HEADER DE NOVO PROTEIN 20-MAR-23 8GL3 TITLE DE NOVO DESIGN OF MONOMERIC HELICAL BUNDLES FOR PH-CONTROLLED MEMBRANE TITLE 2 LYSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRLB-519; 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 PROTEIN DESIGN, PH-RESPONSIVE, MEMBRANE LYSIS, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.GOLDBACH,A.K.BERA,D.BAKER,A.KANG REVDAT 3 08-NOV-23 8GL3 1 JRNL REVDAT 2 20-SEP-23 8GL3 1 REMARK REVDAT 1 06-SEP-23 8GL3 0 JRNL AUTH N.GOLDBACH,I.BENNA,B.I.M.WICKY,J.T.CROFT,L.CARTER,A.K.BERA, JRNL AUTH 2 H.NGUYEN,A.KANG,B.SANKARAN,E.C.YANG,K.K.LEE,D.BAKER JRNL TITL DE NOVO DESIGN OF MONOMERIC HELICAL BUNDLES FOR JRNL TITL 2 PH-CONTROLLED MEMBRANE LYSIS. JRNL REF PROTEIN SCI. V. 32 E4769 2023 JRNL REFN ESSN 1469-896X JRNL PMID 37632837 JRNL DOI 10.1002/PRO.4769 REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.420 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 11502 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) : 0.238 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.410 REMARK 3 FREE R VALUE TEST SET COUNT : 622 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 45.6400 - 3.6500 0.98 2778 158 0.2453 0.2834 REMARK 3 2 3.6500 - 2.9000 1.00 2768 142 0.2257 0.2858 REMARK 3 3 2.9000 - 2.5300 0.97 2676 167 0.2432 0.2635 REMARK 3 4 2.5300 - 2.3000 0.98 2658 155 0.2378 0.3089 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) : 0.217 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.093 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.04 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 : 0.002 1599 REMARK 3 ANGLE : 0.337 2121 REMARK 3 CHIRALITY : 0.026 238 REMARK 3 PLANARITY : 0.003 285 REMARK 3 DIHEDRAL : 14.154 684 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 6:221 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.879 -7.312 36.152 REMARK 3 T TENSOR REMARK 3 T11: 0.1306 T22: 0.1758 REMARK 3 T33: 0.1836 T12: -0.0051 REMARK 3 T13: 0.0214 T23: -0.0607 REMARK 3 L TENSOR REMARK 3 L11: 2.4539 L22: 2.2005 REMARK 3 L33: 2.7245 L12: -0.4912 REMARK 3 L13: -0.8311 L23: -1.3478 REMARK 3 S TENSOR REMARK 3 S11: 0.0751 S12: 0.4572 S13: -0.0930 REMARK 3 S21: -0.1764 S22: 0.0473 S23: -0.0304 REMARK 3 S31: 0.0858 S32: -0.5931 S33: -0.0402 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 8GL3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1000273112. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-NOV-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99998 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 : DIALS REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11502 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 45.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.14400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.390 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM FLUORIDE AND 20% (W/V) REMARK 280 PEG 3350, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 1 2 1 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+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 15.37489 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.35150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 91.28693 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 15.37489 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.35150 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 91.28693 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 GLU A -6 REMARK 465 ASN A -5 REMARK 465 LEU A -4 REMARK 465 TYR A -3 REMARK 465 PHE A -2 REMARK 465 GLN A -1 REMARK 465 GLY A 0 REMARK 465 SER A 1 REMARK 465 GLU A 2 REMARK 465 GLU A 3 REMARK 465 ALA A 4 REMARK 465 ARG A 5 REMARK 465 GLY A 53 REMARK 465 GLU A 54 REMARK 465 LYS A 55 REMARK 465 LYS A 106 REMARK 465 LYS A 107 REMARK 465 LYS A 108 REMARK 465 ALA A 109 REMARK 465 SER A 110 REMARK 465 GLU A 111 REMARK 465 GLU A 112 REMARK 465 GLU A 113 REMARK 465 LYS A 161 REMARK 465 GLY A 162 REMARK 465 GLY A 163 REMARK 465 SER A 164 REMARK 465 GLY A 165 REMARK 465 SER A 166 REMARK 465 GLY A 167 REMARK 465 GLU A 168 REMARK 465 ASN A 169 REMARK 465 LEU A 170 REMARK 465 TYR A 171 REMARK 465 PHE A 172 REMARK 465 GLN A 173 REMARK 465 GLY A 174 REMARK 465 GLY A 175 REMARK 465 SER A 176 REMARK 465 LYS A 222 REMARK 465 PHE A 223 REMARK 465 ARG A 224 REMARK 465 LYS A 225 DBREF 8GL3 A -6 225 PDB 8GL3 8GL3 -6 225 SEQRES 1 A 232 GLU ASN LEU TYR PHE GLN GLY SER GLU GLU ALA ARG GLU SEQRES 2 A 232 VAL ALA GLU GLU ILE LEU ARG LEU LEU ARG GLU HIS GLU SEQRES 3 A 232 GLU LEU LEU ARG GLU HIS GLU ARG LEU LEU LYS GLU ALA SEQRES 4 A 232 ARG GLU LEU ALA GLU ARG LEU GLU GLU LEU ALA ARG ARG SEQRES 5 A 232 LEU GLU GLU LEU ALA ARG ARG GLY GLU LYS ASP GLU GLU SEQRES 6 A 232 ALA VAL ARG GLN VAL GLU GLU ALA ALA ARG GLU ALA GLU SEQRES 7 A 232 ARG VAL ALA ARG GLU LEU GLU LYS SER ALA ARG ARG LEU SEQRES 8 A 232 GLN GLU SER ILE ARG GLU LEU ARG ARG LEU LEU LYS GLU SEQRES 9 A 232 LEU ARG GLU LEU LEU ARG GLU LEU LYS LYS LYS ALA SER SEQRES 10 A 232 GLU GLU GLU ARG LYS ILE ALA GLU GLU LEU GLU ARG ILE SEQRES 11 A 232 ALA GLU GLU ALA GLN ARG ILE LEU GLU GLU THR GLU ARG SEQRES 12 A 232 ILE LEU ARG GLU THR VAL ARG ILE ALA GLN GLU ALA VAL SEQRES 13 A 232 ARG LEU LEU GLN GLU ALA ARG ARG ARG ALA LYS LYS GLY SEQRES 14 A 232 GLY SER GLY SER GLY GLU ASN LEU TYR PHE GLN GLY GLY SEQRES 15 A 232 SER GLY SER GLU GLU ILE GLU LYS LEU ALA ARG GLU ILE SEQRES 16 A 232 LYS ARG ALA VAL GLU GLU LEU GLN LYS ALA LEU GLU GLU SEQRES 17 A 232 ASN GLU ARG ALA ILE ARG LEU ASN LYS GLU ALA ALA ARG SEQRES 18 A 232 LYS PHE GLU GLU ALA VAL GLU LYS PHE ARG LYS FORMUL 2 HOH *31(H2 O) HELIX 1 AA1 GLU A 6 ARG A 52 1 47 HELIX 2 AA2 GLU A 57 GLU A 104 1 48 HELIX 3 AA3 LYS A 115 LYS A 160 1 46 HELIX 4 AA4 SER A 178 GLU A 221 1 44 CRYST1 32.120 44.703 182.579 90.00 90.43 90.00 I 1 2 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 0.031133 0.000000 0.000234 0.00000 SCALE2 0.000000 0.022370 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005477 0.00000