HEADER DE NOVO PROTEIN 29-NOV-22 8FBI TITLE IMPROVING THE SECRETION OF DESIGNED PROTEIN ASSEMBLIES THROUGH TITLE 2 NEGATIVE DESIGN OF CRYPTIC TRANSMEMBRANE DOMAINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: KWOCA_39; 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 DESIGNED PROTEIN, PROTEIN ASSEMBLIES, NEGATIVE DESIGN, CRYPTIC KEYWDS 2 TRANSMEMBRANE DOMAINS, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.Y.WANG,A.KHMELINSKAIA,A.K.BERA,N.P.KING REVDAT 1 22-MAR-23 8FBI 0 JRNL AUTH J.Y.J.WANG,A.KHMELINSKAIA,W.SHEFFLER,M.C.MIRANDA, JRNL AUTH 2 A.ANTANASIJEVIC,A.J.BORST,S.V.TORRES,C.SHU,Y.HSIA, JRNL AUTH 3 U.NATTERMANN,D.ELLIS,C.WALKEY,M.AHLRICHS,S.CHAN,A.KANG, JRNL AUTH 4 H.NGUYEN,C.SYDEMAN,B.SANKARAN,M.WU,A.K.BERA,L.CARTER, JRNL AUTH 5 B.FIALA,M.MURPHY,D.BAKER,A.B.WARD,N.P.KING JRNL TITL IMPROVING THE SECRETION OF DESIGNED PROTEIN ASSEMBLIES JRNL TITL 2 THROUGH NEGATIVE DESIGN OF CRYPTIC TRANSMEMBRANE DOMAINS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 120 56120 2023 JRNL REFN ESSN 1091-6490 JRNL PMID 36888664 JRNL DOI 10.1073/PNAS.2214556120 REMARK 2 REMARK 2 RESOLUTION. 3.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 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) : 3.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 58.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.240 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 4126 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 12.530 REMARK 3 FREE R VALUE TEST SET COUNT : 517 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 58.5100 - 5.7300 1.00 910 126 0.1841 0.2439 REMARK 3 2 5.7300 - 4.5500 1.00 923 101 0.3265 0.3628 REMARK 3 3 4.5500 - 3.9700 1.00 894 141 0.2900 0.2853 REMARK 3 4 3.9700 - 3.6100 1.00 882 149 0.3614 0.3779 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) : 0.520 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 39.890 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 185.1 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 183.8 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 : 0.001 2152 REMARK 3 ANGLE : 0.326 2891 REMARK 3 CHIRALITY : 0.029 347 REMARK 3 PLANARITY : 0.002 377 REMARK 3 DIHEDRAL : 12.436 857 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 8FBI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1000270340. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4127 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.610 REMARK 200 RESOLUTION RANGE LOW (A) : 58.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.21200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.61 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.66300 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE, 0.1 M REMARK 280 NA3C6H5O7, PH 5.6, 30% V/V MPD, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 57.83050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.38845 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.02633 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 57.83050 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 33.38845 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 24.02633 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 57.83050 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 33.38845 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 24.02633 