HEADER DE NOVO PROTEIN 06-MAY-20 6WVS TITLE HYPERSTABLE DE NOVO TIM BARREL VARIANT DENOVOTIM15 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DENOVOTIM15 HYPERSTABLE DE NOVO TIM BARREL; 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 BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS TIM BARREL, HYPERSTABLE, SYMMETRIC, DE NOVO, REPEAT PROTEIN, DE NOVO KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.J.BICK,I.C.HAYDON,S.J.CALDWELL,C.ZEYMER,P.HUANG,D.A.FERNANDEZ- AUTHOR 2 VELASCO,D.BAKER REVDAT 5 03-APR-24 6WVS 1 REMARK REVDAT 4 06-MAR-24 6WVS 1 REMARK REVDAT 3 16-DEC-20 6WVS 1 JRNL REVDAT 2 02-DEC-20 6WVS 1 TITLE COMPND AUTHOR JRNL REVDAT 1 25-NOV-20 6WVS 0 JRNL AUTH S.J.CALDWELL,I.C.HAYDON,N.PIPERIDOU,P.S.HUANG,M.J.BICK, JRNL AUTH 2 H.S.SJOSTROM,D.HILVERT,D.BAKER,C.ZEYMER JRNL TITL TIGHT AND SPECIFIC LANTHANIDE BINDING IN A DE NOVO TIM JRNL TITL 2 BARREL WITH A LARGE INTERNAL CAVITY DESIGNED BY SYMMETRIC JRNL TITL 3 DOMAIN FUSION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 117 30362 2020 JRNL REFN ESSN 1091-6490 JRNL PMID 33203677 JRNL DOI 10.1073/PNAS.2008535117 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18RC2_3793 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 10220 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.610 REMARK 3 FREE R VALUE TEST SET COUNT : 982 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 37.4400 - 4.2100 0.91 1339 126 0.1511 0.1737 REMARK 3 2 4.2100 - 3.3400 0.90 1328 141 0.1644 0.1935 REMARK 3 3 3.3400 - 2.9200 0.90 1329 149 0.2193 0.2035 REMARK 3 4 2.9200 - 2.6600 0.90 1303 146 0.2659 0.2681 REMARK 3 5 2.6500 - 2.4600 0.90 1346 141 0.2828 0.2815 REMARK 3 6 2.4600 - 2.3200 0.91 1307 133 0.3010 0.2645 REMARK 3 7 2.3200 - 2.2000 0.88 1286 146 0.5156 0.5734 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.686 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.91 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 : 0.003 1296 REMARK 3 ANGLE : 0.509 1764 REMARK 3 CHIRALITY : 0.048 235 REMARK 3 PLANARITY : 0.003 222 REMARK 3 DIHEDRAL : 13.792 189 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 6WVS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1000248731. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10232 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.202 REMARK 200 RESOLUTION RANGE LOW (A) : 37.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 9.100 REMARK 200 R MERGE (I) : 0.20380 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.3200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : 2.75900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.310 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: ROSETTA DESIGN MODEL OF PROTEIN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% W/V PEG 20 000, 20% V/V PEG MME REMARK 280 550, 0.02 M EACH OF EACH 1,6-HEXANEDIOL, 1-BUTANOL, (RS)-1,2- REMARK 280 PROPANEDIOL, 2-PROPANOL, 1,4-BUTANEDIOL, 1,3-PROPANEDIOL, 0.1 M REMARK 280 BICINE/TRIZMA BASE PH 8.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 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 42.84667 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 21.42333 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 MET A 1 REMARK 465 GLY A 184 REMARK 465 GLY A 185 REMARK 465 LEU A 186 REMARK 465 GLU A 187 REMARK 465 HIS A 188 REMARK 465 HIS A 189 REMARK 465 HIS A 190 REMARK 465 HIS A 191 REMARK 465 HIS A 192 REMARK 465 HIS A 193 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 THR A 9 OG1 CG2 REMARK 470 ASP A 10 CG OD1 OD2 REMARK 470 GLU A 13 CG CD OE1 OE2 REMARK 470 MET A 14 SD CE REMARK 470 LEU A 15 CG CD1 CD2 REMARK 470 LYS A 16 CG CD CE