HEADER DE NOVO PROTEIN 08-OCT-18 6MPW TITLE DE NOVO DESIGN OF MEMBRANE PROTEIN--MINI-EVGL MEMBRANE PROTEIN, C2221 TITLE 2 FORM-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MINI-EVGL MEMBRANE PROTEIN; COMPND 3 CHAIN: A, B, C, D, E; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS DE NOVO DESIGN, MEMBRANE PROTEIN, PENTAMERIC BUNDLE, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.MRAVIC,L.LIU,W.F.DEGRADO REVDAT 4 11-OCT-23 6MPW 1 REMARK REVDAT 3 27-NOV-19 6MPW 1 REMARK REVDAT 2 17-APR-19 6MPW 1 JRNL REVDAT 1 03-APR-19 6MPW 0 JRNL AUTH M.MRAVIC,J.L.THOMASTON,M.TUCKER,P.E.SOLOMON,L.LIU, JRNL AUTH 2 W.F.DEGRADO JRNL TITL PACKING OF APOLAR SIDE CHAINS ENABLES ACCURATE DESIGN OF JRNL TITL 2 HIGHLY STABLE MEMBRANE PROTEINS. JRNL REF SCIENCE V. 363 1418 2019 JRNL REFN ESSN 1095-9203 JRNL PMID 30923216 JRNL DOI 10.1126/SCIENCE.AAV7541 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 7909 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.610 REMARK 3 FREE R VALUE TEST SET COUNT : 239 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 2.8619 - 2.5002 0.99 2477 152 0.3004 0.3171 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 42.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 50.83 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 : 0.002 1152 REMARK 3 ANGLE : 0.387 1543 REMARK 3 CHIRALITY : 0.031 207 REMARK 3 PLANARITY : 0.002 155 REMARK 3 DIHEDRAL : 24.212 408 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 6MPW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1000237373. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-AUG-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.11583 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4438 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.480 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 12.30 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.7100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.1 REMARK 200 DATA REDUNDANCY IN SHELL : 11.90 REMARK 200 R MERGE FOR SHELL (I) : 0.58000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.840 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: ONE BUNDLE OF 6MCT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M MGCL2, 0.1 %W/V NAN3, 0.1 M NA REMARK 280 CACODYLATE, PH 6.7, 6.6 %W/V PEG 3350, VAPOR DIFFUSION, HANGING REMARK 280 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 24.10350 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 24.10350 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 27.79000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.40100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 27.79000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.40100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 24.10350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 27.79000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.40100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 24.10350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 27.79000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 44.40100 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -66.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 B 26 REMARK 465 NH2 B 27 REMARK 465 GLY C 26 REMARK 465 NH2 C 27 REMARK 465 GLY D 26 REMARK 465 NH2 D 27 REMARK 465 GLY E 26 REMARK 465 NH2 E 27 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 ASP A 1 CG OD1 OD2 REMARK 470 LYS A 4 CG CD CE NZ REMARK 470 LYS B 4 CG CD CE NZ REMARK 470 LYS C 4 CG CD CE NZ REMARK 470 LYS D 4 CG CD CE NZ REMARK 470 LYS E 4 CG CD CE NZ REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 C8E A 101 REMARK 610 C8E A 102 REMARK 610 C8E B 101 REMARK 610 C8E C 101 REMARK 610 C8E C 102 REMARK 610 C8E E 101 REMARK 610 C8E E 102 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C8E A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C8E A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C8E B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C8E C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C8E C 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C8E E 102 DBREF 6MPW A 1 27 PDB 6MPW 6MPW 1 27 DBREF 6MPW B 1 27 PDB 6MPW 6MPW 1 27 DBREF 6MPW C 1 27 PDB 6MPW 6MPW 1 27 DBREF 6MPW D 1 27 PDB 6MPW 6MPW 1 27 DBREF 6MPW E 1 27 PDB 6MPW 6MPW 1 27 SEQRES 1 A 27 ASP SER LEU LYS TRP ILE VAL PHE LEU LEU PHE LEU ILE SEQRES 2 A 27 VAL LEU LEU LEU LEU ALA ILE VAL PHE LEU LEU ARG GLY SEQRES 3 A 27 NH2 SEQRES 1 B 27 ASP SER LEU LYS TRP ILE VAL PHE LEU LEU PHE LEU ILE SEQRES 2 B 27 VAL LEU LEU LEU LEU ALA ILE VAL PHE LEU LEU ARG GLY SEQRES 3 B 27 NH2 SEQRES 1 C 27 ASP SER LEU LYS TRP ILE VAL PHE LEU LEU PHE LEU ILE SEQRES 2 C 27 VAL LEU LEU LEU LEU ALA ILE VAL PHE LEU LEU ARG GLY SEQRES 3 C 27 NH2 SEQRES 1 D 27 ASP SER LEU LYS TRP ILE VAL PHE LEU LEU PHE LEU ILE SEQRES 2 D 27 VAL LEU LEU LEU LEU ALA ILE VAL PHE LEU LEU ARG GLY SEQRES 3 D 27 NH2 SEQRES 1 E 27 ASP SER LEU LYS TRP ILE VAL PHE LEU LEU PHE LEU ILE SEQRES 2 E 27 VAL LEU LEU LEU LEU ALA ILE VAL PHE LEU LEU ARG GLY SEQRES 3 E 27 NH2 HET NH2 A 27 1 HET C8E A 101 12 HET C8E A 102 8 HET C8E B 101 7 HET C8E C 101 9 HET C8E C 102 18 HET C8E E 101 7 HET C8E E 102 18 HETNAM NH2 AMINO GROUP HETNAM C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE FORMUL 1 NH2 H2 N FORMUL 6 C8E 7(C16 H34 O5) HELIX 1 AA1 ASP A 1 GLY A 26 1 26 HELIX 2 AA2 SER B 2 ARG B 25 1 24 HELIX 3 AA3 SER C 2 ARG C 25 1 24 HELIX 4 AA4 SER D 2 ARG D 25 1 24 HELIX 5 AA5 SER E 2 ARG E 25 1 24 LINK C GLY A 26 N NH2 A 27 1555 1555 1.23 SITE 1 AC1 4 LYS A 4 TRP A 5 PHE A 8 PHE B 22 SITE 1 AC2 6 PHE A 11 TRP B 5 C8E B 101 VAL C 21 SITE 2 AC2 6 PHE D 22 ARG D 25 SITE 1 AC3 2 C8E A 102 TRP B 5 SITE 1 AC4 2 LEU B 24 LEU C 24 SITE 1 AC5 10 LEU A 15 ALA A 19 VAL B 7 TRP C 5 SITE 2 AC5 10 PHE C 11 TRP D 5 PHE D 8 LEU D 12 SITE 3 AC5 10 PHE E 22 ARG E 25 SITE 1 AC6 3 VAL D 7 SER E 2 TRP E 5 CRYST1 55.580 88.802 48.207 90.00 90.00 90.00 C 2 2 21 40 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 0.017992 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011261 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020744 0.00000