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 66.77691 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 48.05267 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 66.77691 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 48.05267 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 66.77691 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 48.05267 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 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 MET A 1 REMARK 465 PRO A 2 REMARK 465 GLU A 3 REMARK 465 THR A 4 REMARK 465 PHE A 5 REMARK 465 GLU A 6 REMARK 465 GLY A 281 REMARK 465 SER A 282 REMARK 465 TRP A 283 REMARK 465 SER A 284 REMARK 465 GLY A 285 REMARK 465 GLY A 286 REMARK 465 GLY A 287 REMARK 465 SER A 288 REMARK 465 GLU A 289 REMARK 465 GLN A 290 REMARK 465 LYS A 291 REMARK 465 LEU A 292 REMARK 465 ILE A 293 REMARK 465 SER A 294 REMARK 465 GLU A 295 REMARK 465 GLU A 296 REMARK 465 ASP A 297 REMARK 465 LEU A 298 REMARK 465 GLY A 299 REMARK 465 GLY A 300 REMARK 465 SER A 301 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 ALA A 140 73.85 -158.80 REMARK 500 GLU A 193 36.24 -97.16 REMARK 500 REMARK 500 REMARK: NULL DBREF 8FBI A 1 301 PDB 8FBI 8FBI 1 301 SEQRES 1 A 301 MET PRO GLU THR PHE GLU ALA ILE ALA ARG ALA ILE GLU SEQRES 2 A 301 VAL ALA ARG GLU VAL GLU LYS VAL ALA GLN ARG ALA GLU SEQRES 3 A 301 GLU GLU GLY ASN PRO ASP LEU ARG ASP SER ALA LYS GLU SEQRES 4 A 301 LEU ALA ARG ALA VAL ASP GLU ALA ILE GLU GLU ALA LYS SEQRES 5 A 301 LYS GLN GLY ASN PRO GLU LEU VAL GLU TRP VAL ALA ARG SEQRES 6 A 301 ALA ALA LYS VAL ALA ALA GLU VAL ILE LYS VAL ALA ILE SEQRES 7 A 301 GLN ALA GLU LYS GLU GLY ASN ARG ASP LEU PHE ARG ALA SEQRES 8 A 301 ALA LEU GLU LEU VAL ARG ALA VAL ILE GLU ALA ILE GLU SEQRES 9 A 301 GLU ALA VAL LYS GLN GLY ASN PRO GLU LEU VAL GLU TRP SEQRES 10 A 301 VAL ALA ARG ALA ALA LYS VAL ALA ALA GLU VAL ILE LYS SEQRES 11 A 301 VAL ALA ILE GLN ALA GLU LYS GLU GLY ALA ARG ASP LEU SEQRES 12 A 301 PHE ARG LEU ALA LEU GLU LEU VAL ARG ALA VAL ILE GLU SEQRES 13 A 301 ALA ILE GLU PHE ALA VAL LYS LEU GLY ASP PRO GLU MET SEQRES 14 A 301 VAL GLU ARG ALA ALA ARG ILE ALA LYS THR ALA ALA GLU SEQRES 15 A 301 LEU ILE LYS ARG ALA ILE ARG ALA LYS LYS GLU GLY ASP SEQRES 16 A 301 LYS ASP GLN GLU ARG GLU ALA LYS LYS ARG VAL THR ARG SEQRES 17 A 301 LEU ILE ILE GLU LEU THR LEU MET VAL LEU LYS ALA SER SEQRES 18 A 301 LEU ASP LEU LEU ARG ARG ILE LEU GLU GLU LEU LYS GLU SEQRES 19 A 301 MET LEU GLU ARG LEU GLU LYS ASN PRO ASP LYS ASP VAL SEQRES 20 A 301 ILE VAL LYS VAL LEU LYS VAL ILE VAL LYS ALA ILE GLU SEQRES 21 A 301 ALA SER VAL ASP ASN GLN ARG VAL SER ALA ASP ASN GLN SEQRES 22 A 301 LYS MET LEU ALA GLU LEU ALA GLY SER TRP SER GLY GLY SEQRES 23 A 301 GLY SER GLU GLN LYS LEU ILE SER GLU GLU ASP LEU GLY SEQRES 24 A 301 GLY SER HELIX 1 AA1 ALA A 7 GLU A 27 1 21 HELIX 2 AA2 ASN A 30 GLY A 55 1 26 HELIX 3 AA3 ASN A 56 GLU A 83 1 28 HELIX 4 AA4 ASN A 85 GLN A 109 1 25 HELIX 5 AA5 GLU A 113 GLU A 138 1 26 HELIX 6 AA6 ALA A 140 GLY A 165 1 26 HELIX 7 AA7 ASP A 166 GLU A 193 1 28 HELIX 8 AA8 ASP A 195 ASN A 242 1 48 HELIX 9 AA9 ASP A 244 ALA A 280 1 37 CRYST1 115.661 115.661 72.079 90.00 90.00 120.00 H 3 9 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 0.008646 0.004992 0.000000 0.00000 SCALE2 0.000000 0.009983 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013874 0.00000