NZ REMARK 470 GLU A 19 CG CD OE1 OE2 REMARK 470 ILE A 20 CD1 REMARK 470 LYS A 27 CD CE NZ REMARK 470 ASP A 34 CG OD1 OD2 REMARK 470 GLU A 41 CD OE1 OE2 REMARK 470 LYS A 44 CD CE NZ REMARK 470 LYS A 45 CD CE NZ REMARK 470 ASP A 56 CG OD1 OD2 REMARK 470 GLU A 59 CD OE1 OE2 REMARK 470 GLU A 65 CD OE1 OE2 REMARK 470 ARG A 68 CD NE CZ NH1 NH2 REMARK 470 LYS A 73 CE NZ REMARK 470 ILE A 84 CD1 REMARK 470 GLU A 87 OE1 OE2 REMARK 470 LYS A 90 CD CE NZ REMARK 470 LYS A 91 CD CE NZ REMARK 470 ASP A 102 OD1 OD2 REMARK 470 GLU A 105 CD OE1 OE2 REMARK 470 LEU A 107 CG CD1 CD2 REMARK 470 LYS A 108 CG CD CE NZ REMARK 470 ARG A 115 NE CZ NH1 NH2 REMARK 470 LYS A 119 CE NZ REMARK 470 ASP A 127 CG OD1 OD2 REMARK 470 ARG A 129 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 136 CE NZ REMARK 470 LYS A 137 CD CE NZ REMARK 470 THR A 147 OG1 CG2 REMARK 470 ASP A 148 CG OD1 OD2 REMARK 470 ASP A 150 CG OD1 OD2 REMARK 470 GLU A 151 CG CD OE1 OE2 REMARK 470 LYS A 154 CE NZ REMARK 470 GLU A 157 CD OE1 OE2 REMARK 470 SER A 171 OG REMARK 470 TRP A 174 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 174 CZ3 CH2 REMARK 470 ARG A 175 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 178 CG CD OE1 NE2 REMARK 470 GLU A 179 CD OE1 OE2 REMARK 470 LEU A 181 CG CD1 CD2 REMARK 470 LYS A 182 CG CD CE NZ REMARK 470 LYS A 183 CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD2 ASP A 2 HH22 ARG A 160 1.57 REMARK 500 REMARK 500 REMARK: NULL 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 SER A 125 149.12 -177.91 REMARK 500 REMARK 500 REMARK: NULL DBREF 6WVS A 1 193 PDB 6WVS 6WVS 1 193 SEQRES 1 A 193 MET ASP ILE LEU ILE VAL ASN ALA THR ASP VAL ASP GLU SEQRES 2 A 193 MET LEU LYS GLN VAL GLU ILE LEU ARG ARG LEU GLY ALA SEQRES 3 A 193 LYS GLN ILE ALA VAL VAL SER ASP ASP TRP ARG ILE LEU SEQRES 4 A 193 GLN GLU ALA LEU LYS LYS GLY GLY ASP ILE LEU ILE VAL SEQRES 5 A 193 ASN ALA THR ASP VAL ASP GLU MET LEU LYS GLN VAL GLU SEQRES 6 A 193 ILE LEU ARG ARG LEU GLY ALA LYS GLN ILE ALA VAL VAL SEQRES 7 A 193 SER ASP ASP TRP ARG ILE LEU GLN GLU ALA LEU LYS LYS SEQRES 8 A 193 GLY GLY ASP ILE LEU ILE VAL ASN ALA THR ASP VAL ASP SEQRES 9 A 193 GLU MET LEU LYS GLN VAL GLU ILE LEU ARG ARG LEU GLY SEQRES 10 A 193 ALA LYS GLN ILE ALA VAL VAL SER ASP ASP TRP ARG ILE SEQRES 11 A 193 LEU GLN GLU ALA LEU LYS LYS GLY GLY ASP ILE LEU ILE SEQRES 12 A 193 VAL ASN ALA THR ASP VAL ASP GLU MET LEU LYS GLN VAL SEQRES 13 A 193 GLU ILE LEU ARG ARG LEU GLY ALA LYS GLN ILE ALA VAL SEQRES 14 A 193 VAL SER ASP ASP TRP ARG ILE LEU GLN GLU ALA LEU LYS SEQRES 15 A 193 LYS GLY GLY LEU GLU HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *19(H2 O) HELIX 1 AA1 ASP A 10 LEU A 24 1 15 HELIX 2 AA2 ASP A 35 LYS A 45 1 11 HELIX 3 AA3 ASP A 56 LEU A 70 1 15 HELIX 4 AA4 ASP A 81 LYS A 91 1 11 HELIX 5 AA5 ASP A 102 LEU A 116 1 15 HELIX 6 AA6 ASP A 127 GLY A 138 1 12 HELIX 7 AA7 ASP A 148 LEU A 162 1 15 HELIX 8 AA8 ASP A 173 LYS A 183 1 11 SHEET 1 AA1 9 ILE A 3 VAL A 6 0 SHEET 2 AA1 9 ILE A 29 SER A 33 1 O ALA A 30 N VAL A 6 SHEET 3 AA1 9 ILE A 49 VAL A 52 1 O ILE A 49 N ILE A 29 SHEET 4 AA1 9 GLN A 74 SER A 79 1 O ALA A 76 N LEU A 50 SHEET 5 AA1 9 ILE A 95 VAL A 98 1 O ILE A 97 N VAL A 77 SHEET 6 AA1 9 ILE A 121 SER A 125 1 O ALA A 122 N LEU A 96 SHEET 7 AA1 9 ILE A 141 VAL A 144 1 O ILE A 143 N VAL A 123 SHEET 8 AA1 9 GLN A 166 SER A 171 1 O ALA A 168 N VAL A 144 SHEET 9 AA1 9 ILE A 3 VAL A 6 1 N ILE A 5 O VAL A 169 CRYST1 53.199 53.199 64.270 90.00 90.00 120.00 P 32 3 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 0.018797 0.010853 0.000000 0.00000 SCALE2 0.000000 0.021705 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015559 0.00000