HEADER DE NOVO PROTEIN 24-JUL-22 8DT0 TITLE SCAFFOLDING PROTEIN FUNCTIONAL SITES USING DEEP LEARNING COMPND MOL_ID: 1; COMPND 2 MOLECULE: SCAFFOLDING PROTEIN FUNCTIONAL SITES; 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, SCAFFOLDING PROTEIN FUNCTIONAL SITES, DEEP LEARNING, KEYWDS 2 DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,J.WATSON,D.BAKER REVDAT 3 03-APR-24 8DT0 1 REMARK REVDAT 2 14-FEB-24 8DT0 1 REMARK REVDAT 1 10-AUG-22 8DT0 0 JRNL AUTH J.WANG,S.LISANZA,D.JUERGENS,D.TISCHER,J.L.WATSON,K.M.CASTRO, JRNL AUTH 2 R.RAGOTTE,A.SARAGOVI,L.F.MILLES,M.BAEK,I.ANISHCHENKO,W.YANG, JRNL AUTH 3 D.R.HICKS,M.EXPOSIT,T.SCHLICHTHAERLE,J.H.CHUN,J.DAUPARAS, JRNL AUTH 4 N.BENNETT,B.I.M.WICKY,A.MUENKS,F.DIMAIO,B.CORREIA, JRNL AUTH 5 S.OVCHINNIKOV,D.BAKER JRNL TITL SCAFFOLDING PROTEIN FUNCTIONAL SITES USING DEEP LEARNING. JRNL REF SCIENCE V. 377 387 2022 JRNL REFN ESSN 1095-9203 JRNL PMID 35862514 JRNL DOI 10.1126/SCIENCE.ABN2100 REMARK 2 REMARK 2 RESOLUTION. 2.46 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) : 2.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 8790 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 879 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 31.5900 - 4.4700 0.99 1346 149 0.1967 0.2325 REMARK 3 2 4.4700 - 3.5500 0.99 1330 151 0.2127 0.2487 REMARK 3 3 3.5500 - 3.1000 0.99 1302 138 0.2388 0.3376 REMARK 3 4 3.1000 - 2.8200 0.99 1288 144 0.2720 0.3420 REMARK 3 5 2.8200 - 2.6100 0.99 1338 150 0.2993 0.3859 REMARK 3 6 2.6100 - 2.4600 0.98 1307 147 0.3129 0.4213 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) : 0.443 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.573 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 72.44 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 2157 REMARK 3 ANGLE : 0.519 2889 REMARK 3 CHIRALITY : 0.029 328 REMARK 3 PLANARITY : 0.004 394 REMARK 3 DIHEDRAL : 4.142 296 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 8DT0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1000267326. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 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) : 0.97 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 : 8800 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.460 REMARK 200 RESOLUTION RANGE LOW (A) : 31.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.61800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.470 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 (%): 38.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM CHLORIDE, 0.1 M SODIUM REMARK 280 ACETATE PH 5, 20% (W/V) PEG 6000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 44.45400 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 LEU B 140 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 SER B 104 -56.66 62.56 REMARK 500 GLU B 105 -43.23 68.75 REMARK 500 REMARK 500 REMARK: NULL DBREF 8DT0 A 1 140 PDB 8DT0 8DT0 1 140 DBREF 8DT0 B 1 140 PDB 8DT0 8DT0 1 140 SEQRES 1 A 140 GLU GLU GLU GLU LEU GLU GLU LEU ALA LYS GLU LEU GLU SEQRES 2 A 140 LYS ILE LEU ARG ASP GLU GLU GLY HIS LEU ARG LYS LEU SEQRES 3 A 140 LYS GLU ALA LEU ALA GLU GLY LEU GLY ASP ALA GLU GLU SEQRES 4 A 140 ALA ALA GLU LEU PHE ARG ALA GLU SER ILE ASP GLU MET SEQRES 5 A 140 LYS HIS ALA GLU GLU LEU ALA LYS LEU LEU LYS LYS GLY SEQRES 6 A 140 GLY LEU ASP PRO GLU LEU ARG GLU LEU LEU GLU GLU LEU SEQRES 7 A 140 ALA GLU LEU GLU LEU VAL ALA ILE ASN GLN TYR ARG GLU SEQRES 8 A 140 ALA ALA GLU ALA ALA ALA GLU ALA ALA GLU ASN GLY SER SEQRES 9 A 140 GLU GLU ALA ARG ALA ALA ALA ARG GLU ALA LEU GLU GLU SEQRES 10 A 140 ALA LEU ALA LEU GLU LEU ASP GLY ALA LYS LEU ALA ARG SEQRES 11 A 140 ALA ALA LEU GLU ALA VAL GLU LYS LEU LEU SEQRES 1 B 140 GLU GLU GLU GLU LEU GLU GLU LEU ALA LYS GLU LEU GLU SEQRES 2 B 140 LYS ILE LEU ARG ASP GLU GLU GLY HIS LEU ARG LYS LEU SEQRES 3 B 140 LYS GLU ALA LEU ALA GLU GLY LEU GLY ASP ALA GLU GLU SEQRES 4 B 140 ALA ALA GLU LEU PHE ARG ALA GLU SER ILE ASP GLU MET SEQRES 5 B 140 LYS HIS ALA GLU GLU LEU ALA LYS LEU LEU LYS LYS GLY SEQRES 6 B 140 GLY LEU ASP PRO GLU LEU ARG GLU LEU LEU GLU GLU LEU SEQRES 7 B 140 ALA GLU LEU GLU LEU VAL ALA ILE ASN GLN TYR ARG GLU SEQRES 8 B 140 ALA ALA GLU ALA ALA ALA GLU ALA ALA GLU ASN GLY SER SEQRES 9 B 140 GLU GLU ALA ARG ALA ALA ALA ARG GLU ALA LEU GLU GLU SEQRES 10 B 140 ALA LEU ALA LEU GLU LEU ASP GLY ALA LYS LEU ALA ARG SEQRES 11 B 140 ALA ALA LEU GLU ALA VAL GLU LYS LEU LEU HELIX 1 AA1 GLU A 1 GLU A 32 1 32 HELIX 2 AA2 ASP A 36 LYS A 63 1 28 HELIX 3 AA3 ASP A 68 GLY A 103 1 36 HELIX 4 AA4 SER A 104 LEU A 140 1 37 HELIX 5 AA5 GLU B 2 GLU B 32 1 31 HELIX 6 AA6 ASP B 36 LYS B 63 1 28 HELIX 7 AA7 ASP B 68 GLY B 103 1 36 HELIX 8 AA8 GLU B 105 LEU B 139 1 35 CRYST1 31.038 88.908 47.516 90.00 109.06 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 0.032219 0.000000 0.011131 0.00000 SCALE2 0.000000 0.011248 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022266 0.00000