HEADER DE NOVO PROTEIN 09-MAR-20 6W40 TITLE AN ENUMERATIVE ALGORITHM FOR DE NOVO DESIGN OF PROTEINS WITH DIVERSE TITLE 2 POCKET STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DENOVO NTF2; 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: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS NTF2, DE NOVO DESIGN, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,B.BASANTA,B.SANKARAN,D.BAKER REVDAT 6 03-APR-24 6W40 1 REMARK REVDAT 5 06-MAR-24 6W40 1 REMARK REVDAT 4 16-SEP-20 6W40 1 JRNL REVDAT 3 09-SEP-20 6W40 1 JRNL REVDAT 2 19-AUG-20 6W40 1 TITLE JRNL REVDAT 1 08-APR-20 6W40 0 JRNL AUTH B.BASANTA,M.J.BICK,A.K.BERA,C.NORN,C.M.CHOW,L.P.CARTER, JRNL AUTH 2 I.GORESHNIK,F.DIMAIO,D.BAKER JRNL TITL AN ENUMERATIVE ALGORITHM FOR DE NOVO DESIGN OF PROTEINS WITH JRNL TITL 2 DIVERSE POCKET STRUCTURES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 117 22135 2020 JRNL REFN ESSN 1091-6490 JRNL PMID 32839327 JRNL DOI 10.1073/PNAS.2005412117 REMARK 2 REMARK 2 RESOLUTION. 2.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15RC3_3435 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 8801 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.243 REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.292 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 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 23.6400 - 4.5200 1.00 1413 156 0.2243 0.2689 REMARK 3 2 4.5200 - 3.5900 0.99 1317 148 0.2188 0.2996 REMARK 3 3 3.5900 - 3.1400 1.00 1306 145 0.2363 0.2986 REMARK 3 4 3.1400 - 2.8500 1.00 1291 144 0.2664 0.2834 REMARK 3 5 2.8500 - 2.6500 1.00 1312 144 0.2808 0.3432 REMARK 3 6 2.6500 - 2.4900 1.00 1283 142 0.2792 0.3247 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.302 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.672 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.12 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.50 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 2005 REMARK 3 ANGLE : 0.425 2694 REMARK 3 CHIRALITY : 0.049 296 REMARK 3 PLANARITY : 0.002 343 REMARK 3 DIHEDRAL : 14.272 1210 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 6W40 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1000247580. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL 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) : 0.9771 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8867 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.490 REMARK 200 RESOLUTION RANGE LOW (A) : 43.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.14300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 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 PROTEIN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE PH 4.5 AND 1.0 M REMARK 280 DI-AMMONIUM PHOSPHATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 18.76600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.03150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.87100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.03150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.76600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.87100 