 SER A 135 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 89 -113.87 59.85 REMARK 500 ASP A 89 -110.16 51.98 REMARK 500 REMARK 500 REMARK: NULL DBREF 8CYK B 1 135 PDB 8CYK 8CYK 1 135 DBREF 8CYK A 1 135 PDB 8CYK 8CYK 1 135 SEQRES 1 B 135 MET SER GLY MET LYS LYS LEU TYR GLU TYR THR VAL THR SEQRES 2 B 135 THR LEU ASP GLU PHE LEU GLU LYS LEU LYS GLU PHE ILE SEQRES 3 B 135 LEU ASN THR SER LYS ASP LYS ILE TYR LYS LEU THR ILE SEQRES 4 B 135 THR ASN PRO LYS LEU ILE LYS ASP ILE GLY LYS ALA ILE SEQRES 5 B 135 ALA LYS ALA ALA GLU ILE ALA ASP VAL ASP PRO LYS GLU SEQRES 6 B 135 ILE GLU GLU MET ILE LYS ALA VAL GLU GLU ASN GLU LEU SEQRES 7 B 135 THR LYS LEU VAL ILE THR ILE GLU GLN THR ASP ASP LYS SEQRES 8 B 135 TYR VAL ILE LYS VAL GLU LEU GLU ASN GLU ASP GLY LEU SEQRES 9 B 135 VAL HIS SER PHE GLU ILE TYR PHE LYS ASN LYS GLU GLU SEQRES 10 B 135 MET GLU LYS PHE LEU GLU LEU LEU GLU LYS LEU ILE SER SEQRES 11 B 135 LYS LEU SER GLY SER SEQRES 1 A 135 MET SER GLY MET LYS LYS LEU TYR GLU TYR THR VAL THR SEQRES 2 A 135 THR LEU ASP GLU PHE LEU GLU LYS LEU LYS GLU PHE ILE SEQRES 3 A 135 LEU ASN THR SER LYS ASP LYS ILE TYR LYS LEU THR ILE SEQRES 4 A 135 THR ASN PRO LYS LEU ILE LYS ASP ILE GLY LYS ALA ILE SEQRES 5 A 135 ALA LYS ALA ALA GLU ILE ALA ASP VAL ASP PRO LYS GLU SEQRES 6 A 135 ILE GLU GLU MET ILE LYS ALA VAL GLU GLU ASN GLU LEU SEQRES 7 A 135 THR LYS LEU VAL ILE THR ILE GLU GLN THR ASP ASP LYS SEQRES 8 A 135 TYR VAL ILE LYS VAL GLU LEU GLU ASN GLU ASP GLY LEU SEQRES 9 A 135 VAL HIS SER PHE GLU ILE TYR PHE LYS ASN LYS GLU GLU SEQRES 10 A 135 MET GLU LYS PHE LEU GLU LEU LEU GLU LYS LEU ILE SER SEQRES 11 A 135 LYS LEU SER GLY SER FORMUL 3 HOH *215(H2 O) HELIX 1 AA1 THR B 14 ASN B 28 1 15 HELIX 2 AA2 ASN B 41 ALA B 59 1 19 HELIX 3 AA3 ASP B 62 GLU B 74 1 13 HELIX 4 AA4 ASN B 114 LYS B 131 1 18 HELIX 5 AA5 THR A 14 ASN A 28 1 15 HELIX 6 AA6 ASN A 41 ALA A 59 1 19 HELIX 7 AA7 ASP A 62 GLU A 74 1 13 HELIX 8 AA8 ASN A 114 SER A 133 1 20 SHEET 1 AA111 MET A 4 LYS A 6 0 SHEET 2 AA111 LEU B 104 PHE B 112 -1 N VAL B 105 O LYS A 5 SHEET 3 AA111 LYS B 91 ASN B 100 -1 N VAL B 96 O PHE B 108 SHEET 4 AA111 LEU B 78 THR B 88 -1 N GLU B 86 O VAL B 93 SHEET 5 AA111 LYS B 33 ILE B 39 -1 N TYR B 35 O ILE B 85 SHEET 6 AA111 LYS B 6 THR B 11 1 N TYR B 10 O THR B 38 SHEET 7 AA111 LEU A 104 TYR A 111 -1 O VAL A 105 N LEU B 7 SHEET 8 AA111 LYS A 91 ASN A 100 -1 N VAL A 96 O PHE A 108 SHEET 9 AA111 LEU A 78 THR A 88 -1 N LYS A 80 O GLU A 99 SHEET 10 AA111 LYS A 33 ILE A 39 -1 N LEU A 37 O ILE A 83 SHEET 11 AA111 TYR A 8 THR A 11 1 N TYR A 8 O LYS A 36 CRYST1 64.174 55.453 82.807 90.00 94.00 90.00 I 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 0.015583 0.000000 0.001090 0.00000 SCALE2 0.000000 0.018033 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012106 0.00000