HEADER DE NOVO PROTEIN 28-JUL-21 7RMX TITLE STRUCTURE OF DE NOVO DESIGNED TUNABLE SYMMETRIC PROTEIN POCKETS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUNABLE SYMMETRIC PROTEIN, D_3_212; 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, TUNABLE, SYMMETRIC PROTEIN, POCKETS, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,D.R.HICKS,A.KANG,B.SANKARAN,D.BAKER REVDAT 3 03-APR-24 7RMX 1 REMARK REVDAT 2 10-AUG-22 7RMX 1 JRNL REVDAT 1 03-AUG-22 7RMX 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. 1.65 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 : 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) : 48.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 25315 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) : 0.186 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.170 REMARK 3 FREE R VALUE TEST SET COUNT : 1309 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 3.4300 - 2.7200 1.00 2738 161 0.1875 0.2062 REMARK 3 2 2.7200 - 2.3800 1.00 2681 144 0.1783 0.2332 REMARK 3 3 2.3800 - 2.1600 1.00 2670 145 0.1771 0.2179 REMARK 3 4 2.1600 - 2.0000 0.99 2656 150 0.1861 0.1933 REMARK 3 5 2.0000 - 1.8900 0.99 2646 150 0.2143 0.2421 REMARK 3 6 1.8900 - 1.7900 0.99 2640 126 0.2353 0.2927 REMARK 3 7 1.7900 - 1.7100 0.99 2598 151 0.2643 0.3104 REMARK 3 8 1.7100 - 1.6500 0.97 2565 130 0.2925 0.3230 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) : 0.205 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.069 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.04 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 1919 REMARK 3 ANGLE : 0.966 2586 REMARK 3 CHIRALITY : 0.051 307 REMARK 3 PLANARITY : 0.006 331 REMARK 3 DIHEDRAL : 20.686 1228 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): 1.2070 -11.7882 6.0997 REMARK 3 T TENSOR REMARK 3 T11: 0.2132 T22: 0.2043 REMARK 3 T33: 0.1534 T12: 0.0156 REMARK 3 T13: -0.0220 T23: -0.0189 REMARK 3 L TENSOR REMARK 3 L11: 1.7184 L22: 1.4110 REMARK 3 L33: 0.2793 L12: 0.4551 REMARK 3 L13: 0.0857 L23: -0.0738 REMARK 3 S TENSOR REMARK 3 S11: 0.0115 S12: 0.0344 S13: -0.0350 REMARK 3 S21: 0.0466 S22: -0.0456 S23: 0.0779 REMARK 3 S31: -0.0166 S32: -0.0337 S33: 0.0238 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 7RMX 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_1000258571. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-APR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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) : 0.99997 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 : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25328 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 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 : 1.270 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 (%): 36.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 20000, GLYCEROL, SODIUM L REMARK 280 -GLUTAMATE, DL-ALANINE, GLYCINE, DL-LYSINE HCL, DL-SERINE, MES/ REMARK 280 IMIDAZOLE, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 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 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 29.04550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.60600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.04550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.60600 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: 3370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 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 365 O HOH A 384 1.98 REMARK 500 O HOH A 327 O HOH A 381 2.02 REMARK 500 O HOH A 327 O HOH A 384 2.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 374 O HOH A 382 1455 2.01 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 228 45.03 -96.60 REMARK 500 REMARK 500 REMARK: NULL DBREF 7RMX A 1 229 PDB 7RMX 7RMX 1 229 SEQRES 1 A 229 SER GLY SER GLY SER THR GLU GLU GLU GLU ALA LEU LEU SEQRES 2 A 229 ARG TRP PHE GLN THR LEU LEU ALA LYS PHE ASP GLU LEU SEQRES 3 A 229 VAL LYS GLN LEU GLY ASP PRO ARG LEU LEU GLU GLU ALA SEQRES 4 A 229 ARG ARG LEU GLN GLU ARG LEU GLU GLU ALA LYS LYS ARG SEQRES 5 A 229 GLY ASP LYS ARG THR ILE LYS GLN LEU ALA ALA LEU LEU SEQRES 6 A 229 GLN MET PHE VAL LEU ILE ALA GLN ILE PHE GLN LEU VAL SEQRES 7 A 229 GLU GLU LEU GLY ASP PRO LYS LEU LEU GLU GLN ALA LYS SEQRES 8 A 229 ARG LEU LEU GLU ARG LEU LYS GLU ALA VAL GLU ARG GLY SEQRES 9 A 229 ASP GLU GLU THR ILE LYS GLU LEU LEU ASP LEU ALA HIS SEQRES 10 A 229 MET THR TYR LEU ILE ALA GLN ILE PHE GLN LEU VAL GLU SEQRES 11 A 229 GLN LEU GLY ASP PRO ARG LEU LEU GLU LEU ALA LYS GLU SEQRES 12 A 229 LEU LEU LYS ARG LEU LYS GLU ALA GLN GLU ARG GLY ASP SEQRES 13 A 229 ARG ARG THR ILE GLU ARG LEU LEU ARG LEU VAL GLN MET SEQRES 14 A 229 THR TYR LEU ILE ALA GLN ILE PHE GLN LEU VAL ARG GLN SEQRES 15 A 229 LEU GLY ASP PRO ARG LEU LEU GLU THR ALA LYS THR LEU SEQRES 16 A 229 LEU THR LEU LEU LYS LEU ALA PHE GLU GLU GLY ASP GLU SEQRES 17 A 229 LEU LEU ILE LYS SER LEU LEU THR LEU VAL ALA GLU THR SEQRES 18 A 229 TYR ARG GLN ALA ALA ALA GLU GLN FORMUL 2 HOH *96(H2 O) HELIX 1 AA1 THR A 6 GLY A 31 1 26 HELIX 2 AA2 ASP A 32 GLY A 53 1 22 HELIX 3 AA3 ASP A 54 GLY A 82 1 29 HELIX 4 AA4 ASP A 83 GLY A 104 1 22 HELIX 5 AA5 ASP A 105 GLY A 133 1 29 HELIX 6 AA6 ASP A 134 GLY A 155 1 22 HELIX 7 AA7 ASP A 156 GLY A 184 1 29 HELIX 8 AA8 ASP A 185 GLU A 205 1 21 HELIX 9 AA9 ASP A 207 GLU A 228 1 22 CRYST1 58.091 97.212 36.266 90.00 90.00 90.00 P 21 21 2 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 0.017214 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010287 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027574 0.00000