HEADER DE NOVO PROTEIN 25-AUG-22 8GOI TITLE 23-RESIDUES HETEROTETRAMIC ANTIPARALLEL COILED-COIL DERIVED FROM LACI COMPND MOL_ID: 1; COMPND 2 MOLECULE: LAC23YS_AEE, AN ACIDIC MUTANT OF LACI C-TERMINAL COMPND 3 TETRAMERIZATION HELIX; COMPND 4 CHAIN: A, C, E, G; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: AN ACIDIC PEPTIDE DESIGNED FROM LAC REPRESSOR COMPND 7 TETRAMERIZATION DOMAIN.; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: LAC23YS_BRR, A BASIC MUTANT OF LACI C-TERMINAL COMPND 10 TETRAMERIZATION HELIX; COMPND 11 CHAIN: B, D, F, H; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: A BASIC PEPTIDE DESIGNED FROM LAC REPRESSOR COMPND 14 TETRAMERIZATION DOMAIN. SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 4 ORGANISM_TAXID: 562; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 8 ORGANISM_TAXID: 562 KEYWDS DE NOVO PROTEIN, COILED-COIL, TETRAMER EXPDTA X-RAY DIFFRACTION AUTHOR T.KUMASAKA REVDAT 1 30-AUG-23 8GOI 0 JRNL AUTH Y.OTSUKA,A.OSAKI,Y.NAKAMURA,N.MIZUNO,T.KAWAMURA,K.HASEGAWA, JRNL AUTH 2 H.YAMAGUCHI,T.KUMASAKA JRNL TITL DESIGN OF INTERCHAIN GLU-ARG SALT-BRIDGES STABILIZING JRNL TITL 2 HETEROTETRAMERIC COILED-COIL DERIVED FROM LAC REPRESSOR. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.54 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) : 1.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 22984 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1171 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 42.9600 - 3.0800 1.00 2893 162 0.2027 0.2563 REMARK 3 2 3.0800 - 2.4500 1.00 2802 141 0.2360 0.2858 REMARK 3 3 2.4500 - 2.1400 1.00 2744 125 0.2253 0.3053 REMARK 3 4 2.1400 - 1.9400 1.00 2741 135 0.2339 0.2917 REMARK 3 5 1.9400 - 1.8000 1.00 2706 137 0.2485 0.3037 REMARK 3 6 1.8000 - 1.7000 1.00 2688 164 0.2532 0.3286 REMARK 3 7 1.7000 - 1.6100 1.00 2669 160 0.2851 0.3320 REMARK 3 8 1.6100 - 1.5400 0.96 2570 147 0.3062 0.2991 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) : 0.211 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.251 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.12 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.71 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 : 0.007 1395 REMARK 3 ANGLE : 0.891 1887 REMARK 3 CHIRALITY : 0.044 218 REMARK 3 PLANARITY : 0.008 248 REMARK 3 DIHEDRAL : 6.398 205 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 8GOI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1300031769. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-NOV-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL45XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22984 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 REMARK 200 RESOLUTION RANGE LOW (A) : 42.