HEADER DE NOVO PROTEIN 05-MAY-23 8SRN TITLE DE NOVO DESIGNED TRANSMEMBRANE ANTIPARALLEL HOMO-DIMER G-X6-G 01322-42 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GX6G_DENOVO_DESIGN_01322-42; COMPND 3 CHAIN: A, B, C, D, E, F; 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; SOURCE 6 EXPRESSION_SYSTEM_VARIANT: C43 KEYWDS HOMO-DIMER, MEMBRANE PROTEIN, COMPUTATIONAL DESIGN, SINGLE-PASS, DE KEYWDS 2 NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.GOLDEN,X.DAI,M.MRAVIC REVDAT 1 04-SEP-24 8SRN 0 JRNL AUTH M.MRAVIC,J.GOLDEN,X.DAI,C.T.ANDERSON JRNL TITL DE NOVO DESIGN REVEALS PRINCIPLES OF A COMMON MEMBRANE JRNL TITL 2 PROTEIN STRUCTURAL BUILDING BLOCK: THE G-X6-G MOTIF JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 3 NUMBER OF REFLECTIONS : 2984 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.253 REMARK 3 R VALUE (WORKING SET) : 0.253 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 299 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 39.6260 - 4.1261 0.98 1447 161 0.2340 0.2280 REMARK 3 2 4.1261 - 3.2755 0.88 1238 138 0.3066 0.3323 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.460 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.004 1046 REMARK 3 ANGLE : 0.757 1427 REMARK 3 CHIRALITY : 0.044 200 REMARK 3 PLANARITY : 0.006 157 REMARK 3 DIHEDRAL : 9.919 319 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 8SRN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1000274143. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAR-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 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 : 3003 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.275 REMARK 200 RESOLUTION RANGE LOW (A) : 60.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.4 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 0.46900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 (%): 52.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CHLORIDE, 0.1 M LITHIUM REMARK 280 SULFATE, 0.1 M SODIUM CITRATE PH 3.5, 30% PEG400, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 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 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 50.53200 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 50.53200 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 SMTRY1 5 1.000000 0.000000 0.000000 27.00400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.70400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 27.00400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.70400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 50.53200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 27.00400 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 35.70400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 50.53200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 27.00400 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 35.70400 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: 1230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 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: 1270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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: 3 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: 1360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 GLY A 1 REMARK 465 ALA A 2 REMARK 465 PRO A 3 REMARK 465 ASP A 4 REMARK 465 LYS A 28 REMARK 465 PHE A 29 REMARK 465 ALA A 30 REMARK 465 GLY B 1 REMARK 465 ALA B 2 REMARK 465 PRO B 3 REMARK 465 ASP B 4 REMARK 465 PHE B 29 REMARK 465 ALA B 30 REMARK 465 GLY C 1 REMARK 465 ALA C 2 REMARK 465 PRO C 3 REMARK 465 ASP C 4 REMARK 465 SER C 5 REMARK 465 ALA C 30 REMARK 465 GLY D 1 REMARK 465 ALA D 2 REMARK 465 PRO D 3 REMARK 465 PHE D 29 REMARK 465 ALA D 30 REMARK 465 GLY E 1 REMARK 465 ALA E 2 REMARK 465 PRO E 3 REMARK 465 ASP E 4 REMARK 465 ALA E 30 REMARK 465 GLY F 1 REMARK 465 ALA F 2 REMARK 465 PRO F 3 REMARK 465 PHE F 29 REMARK 465 ALA F 30 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 TRP A 6 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 6 CZ3 CH2 REMARK 470 GLU A 7 CG CD OE1 OE2 REMARK 470 PHE A 18 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 25 CG CD CE NZ REMARK 470 SER B 5 OG REMARK 470 GLU B 7 CG CD OE1 OE2 REMARK 470 TYR B 21 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS B 25 CG CD CE NZ REMARK 470 LYS B 28 CG CD CE NZ REMARK 470 TRP C 6 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP C 6 CZ3 CH2 REMARK 470 GLU C 7 CG CD OE1 OE2 REMARK 470 LYS C 25 CG CD CE NZ REMARK 470 GLU D 7 CG CD OE1 OE2 REMARK 470 GLU E 7 CG CD OE1 OE2 REMARK 470 LYS E 28 CG CD CE NZ REMARK 470 PHE E 29 CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR F 21 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS F 25 CG CD CE NZ REMARK 470 LYS F 28 CG CD CE NZ 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 TRP D 6 -74.42 -46.45 REMARK 500 TRP F 6 -73.85 -62.02 REMARK 500 REMARK 500 REMARK: NULL DBREF 8SRN A 1 30 PDB 8SRN 8SRN 1 30 DBREF 8SRN B 1 30 PDB 8SRN 8SRN 1 30 DBREF 8SRN C 1 30 PDB 8SRN 8SRN 1 30 DBREF 8SRN D 1 30 PDB 8SRN 8SRN 1 30 DBREF 8SRN E 1 30 PDB 8SRN 8SRN 1 30 DBREF 8SRN F 1 30 PDB 8SRN 8SRN 1 30 SEQRES 1 A 30 GLY ALA PRO ASP SER TRP GLU ALA GLY VAL ILE LEU ILE SEQRES 2 A 30 ALA LEU GLY VAL PHE VAL LEU TYR LEU GLY VAL LYS LEU SEQRES 3 A 30 LEU LYS PHE ALA SEQRES 1 B 30 GLY ALA PRO ASP SER TRP GLU ALA GLY VAL ILE LEU ILE SEQRES 2 B 30 ALA LEU GLY VAL PHE VAL LEU TYR LEU GLY VAL LYS LEU SEQRES 3 B 30 LEU LYS PHE ALA SEQRES 1 C 30 GLY ALA PRO ASP SER TRP GLU ALA GLY VAL ILE LEU ILE SEQRES 2 C 30 ALA LEU GLY VAL PHE VAL LEU TYR LEU GLY VAL LYS LEU SEQRES 3 C 30 LEU LYS PHE ALA SEQRES 1 D 30 GLY ALA PRO ASP SER TRP GLU ALA GLY VAL ILE LEU ILE SEQRES 2 D 30 ALA LEU GLY VAL PHE VAL LEU TYR LEU GLY VAL LYS LEU SEQRES 3 D 30 LEU LYS PHE ALA SEQRES 1 E 30 GLY ALA PRO ASP SER TRP GLU ALA GLY VAL ILE LEU ILE SEQRES 2 E 30 ALA LEU GLY VAL PHE VAL LEU TYR LEU GLY VAL LYS LEU SEQRES 3 E 30 LEU LYS PHE ALA SEQRES 1 F 30 GLY ALA PRO ASP SER TRP GLU ALA GLY VAL ILE LEU ILE SEQRES 2 F 30 ALA LEU GLY VAL PHE VAL LEU TYR LEU GLY VAL LYS LEU SEQRES 3 F 30 LEU LYS PHE ALA HELIX 1 AA1 SER A 5 LEU A 27 1 23 HELIX 2 AA2 TRP B 6 LEU B 27 1 22 HELIX 3 AA3 GLU C 7 LYS C 28 1 22 HELIX 4 AA4 SER D 5 LEU D 27 1 23 HELIX 5 AA5 TRP E 6 LYS E 28 1 23 HELIX 6 AA6 SER F 5 LEU F 27 1 23 CRYST1 54.008 71.408 101.064 90.00 90.00 90.00 C 2 2 21 48 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 0.018516 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014004 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009895 0.00000