HEADER DE NOVO PROTEIN 07-JAN-25 9MRF TITLE DE NOVO DESIGNED APOLAR RESIDUE MOTIF TRANSMEMBRANE HELIX COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOLARRESIDUE_DENOVO_DESIGN_46727_KFYK; COMPND 3 CHAIN: A, B; 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 BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS MEMBRANE PROTEIN, DE NOVO DESIGN, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.MRAVIC,M.ZHANG,C.T.ANDERSON REVDAT 1 22-JAN-25 9MRF 0 JRNL AUTH M.MRAVIC,M.ZHANG,C.T.ANDERSON JRNL TITL DE NOVO DESIGNED APOLAR RESIDUE MOTIF TRANSMEMBRANE HELIX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.LIEBSCHNER,P.V.AFONINE,M.L.BAKER,G.BUNKOCZI,V.B.CHEN, REMARK 1 AUTH 2 T.I.CROLL,B.HINTZE,L.W.HUNG,S.JAIN,A.J.MCCOY,N.W.MORIARTY, REMARK 1 AUTH 3 R.D.OEFFNER,B.K.POON,M.G.PRISANT,R.J.READ,J.S.RICHARDSON, REMARK 1 AUTH 4 D.C.RICHARDSON,M.D.SAMMITO,O.V.SOBOLEV,D.H.STOCKWELL, REMARK 1 AUTH 5 T.C.TERWILLIGER,A.G.URZHUMTSEV,L.L.VIDEAU,C.J.WILLIAMS, REMARK 1 AUTH 6 P.D.ADAMS REMARK 1 TITL MACROMOLECULAR STRUCTURE DETERMINATION USING X-RAYS, REMARK 1 TITL 2 NEUTRONS AND ELECTRONS: RECENT DEVELOPMENTS IN PHENIX REMARK 1 REF ACTA CRYSTALLOGR D STRUCT 2019 REMARK 1 REF 2 BIOL REMARK 1 REFN REMARK 1 PMID 31588918 REMARK 1 DOI 10.1107/S2059798319011471 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.090 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 4146 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 203 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 25.4000 - 2.0000 0.98 3943 203 0.2139 0.2524 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) : 0.135 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.678 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.96 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 : 0.011 486 REMARK 3 ANGLE : 1.166 662 REMARK 3 CHIRALITY : 0.063 89 REMARK 3 PLANARITY : 0.007 76 REMARK 3 DIHEDRAL : 12.475 161 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 9MRF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1000291108. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-OCT-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4159 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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 (%): 41.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01M HEPES PH7.5, 3.5M 1,6 REMARK 280 -HEXANEDIOL, LIPIDIC CUBIC PHASE, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-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 14.87800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 14.87800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 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: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 213 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 216 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 217 LIES ON A SPECIAL POSITION. 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 LYS A 24 CG CD CE NZ REMARK 470 PHE A 25 CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 27 CG CD CE NZ REMARK 470 LYS B 24 CG CD CE NZ REMARK 470 PHE B 25 CD1 CE1 CE2 CZ REMARK 470 LYS B 27 NZ REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 217 DISTANCE = 6.21 ANGSTROMS DBREF 9MRF A -3 27 PDB 9MRF 9MRF -3 27 DBREF 9MRF B -3 27 PDB 9MRF 9MRF -3 27 SEQRES 1 A 31 SER ALA ALA SER ASP LEU ASP GLU LEU LEU TRP VAL ILE SEQRES 2 A 31 ALA VAL THR ILE PHE GLY LEU VAL LEU ILE ALA SER ILE SEQRES 3 A 31 LEU LYS PHE TYR LYS SEQRES 1 B 31 SER ALA ALA SER ASP LEU ASP