HEADER DE NOVO PROTEIN 02-AUG-23 8TNM TITLE UNC_079 FROM CHROMA GENERATIVE MODEL COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNC_079; 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: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS CHROMA, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.NG-THOW-HING,E.R.VAN VLACK,D.M.LORD REVDAT 3 13-DEC-23 8TNM 1 JRNL REVDAT 2 29-NOV-23 8TNM 1 JRNL REVDAT 1 22-NOV-23 8TNM 0 JRNL AUTH J.B.INGRAHAM,M.BARANOV,Z.COSTELLO,K.W.BARBER,W.WANG, JRNL AUTH 2 A.ISMAIL,V.FRAPPIER,D.M.LORD,C.NG-THOW-HING,E.R.VAN VLACK, JRNL AUTH 3 S.TIE,V.XUE,S.C.COWLES,A.LEUNG,J.V.RODRIGUES, JRNL AUTH 4 C.L.MORALES-PEREZ,A.M.AYOUB,R.GREEN,K.PUENTES,F.OPLINGER, JRNL AUTH 5 N.V.PANWAR,F.OBERMEYER,A.R.ROOT,A.L.BEAM,F.J.POELWIJK, JRNL AUTH 6 G.GRIGORYAN JRNL TITL ILLUMINATING PROTEIN SPACE WITH A PROGRAMMABLE GENERATIVE JRNL TITL 2 MODEL. JRNL REF NATURE V. 623 1070 2023 JRNL REFN ESSN 1476-4687 JRNL PMID 37968394 JRNL DOI 10.1038/S41586-023-06728-8 REMARK 2 REMARK 2 RESOLUTION. 1.10 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) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.320 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 64846 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 3248 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 35.6900 - 3.1300 1.00 2942 172 0.1784 0.1958 REMARK 3 2 3.1300 - 2.4800 1.00 2802 147 0.1819 0.2106 REMARK 3 3 2.4800 - 2.1700 1.00 2771 155 0.1622 0.1814 REMARK 3 4 2.1700 - 1.9700 1.00 2776 123 0.1685 0.1780 REMARK 3 5 1.9700 - 1.8300 1.00 2711 152 0.1756 0.2110 REMARK 3 6 1.8300 - 1.7200 1.00 2714 159 0.1665 0.2037 REMARK 3 7 1.7200 - 1.6400 1.00 2728 131 0.1597 0.1738 REMARK 3 8 1.6400 - 1.5600 1.00 2708 126 0.1456 0.1767 REMARK 3 9 1.5600 - 1.5000 1.00 2686 164 0.1456 0.1810 REMARK 3 10 1.5000 - 1.4500 1.00 2675 148 0.1685 0.1851 REMARK 3 11 1.4500 - 1.4100 1.00 2688 158 0.1976 0.2141 REMARK 3 12 1.4100 - 1.3700 1.00 2688 146 0.1951 0.2201 REMARK 3 13 1.3700 - 1.3300 1.00 2677 136 0.2100 0.2223 REMARK 3 14 1.3300 - 1.3000 1.00 2686 140 0.2259 0.2515 REMARK 3 15 1.3000 - 1.2700 1.00 2697 129 0.2449 0.2892 REMARK 3 16 1.2700 - 1.2400 1.00 2643 143 0.2703 0.2780 REMARK 3 17 1.2400 - 1.2200 1.00 2703 120 0.2844 0.3003 REMARK 3 18 1.2200 - 1.1900 1.00 2662 155 0.3067 0.3259 REMARK 3 19 1.1900 - 1.1700 1.00 2689 121 0.3259 0.3291 REMARK 3 20 1.1700 - 1.1500 1.00 2662 131 0.3570 0.3780 REMARK 3 21 1.1500 - 1.1300 0.97 2614 132 0.3784 0.3789 REMARK 3 22 1.1300 - 1.1200 0.93 2466 135 0.4060 0.4111 REMARK 3 23 1.1200 - 1.1000 0.83 2210 125 0.4313 0.4014 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) : 0.158 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.341 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.64 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 : 0.005 1094 REMARK 3 ANGLE : 0.839 1477 REMARK 3 CHIRALITY : 0.065 172 REMARK 3 PLANARITY : 0.006 193 REMARK 3 DIHEDRAL : 3.995 154 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 8TNM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1000275124. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-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 : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97624 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 : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65204 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 35.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 12.40 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.13 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 2.34000 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 (%): 52.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.1 M DL-MALIC ACID, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 44.58900 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 29.76600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.76600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 66.88350 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.76600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.76600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.29450 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.76600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.76600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 66.88350 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.76600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.76600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 22.29450 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 44.58900 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 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 A 1 REMARK 465 GLY A 2 REMARK 465 VAL A 139 REMARK 465 GLY A 140 REMARK 465 SER A 141 REMARK 465 GLU A 142 REMARK 465 ASN A 143 REMARK 465 LEU A 144 REMARK 465 TYR A 145 REMARK 465 PHE A 146 REMARK 465 GLN A 147 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 SER A 3 OG REMARK 470 LYS A 117 CG CD CE NZ REMARK 470 GLN A 138 CG CD OE1 NE2 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 HOH A 218 O HOH A 287 2.19 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 A 317 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A 318 DISTANCE = 6.51 ANGSTROMS REMARK 525 HOH A 319 DISTANCE = 6.81 ANGSTROMS DBREF 8TNM A 1 147 PDB 8TNM 8TNM 1 147 SEQRES 1 A 147 MET GLY SER ASN ASP TYR VAL ASN GLN MET ILE SER GLN SEQRES 2 A 147 MET THR ASP LEU ALA LYS SER LEU ASN VAL ASP VAL THR SEQRES 3 A 147 GLU LEU ILE THR SER VAL THR GLN ALA LEU GLU ALA LEU SEQRES 4 A 147 LEU GLU GLU TYR ARG ARG GLU GLY ARG LEU THR ASP GLN SEQRES 5 A 147 VAL GLU LYS MET ALA SER SER VAL ALA LEU GLN LEU ALA SEQRES 6 A 147 ALA GLU LEU LEU ALA GLN LYS ALA LEU GLU GLU GLY HIS SEQRES 7 A 147 ASP LYS LYS GLN THR THR ALA LYS ARG ASN GLN ILE SER SEQRES 8 A 147 ASN SER TYR SER SER GLU ALA MET SER HIS ALA ARG ALA SEQRES 9 A 147 TRP ALA ALA SER ARG HIS SER GLU GLU GLU ALA GLU LYS SEQRES 10 A 147 LEU ALA GLU GLU LEU TYR LYS ASP MET LYS GLU SER LEU SEQRES 11 A 147 LYS GLN ARG ILE ASP THR GLU GLN VAL GLY SER GLU ASN SEQRES 12 A 147 LEU TYR PHE GLN FORMUL 2 HOH *119(H2 O) HELIX 1 AA1 SER A 3 ASN A 22 1 20 HELIX 2 AA2 VAL A 25 GLU A 46 1 22 HELIX 3 AA3 THR A 50 GLU A 76 1 27 HELIX 4 AA4 ASP A 79 SER A 108 1 30 HELIX 5 AA5 SER A 111 GLN A 138 1 28 CRYST1 59.532 59.532 89.178 90.00 90.00 90.00 P 43 21 2 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 0.016798 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016798 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011214 0.00000