HEADER DE NOVO PROTEIN 15-OCT-18 6MRR TITLE DE NOVO DESIGNED PROTEIN FOLDIT1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: FOLDIT1; 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 DE NOVO PROTEIN, FOLDIT EXPDTA X-RAY DIFFRACTION AUTHOR B.KOEPNICK,M.J.BICK,R.D.ESTEP,S.KLEINFELTER,L.WEI,D.BAKER REVDAT 6 03-APR-24 6MRR 1 REMARK REVDAT 5 13-MAR-24 6MRR 1 REMARK REVDAT 4 20-NOV-19 6MRR 1 REMARK REVDAT 3 26-JUN-19 6MRR 1 JRNL REVDAT 2 19-JUN-19 6MRR 1 JRNL REVDAT 1 12-JUN-19 6MRR 0 JRNL AUTH B.KOEPNICK,J.FLATTEN,T.HUSAIN,A.FORD,D.A.SILVA,M.J.BICK, JRNL AUTH 2 A.BAUER,G.LIU,Y.ISHIDA,A.BOYKOV,R.D.ESTEP,S.KLEINFELTER, JRNL AUTH 3 T.NORGARD-SOLANO,L.WEI,F.PLAYERS,G.T.MONTELIONE,F.DIMAIO, JRNL AUTH 4 Z.POPOVIC,F.KHATIB,S.COOPER,D.BAKER JRNL TITL DE NOVO PROTEIN DESIGN BY CITIZEN SCIENTISTS. JRNL REF NATURE V. 570 390 2019 JRNL REFN ESSN 1476-4687 JRNL PMID 31168091 JRNL DOI 10.1038/S41586-019-1274-4 REMARK 2 REMARK 2 RESOLUTION. 1.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_3112: ???) 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) : 1.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 3 NUMBER OF REFLECTIONS : 18279 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1829 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 28.9244 - 2.7739 0.97 1364 153 0.1719 0.2144 REMARK 3 2 2.7739 - 2.2020 0.96 1315 145 0.1598 0.1838 REMARK 3 3 2.2020 - 1.9237 0.95 1300 145 0.1254 0.1402 REMARK 3 4 1.9237 - 1.7479 0.95 1288 144 0.1409 0.1734 REMARK 3 5 1.7479 - 1.6226 0.94 1280 141 0.1255 0.1625 REMARK 3 6 1.6226 - 1.5269 0.94 1290 144 0.1242 0.1492 REMARK 3 7 1.5269 - 1.4505 0.93 1243 137 0.1178 0.1563 REMARK 3 8 1.4505 - 1.3873 0.92 1252 139 0.1232 0.1918 REMARK 3 9 1.3873 - 1.3339 0.92 1237 139 0.1324 0.1737 REMARK 3 10 1.3339 - 1.2879 0.91 1253 141 0.1315 0.1703 REMARK 3 11 1.2879 - 1.2476 0.90 1219 135 0.1369 0.1953 REMARK 3 12 1.2476 - 1.2120 0.88 1189 132 0.1289 0.2107 REMARK 3 13 1.2120 - 1.1801 0.88 1220 134 0.1296 0.1712 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.420 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 : 0.008 582 REMARK 3 ANGLE : 0.833 781 REMARK 3 CHIRALITY : 0.075 86 REMARK 3 PLANARITY : 0.004 102 REMARK 3 DIHEDRAL : 18.886 232 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 6MRR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1000236328. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-APR-17 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 : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS JUN 17, 2015 REMARK 200 DATA SCALING SOFTWARE : XDS JUN 17, 2015 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22566 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.070 REMARK 200 RESOLUTION RANGE LOW (A) : 43.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.3 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.02600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 32.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.17700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.2. REMARK 200 STARTING MODEL: COMPUTATIONAL DESIGN GENERATED BY FOLDIT SOFTWARE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM CHLORIDE, 0.05 M REMARK 280 HEPES, PH 7.5, 35% V/V PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH), REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 21.79200 REMARK 290 SMTRY3 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 GLU A 11 CD OE1 OE2 REMARK 470 GLU A 43 CD OE1 OE2 REMARK 470 GLU A 51 CD OE1 OE2 REMARK 470 LYS A 55 CD CE NZ REMARK 470 LYS A 58 CD CE NZ REMARK 470 LYS A 59 CE NZ REMARK 470 LYS A 66 CE NZ REMARK 470 GLU A 68 CG CD OE1 OE2 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 HH21 ARG A 47 O HOH A 102 1.55 REMARK 500 O HOH A 113 O HOH A 178 1.85 REMARK 500 O HOH A 112 O HOH A 169 1.97 REMARK 500 O HOH A 104 O HOH A 135 2.04 REMARK 500 OE1 GLU A 15 O HOH A 101 2.10 REMARK 500 NH2 ARG A 47 O HOH A 102 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 168 O HOH A 202 1655 2.19 REMARK 500 REMARK 500 REMARK: NULL DBREF 6MRR A 1 68 PDB 6MRR 6MRR 1 68 SEQRES 1 A 68 GLY TRP SER THR GLU LEU GLU LYS HIS ARG GLU GLU LEU SEQRES 2 A 68 LYS GLU PHE LEU LYS LYS GLU GLY ILE THR ASN VAL GLU SEQRES 3 A 68 ILE ARG ILE ASP ASN GLY ARG LEU GLU VAL ARG VAL GLU SEQRES 4 A 68 GLY GLY THR GLU ARG LEU LYS ARG PHE LEU GLU GLU LEU SEQRES 5 A 68 ARG GLN LYS LEU GLU LYS LYS GLY TYR THR VAL ASP ILE SEQRES 6 A 68 LYS ILE GLU FORMUL 2 HOH *116(H2 O) HELIX 1 AA1 SER A 3 GLY A 21 1 19 HELIX 2 AA2 THR A 42 LYS A 59 1 18 SHEET 1 AA1 3 VAL A 25 ASP A 30 0 SHEET 2 AA1 3 ARG A 33 VAL A 38 -1 O GLU A 35 N ARG A 28 SHEET 3 AA1 3 THR A 62 ILE A 67 1 O ASP A 64 N LEU A 34 CRYST1 24.045 43.584 29.276 90.00 99.00 90.00 P 1 21 1 2 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 0.041589 0.000000 0.006586 0.00000 SCALE2 0.000000 0.022944 0.000000 0.00000 SCALE3 0.000000 0.000000 0.034583 0.00000