GLU LEU LEU TRP VAL ILE SEQRES 2 B 31 ALA VAL THR ILE PHE GLY LEU VAL LEU ILE ALA SER ILE SEQRES 3 B 31 LEU LYS PHE TYR LYS HET PEG A 101 7 HET PEG B 101 7 HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 3 PEG 2(C4 H10 O3) FORMUL 5 HOH *32(H2 O) HELIX 1 AA1 SER A -3 TYR A 26 1 30 HELIX 2 AA2 ALA B -2 TYR B 26 1 29 CRYST1 39.599 48.745 29.756 90.00 90.00 90.00 P 2 2 21 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 0.025253 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020515 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033607 0.00000 TER 235 LYS A 27 TER 469 LYS B 27 HETATM 470 C1 PEG A 101 -3.204 1.029 5.508 1.00 32.39 C HETATM 471 O1 PEG A 101 -3.907 1.124 4.292 1.00 39.32 O HETATM 472 C2 PEG A 101 -3.325 2.263 6.335 1.00 34.43 C HETATM 473 O2 PEG A 101 -4.688 2.505 6.655 1.00 34.86 O HETATM 474 C3 PEG A 101 -5.224 1.516 7.523 1.00 35.43 C HETATM 475 C4 PEG A 101 -6.042 2.156 8.590 1.00 32.02 C HETATM 476 O4 PEG A 101 -6.654 1.198 9.427 1.00 45.09 O HETATM 477 C1 PEG B 101 -3.285 22.733 -5.745 1.00 31.92 C HETATM 478 O1 PEG B 101 -4.557 22.720 -6.348 1.00 36.09 O HETATM 479 C2 PEG B 101 -3.331 23.244 -4.344 1.00 32.32 C HETATM 480 O2 PEG B 101 -2.342 24.249 -4.158 1.00 38.37 O HETATM 481 C3 PEG B 101 -1.580 24.066 -2.971 1.00 32.55 C HETATM 482 C4 PEG B 101 -1.881 25.163 -2.009 1.00 31.45 C HETATM 483 O4 PEG B 101 -0.836 25.367 -1.085 1.00 37.65 O HETATM 484 O HOH A 201 -12.340 2.939 5.873 1.00 27.74 O HETATM 485 O HOH A 202 -13.229 10.471 1.021 1.00 29.72 O HETATM 486 O HOH A 203 14.870 10.192 -13.530 1.00 28.45 O HETATM 487 O HOH A 204 -15.539 12.596 12.112 1.00 37.03 O HETATM 488 O HOH A 205 -16.233 6.001 5.499 1.00 22.41 O HETATM 489 O HOH A 206 -17.233 7.143 7.543 1.00 27.60 O HETATM 490 O HOH A 207 12.330 10.194 -7.364 1.00 23.83 O HETATM 491 O HOH A 208 -14.945 4.047 6.779 1.00 27.27 O HETATM 492 O HOH A 209 -14.404 1.198 9.501 1.00 39.69 O HETATM 493 O HOH A 210 12.898 2.717 -8.116 1.00 32.14 O HETATM 494 O HOH A 211 -13.302 11.200 13.040 1.00 29.34 O HETATM 495 O HOH A 212 23.103 6.980 -12.697 1.00 35.10 O HETATM 496 O HOH A 213 -19.799 6.517 7.439 0.50 41.03 O HETATM 497 O HOH A 214 2.812 3.113 1.157 1.00 38.93 O HETATM 498 O HOH A 215 1.729 4.015 3.775 1.00 36.30 O HETATM 499 O HOH A 216 0.000 7.201 7.439 0.50 53.72 O HETATM 500 O HOH A 217 0.000 10.262 7.439 0.50 39.86 O HETATM 501 O HOH B 201 -14.957 12.296 -3.060 1.00 39.58 O HETATM 502 O HOH B 202 -14.313 13.529 0.201 1.00 21.46 O HETATM 503 O HOH B 203 -11.181 20.394 -12.114 1.00 35.91 O HETATM 504 O HOH B 204 -12.514 13.391 -12.577 1.00 37.08 O HETATM 505 O HOH B 205 -10.916 12.188 -8.433 1.00 36.08 O HETATM 506 O HOH B 206 22.717 18.183 14.711 1.00 30.46 O HETATM 507 O HOH B 207 13.975 21.314 9.326 1.00 35.09 O HETATM 508 O HOH B 208 -9.173 24.883 -6.230 1.00 41.75 O HETATM 509 O HOH B 209 -13.261 23.496 -11.171 1.00 48.06 O HETATM 510 O HOH B 210 17.615 16.786 19.396 1.00 31.98 O HETATM 511 O HOH B 211 21.661 12.612 14.204 1.00 34.69 O HETATM 512 O HOH B 212 -10.266 12.051 -10.811 1.00 36.32 O HETATM 513 O HOH B 213 2.639 21.861 -1.961 1.00 43.20 O HETATM 514 O HOH B 214 1.621 20.941 -4.110 1.00 40.91 O HETATM 515 O HOH B 215 -7.561 21.558 -13.646 1.00 52.28 O CONECT 470 471 472 CONECT 471 470 CONECT 472 470 473 CONECT 473 472 474 CONECT 474 473 475 CONECT 475 474 476 CONECT 476 475 CONECT 477 478 479 CONECT 478 477 CONECT 479 477 480 CONECT 480 479 481 CONECT 481 480 482 CONECT 482 481 483 CONECT 483 482 MASTER 244 0 2 2 0 0 0 6 508 2 14 6 END