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 18.00 REMARK 200 R MERGE (I) : 0.24400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.9600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 3.08900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.280 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: D_1300031768 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE PH 5.5, 0.2 M REMARK 280 POTASSIUM BROMIDE, 8% PEG20000, 8% PEG MME 500, VAPOR DIFFUSION, REMARK 280 SITTING DROP, 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 20.48350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.96150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.48650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.96150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.48350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.48650 REMARK 290 SMTRY3 4 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, G, H 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 THR A 1 REMARK 465 ALA A 2 REMARK 465 THR C 1 REMARK 465 THR F 1 REMARK 465 SER F 23 REMARK 465 SER H 23 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 THR B 1 N CA CB OG1 CG2 REMARK 470 SER B 23 OG REMARK 470 ALA C 2 N CA CB REMARK 470 SER C 23 OG REMARK 470 THR D 1 OG1 CG2 REMARK 470 SER D 23 OG REMARK 470 THR E 1 OG1 CG2 REMARK 470 SER F 22 OG REMARK 470 THR G 1 OG1 CG2 REMARK 470 SER G 23 OG REMARK 470 THR H 1 OG1 CG2 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 NH1 ARG B 17 O HOH B 201 1.97 REMARK 500 O HOH B 201 O HOH B 209 2.11 REMARK 500 OH TYR B 16 OE1 GLN E 13 2.11 REMARK 500 REMARK 500 REMARK: NULL DBREF 8GOI A 1 23 PDB 8GOI 8GOI 1 23 DBREF 8GOI B 1 23 PDB 8GOI 8GOI 1 23 DBREF 8GOI C 1 23 PDB 8GOI 8GOI 1 23 DBREF 8GOI D 1 23 PDB 8GOI 8GOI 1 23 DBREF 8GOI E 1 23 PDB 8GOI 8GOI 1 23 DBREF 8GOI F 1 23 PDB 8GOI 8GOI 1 23 DBREF 8GOI G 1 23 PDB 8GOI 8GOI 1 23 DBREF 8GOI H 1 23 PDB 8GOI 8GOI 1 23 SEQRES 1 A 23 THR ALA SER PRO SER ALA LEU ALA ASP GLU LEU GLU GLN SEQRES 2 A 23 LEU ALA TYR GLU VAL GLU HIS LEU SER SER SEQRES 1 B 23 THR ALA SER PRO HIS ALA LEU ALA ASN ARG LEU ARG GLN SEQRES 2 B 23 LEU ALA TYR ARG VAL ARG SER LEU SER SER SEQRES 1 C 23 THR ALA SER PRO SER ALA LEU ALA ASP GLU LEU GLU GLN SEQRES 2 C 23 LEU ALA TYR GLU VAL GLU HIS LEU SER SER SEQRES 1 D 23 THR ALA SER PRO HIS ALA LEU ALA ASN ARG LEU ARG GLN SEQRES 2 D 23 LEU ALA TYR ARG VAL ARG SER LEU SER SER SEQRES 1 E 23 THR ALA SER PRO SER ALA LEU ALA ASP GLU LEU GLU GLN SEQRES 2 E 23 LEU ALA TYR GLU VAL GLU HIS LEU SER SER SEQRES 1 F 23 THR ALA SER PRO HIS ALA LEU ALA ASN ARG LEU ARG GLN SEQRES 2 F 23 LEU ALA TYR ARG VAL ARG SER LEU SER SER SEQRES 1 G 23 THR ALA SER PRO SER ALA LEU ALA ASP GLU LEU GLU GLN SEQRES 2 G 23 LEU ALA TYR GLU VAL GLU HIS LEU SER SER SEQRES 1 H 23 THR ALA SER PRO HIS ALA LEU ALA ASN ARG LEU ARG GLN SEQRES 2 H 23 LEU ALA TYR ARG VAL ARG SER LEU SER SER HET GOL B 101 6 HET GOL G 101 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 9 GOL 2(C3 H8 O3) FORMUL 11 HOH *78(H2 O) HELIX 1 AA1 SER A 3 HIS A 20 1 18 HELIX 2 AA2 SER B 3 SER B 20 1 18 HELIX 3 AA3 SER C 3 HIS C 20 1 18 HELIX 4 AA4 SER D 3 SER D 20 1 18 HELIX 5 AA5 SER E 3 HIS E 20 1 18 HELIX 6 AA6 SER F 3 SER F 20 1 18 HELIX 7 AA7 SER G 3 GLU G 19 1 17 HELIX 8 AA8 SER H 3 SER H 20 1 18 CRYST1 40.967 42.973 85.923 90.00 90.00 90.00 P 21 21 21 16 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 0.024410 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023270 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011638 0.00000