HEADER DE NOVO PROTEIN 17-NOV-15 5ET3 TITLE CRYSTAL STRUCTURE OF DE NOVO DESIGNED FULLERENE ORGANIZING PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FULLERENE ORGANIZING PROTEIN (C60SOL-COP-3); COMPND 3 CHAIN: A, B; 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 PROTEIN, FULLERENE, COMPLEX, HELICAL ASSEMBLY EXPDTA X-RAY DIFFRACTION AUTHOR K.-H.KIM,Y.H.KIM,R.ACHARYA,N.H.KIM,J.PAUL,G.GRIGORYAN,W.F.DEGRADO REVDAT 3 08-NOV-23 5ET3 1 REMARK REVDAT 2 25-DEC-19 5ET3 1 JRNL REMARK REVDAT 1 04-MAY-16 5ET3 0 JRNL AUTH K.-H.KIM,D.-K.KO,Y.-T.KIM,N.H.KIM,J.PAUL,S.-Q.ZHANG, JRNL AUTH 2 C.B.MURRAY,R.ACHARYA,W.F.DEGRADO,Y.H.KIM,G.GRIGORYAN JRNL TITL PROTEIN-DIRECTED SELF-ASSEMBLY OF A FULLERENE CRYSTAL. JRNL REF NAT COMMUN V. 7 11429 2016 JRNL REFN ESSN 2041-1723 JRNL PMID 27113637 JRNL DOI 10.1038/NCOMMS11429 REMARK 2 REMARK 2 RESOLUTION. 1.67 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_2306: ??? 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) : 1.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.520 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 7487 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.040 REMARK 3 FREE R VALUE TEST SET COUNT : 752 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 15.3045 - 2.8532 0.81 1161 135 0.2570 0.2764 REMARK 3 2 2.8532 - 2.2671 0.99 1399 150 0.1985 0.2228 REMARK 3 3 2.2671 - 1.9812 1.00 1400 155 0.1947 0.2132 REMARK 3 4 1.9812 - 1.8003 1.00 1403 158 0.2060 0.2475 REMARK 3 5 1.8003 - 1.6715 0.98 1372 154 0.2141 0.2521 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.04 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.50 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 : 0.008 536 REMARK 3 ANGLE : 0.893 778 REMARK 3 CHIRALITY : 0.033 70 REMARK 3 PLANARITY : 0.222 81 REMARK 3 DIHEDRAL : 21.212 166 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 30 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.4210 40.8730 4.3230 REMARK 3 T TENSOR REMARK 3 T11: 0.0837 T22: 0.1210 REMARK 3 T33: 0.1141 T12: 0.0355 REMARK 3 T13: 0.0319 T23: 0.0684 REMARK 3 L TENSOR REMARK 3 L11: 1.8346 L22: 2.5477 REMARK 3 L33: 5.4979 L12: -0.1720 REMARK 3 L13: 1.0512 L23: -1.6405 REMARK 3 S TENSOR REMARK 3 S11: 0.1284 S12: 0.0549 S13: 0.2451 REMARK 3 S21: 0.0067 S22: -0.0784 S23: -0.1052 REMARK 3 S31: -0.2886 S32: -0.2235 S33: 0.2840 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 30 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.4242 40.8829 6.3203 REMARK 3 T TENSOR REMARK 3 T11: 0.0830 T22: 0.1131 REMARK 3 T33: 0.1202 T12: -0.0270 REMARK 3 T13: 0.0304 T23: -0.0455 REMARK 3 L TENSOR REMARK 3 L11: 2.0786 L22: 2.6851 REMARK 3 L33: 5.5269 L12: 0.0497 REMARK 3 L13: 1.1035 L23: 1.7197 REMARK 3 S TENSOR REMARK 3 S11: 0.1036 S12: -0.0354 S13: 0.1369 REMARK 3 S21: -0.0869 S22: -0.0989 S23: 0.0519 REMARK 3 S31: -0.3586 S32: 0.1926 S33: 0.2743 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 5ET3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-NOV-15. REMARK 100 THE DEPOSITION ID IS D_1000215326. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7537 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.670 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 (%) : 95.9 REMARK 200 DATA REDUNDANCY : 16.30 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 11.30 REMARK 200 R MERGE FOR SHELL (I) : 0.18800 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: 3S0R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE 2 UL DROP CONSISTED OF A 1:1 V/V REMARK 280 MIXTURE OF 8 MG/ML COMPLEX SOLUTION IN 25 MM TRIS PH 8.0 AND REMARK 280 RESERVOIR SOLUTION CONSISTING OF 0.2 M AMMONIUM ACETATE, 0.1 M REMARK 280 SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.6, 30% W/V POLYETHYLENE REMARK 280 GLYCOL 4,000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 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 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 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 44.52467 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 22.26233 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 44.52467 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 22.26233 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 72.99728 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 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 O HOH B 114 O HOH B 115 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 60C A 101 DBREF 5ET3 A 1 30 PDB 5ET3 5ET3 1 30 DBREF 5ET3 B 1 30 PDB 5ET3 5ET3 1 30 SEQRES 1 A 30 ALA GLU ALA GLU SER ALA LEU GLU TYR ALA GLN GLN ALA SEQRES 2 A 30 LEU GLU LYS ALA GLN LEU ALA LEU GLN ALA ALA ARG GLN SEQRES 3 A 30 ALA LEU LYS ALA SEQRES 1 B 30 ALA GLU ALA GLU SER ALA LEU GLU TYR ALA GLN GLN ALA SEQRES 2 B 30 LEU GLU LYS ALA GLN LEU ALA LEU GLN ALA ALA ARG GLN SEQRES 3 B 30 ALA LEU LYS ALA HET 60C A 101 60 HETNAM 60C (C_{60}-I_{H})[5,6]FULLERENE HETSYN 60C BUCKMINSTERFULLERENE, BUCKYBALL FORMUL 3 60C C60 FORMUL 4 HOH *29(H2 O) HELIX 1 AA1 ALA A 1 ALA A 30 1 30 HELIX 2 AA2 GLU B 2 ALA B 30 1 29 SITE 1 AC1 8 SER A 5 ALA A 6 TYR A 9 LEU A 19 SITE 2 AC1 8 ALA B 6 TYR B 9 LEU B 19 ALA B 23 CRYST1 42.145 42.145 66.787 90.00 90.00 120.00 P 62 12 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 0.023728 0.013699 0.000000 0.00000 SCALE2 0.000000 0.027398 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014973 0.00000