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: 2000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 GLY B 0 REMARK 465 ASP B 1 REMARK 465 GLU B 2 REMARK 465 GLU B 3 REMARK 465 GLU B 4 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 PHE A 18 -78.79 -132.86 REMARK 500 MET A 19 92.54 -48.02 REMARK 500 THR A 20 -135.11 28.29 REMARK 500 ASP A 93 -150.28 -159.15 REMARK 500 LYS B 16 0.89 -67.94 REMARK 500 LEU B 60 -61.28 -92.54 REMARK 500 REMARK 500 REMARK: NULL DBREF 6W40 A 0 119 PDB 6W40 6W40 0 119 DBREF 6W40 B 0 119 PDB 6W40 6W40 0 119 SEQRES 1 A 120 GLY ASP GLU GLU GLU LYS HIS LEU ARG ASP MET MET GLU SEQRES 2 A 120 ILE VAL ILE LYS LEU PHE MET THR GLY ASP TRP ASP ALA SEQRES 3 A 120 PHE HIS GLU MET ALA ASP PRO ASP VAL LYS PHE GLN VAL SEQRES 4 A 120 ASP VAL GLY ASP LYS HIS ILE HIS ARG HIS GLY ARG GLU SEQRES 5 A 120 GLU VAL VAL GLU GLU LEU ILE ARG LEU LEU GLU HIS TRP SEQRES 6 A 120 ARG VAL ARG ASN ILE ARG ILE HIS ASP ILE LYS LEU ILE SEQRES 7 A 120 GLY ASP LYS LEU VAL VAL GLU GLY ARG TRP GLU THR SER SEQRES 8 A 120 TYR GLY ASP LYS SER HIS ASP GLU ASP VAL GLU LEU ILE SEQRES 9 A 120 VAL ILE VAL VAL ASP GLY LYS ILE LYS LYS VAL ARG ILE SEQRES 10 A 120 ILE ILE ARG SEQRES 1 B 120 GLY ASP GLU GLU GLU LYS HIS LEU ARG ASP MET MET GLU SEQRES 2 B 120 ILE VAL ILE LYS LEU PHE MET THR GLY ASP TRP ASP ALA SEQRES 3 B 120 PHE HIS GLU MET ALA ASP PRO ASP VAL LYS PHE GLN VAL SEQRES 4 B 120 ASP VAL GLY ASP LYS HIS ILE HIS ARG HIS GLY ARG GLU SEQRES 5 B 120 GLU VAL VAL GLU GLU LEU ILE ARG LEU LEU GLU HIS TRP SEQRES 6 B 120 ARG VAL ARG ASN ILE ARG ILE HIS ASP ILE LYS LEU ILE SEQRES 7 B 120 GLY ASP LYS LEU VAL VAL GLU GLY ARG TRP GLU THR SER SEQRES 8 B 120 TYR GLY ASP LYS SER HIS ASP GLU ASP VAL GLU LEU ILE SEQRES 9 B 120 VAL ILE VAL VAL ASP GLY LYS ILE LYS LYS VAL ARG ILE SEQRES 10 B 120 ILE ILE ARG FORMUL 3 HOH *35(H2 O) HELIX 1 AA1 GLY A 0 PHE A 18 1 19 HELIX 2 AA2 ASP A 22 ASP A 24 5 3 HELIX 3 AA3 ALA A 25 MET A 29 1 5 HELIX 4 AA4 GLY A 49 ARG A 65 1 17 HELIX 5 AA5 HIS B 6 LYS B 16 1 11 HELIX 6 AA6 LEU B 17 MET B 19 5 3 HELIX 7 AA7 TRP B 23 MET B 29 1 7 HELIX 8 AA8 GLY B 49 GLU B 62 1 14 SHEET 1 AA1 6 LYS A 43 HIS A 48 0 SHEET 2 AA1 6 ALA A 30 VAL A 40 -1 N PHE A 36 O ARG A 47 SHEET 3 AA1 6 LYS A 110 ILE A 118 1 O ILE A 118 N ASP A 39 SHEET 4 AA1 6 ASP A 99 VAL A 107 -1 N VAL A 107 O LYS A 110 SHEET 5 AA1 6 LYS A 80 THR A 89 -1 N LEU A 81 O VAL A 104 SHEET 6 AA1 6 VAL A 66 ILE A 77 -1 N ARG A 67 O GLU A 88 SHEET 1 AA2 6 LYS B 43 HIS B 48 0 SHEET 2 AA2 6 ALA B 30 VAL B 40 -1 N VAL B 38 O ILE B 45 SHEET 3 AA2 6 LYS B 110 ILE B 118 1 O VAL B 114 N GLN B 37 SHEET 4 AA2 6 LYS B 94 VAL B 107 -1 N ILE B 105 O LYS B 112 SHEET 5 AA2 6 LYS B 80 TYR B 91 -1 N VAL B 83 O LEU B 102 SHEET 6 AA2 6 ARG B 65 ILE B 77 -1 N ARG B 67 O GLU B 88 CRYST1 37.532 73.742 86.063 90.00 90.00 90.00 P 21 21 21 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 0.026644 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013561 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011619 0.00000