HEADER DE NOVO PROTEIN 28-JUL-21 7RMY TITLE DE NOVO DESIGNED TUNABLE PROTEIN POCKETS, D_3-337 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGNED TUNABLE HOMODIMER, D_3-337; 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: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DE NOVO DESIGN, HOMODIMER, REPEAT PROTEIN, TUNABLE POCKET, DE NOVO KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,D.R.HICKS,A.KANG,B.SANKARAN,D.BAKER REVDAT 3 03-APR-24 7RMY 1 REMARK REVDAT 2 10-AUG-22 7RMY 1 JRNL REVDAT 1 03-AUG-22 7RMY 0 JRNL AUTH D.R.HICKS,M.A.KENNEDY,K.A.THOMPSON,M.DEWITT,B.COVENTRY, JRNL AUTH 2 A.KANG,A.K.BERA,T.J.BRUNETTE,B.SANKARAN,B.STODDARD,D.BAKER JRNL TITL DE NOVO DESIGN OF PROTEIN HOMODIMERS CONTAINING TUNABLE JRNL TITL 2 SYMMETRIC PROTEIN POCKETS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 119 00119 2022 JRNL REFN ESSN 1091-6490 JRNL PMID 35862457 JRNL DOI 10.1073/PNAS.2113400119 REMARK 2 REMARK 2 RESOLUTION. 3.17 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 3.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 7675 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.240 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 768 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 5.4200 - 4.3000 0.99 1456 164 0.1829 0.2431 REMARK 3 2 4.3000 - 3.7600 0.98 1424 160 0.2294 0.2780 REMARK 3 3 3.7600 - 3.4200 0.96 1367 147 0.3155 0.3566 REMARK 3 4 3.4100 - 3.1700 0.81 1159 129 0.3027 0.3474 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.470 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.973 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.05 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.56 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : 12.803 828 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -25.9770 -3.7942 -2.2021 REMARK 3 T TENSOR REMARK 3 T11: 0.0979 T22: 0.0754 REMARK 3 T33: 0.0850 T12: -0.0877 REMARK 3 T13: 0.0534 T23: 0.0329 REMARK 3 L TENSOR REMARK 3 L11: 0.2499 L22: 0.5970 REMARK 3 L33: 0.3291 L12: 0.0055 REMARK 3 L13: -0.0042 L23: -0.2502 REMARK 3 S TENSOR REMARK 3 S11: -0.1658 S12: 0.1069 S13: -0.1608 REMARK 3 S21: 0.1515 S22: 0.0381 S23: -0.3375 REMARK 3 S31: -0.1761 S32: -0.0554 S33: -0.1154 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 7RMY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1000258572. 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) : 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 : 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) : 0.99996 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 : 7677 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.170 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : 14.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.28 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: DE NOVO DESIGNED MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, GLYCEROL, MAGNESIUM REMARK 280 CHLORIDE, CALCIUM CHLORIDE, AND BICINE-TRIZMA BASE, PH 8.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 54.35450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 45.36150 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 45.36150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.17725 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 45.36150 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 45.36150 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 81.53175 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 45.36150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.36150 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.17725 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 45.36150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.36150 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 81.53175 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 54.35450 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 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 SER A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 TRP A 267 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 PRO A 31 41.25 -93.52 REMARK 500 GLU A 56 7.69 59.96 REMARK 500 LEU A 89 -117.42 62.21 REMARK 500 ASP A 91 116.14 -170.67 REMARK 500 PRO A 92 49.60 -71.91 REMARK 500 ASP A 116 151.79 67.75 REMARK 500 GLU A 149 -44.05 -169.44 REMARK 500 REMARK 500 REMARK: NULL DBREF 7RMY A -4 267 PDB 7RMY 7RMY -4 267 SEQRES 1 A 272 SER GLY SER GLY SER SER GLU GLU LEU LYS LYS VAL GLN SEQRES 2 A 272 LYS MET VAL SER GLN ILE LEU ALA THR ALA GLU ALA VAL SEQRES 3 A 272 LEU LYS LEU ALA LYS VAL LEU GLY ASP PRO LYS ALA VAL SEQRES 4 A 272 GLU LEU ALA GLU ARG ILE LEU GLU ASP ALA LYS GLU LEU SEQRES 5 A 272 ALA LYS ARG ALA GLU SER GLY ASP GLU GLU THR LEU ARG SEQRES 6 A 272 ARG ALA GLN THR LEU LEU LYS VAL LEU LYS MET VAL LEU SEQRES 7 A 272 GLU ILE LEU LEU LEU ALA ILE LYS VAL GLU LEU ALA ALA SEQRES 8 A 272 LYS GLU LEU GLY ASP PRO LYS ALA VAL GLU ALA ALA GLN SEQRES 9 A 272 ARG ILE LEU LYS GLN ALA LEU ARG LEU LEU ALA GLU ILE SEQRES 10 A 272 LYS SER GLY ASP GLU GLU THR LEU LYS ARG ALA GLN GLU SEQRES 11 A 272 LEU LEU LYS VAL LEU LYS MET VAL LEU ARG ILE ILE TYR SEQRES 12 A 272 LEU ALA ILE GLU VAL GLU LYS ALA ALA LYS GLU LEU GLY SEQRES 13 A 272 ASP PRO THR ALA VAL GLU ALA ALA GLN ARG ILE LEU GLU SEQRES 14 A 272 LEU ALA LEU ARG LEU LEU GLN LYS VAL GLU SER GLY ASP SEQRES 15 A 272 GLU ASP THR LEU ARG LYS ALA LEU GLU LEU LEU GLU VAL SEQRES 16 A 272 LEU TYR MET VAL LEU ARG ILE ILE ARG LEU ALA ILE GLU SEQRES 17 A 272 VAL GLU LYS LEU ALA LYS LYS ALA GLY ASP PRO SER ALA SEQRES 18 A 272 VAL GLU GLU ALA GLN ARG ILE LEU LYS GLN ALA LEU ARG SEQRES 19 A 272 LEU LEU LYS GLU ILE SER SER GLY ASP GLU GLN THR LEU SEQRES 20 A 272 ASP GLU ALA ALA LYS THR LEU SER PHE LEU ALA ALA GLU SEQRES 21 A 272 LEU GLU ALA ILE ALA PHE ALA ILE ARG VAL LYS TRP FORMUL 2 HOH *5(H2 O) HELIX 1 AA1 SER A 1 LEU A 28 1 28 HELIX 2 AA2 LYS A 32 ARG A 50 1 19 HELIX 3 AA3 ARG A 60 LEU A 84 1 25 HELIX 4 AA4 PRO A 92 GLY A 115 1 24 HELIX 5 AA5 THR A 119 LYS A 148 1 30 HELIX 6 AA6 ASP A 152 VAL A 173 1 22 HELIX 7 AA7 ASP A 177 ALA A 211 1 35 HELIX 8 AA8 ASP A 213 ARG A 229 1 17 HELIX 9 AA9 LEU A 230 GLU A 233 5 4 HELIX 10 AB1 ASP A 238 ARG A 264 1 27 CRYST1 90.723 90.723 108.709 90.00 90.00 90.00 P 41 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 0.011023 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011023 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009199 0.00000