HEADER DE NOVO PROTEIN 14-JAN-16 5HKN TITLE CRYSTAL STRUCTURE DE NOVO DESIGNED FULLERENE ORGANIZING PROTEIN TITLE 2 COMPLEX WITH FULLERENE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FULLERENE ORGANIZING PROTEIN; 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 FULLERENE PROTEIN COMPLEX, DE NOVO PROTEIN DESIGN, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.PAUL,R.ACHARYA,K.-H.KIM,Y.H.KIM,N.H.KIM,G.GRIGORYAN,W.F.DEGARDO REVDAT 3 08-NOV-23 5HKN 1 REMARK REVDAT 2 01-JAN-20 5HKN 1 JRNL REMARK REVDAT 1 04-MAY-16 5HKN 0 JRNL AUTH K.H.KIM,D.K.KO,Y.T.KIM,N.H.KIM,J.PAUL,S.Q.ZHANG,C.B.MURRAY, JRNL AUTH 2 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. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 3 NUMBER OF REFLECTIONS : 5916 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.180 REMARK 3 FREE R VALUE TEST SET COUNT : 603 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 24.6104 - 3.6593 1.00 1286 154 0.1953 0.2420 REMARK 3 2 3.6593 - 2.9060 1.00 1296 148 0.2043 0.2369 REMARK 3 3 2.9060 - 2.5391 1.00 1295 142 0.1939 0.2015 REMARK 3 4 2.5391 - 2.3071 1.00 1272 147 0.2084 0.2279 REMARK 3 5 2.3071 - 2.1418 0.99 1298 145 0.1835 0.2292 REMARK 3 6 2.1418 - 2.0156 1.00 1286 142 0.2017 0.2809 REMARK 3 7 2.0156 - 1.9147 0.97 1246 148 0.2331 0.2772 REMARK 3 8 1.9147 - 1.8314 0.78 1008 115 0.2407 0.2463 REMARK 3 9 1.8314 - 1.7609 0.49 640 64 0.2815 0.3260 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.260 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 : 0.007 536 REMARK 3 ANGLE : 0.828 778 REMARK 3 CHIRALITY : 0.054 70 REMARK 3 PLANARITY : 0.004 80 REMARK 3 DIHEDRAL : 17.975 166 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 16.4414 -19.6818 3.3308 REMARK 3 T TENSOR REMARK 3 T11: 0.1920 T22: 0.1741 REMARK 3 T33: 0.1823 T12: -0.0224 REMARK 3 T13: 0.0157 T23: 0.0064 REMARK 3 L TENSOR REMARK 3 L11: 0.4948 L22: 0.3439 REMARK 3 L33: 0.2875 L12: -0.2164 REMARK 3 L13: -0.3224 L23: -0.0025 REMARK 3 S TENSOR REMARK 3 S11: 0.0933 S12: -0.0729 S13: 0.0452 REMARK 3 S21: 0.1341 S22: -0.1163 S23: -0.0878 REMARK 3 S31: -0.2803 S32: 0.0663 S33: -0.0031 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 9.591 -11.514 2.671 REMARK 3 T TENSOR REMARK 3 T11: 0.1662 T22: 0.1919 REMARK 3 T33: 0.1772 T12: -0.0034 REMARK 3 T13: -0.0230 T23: -0.0191 REMARK 3 L TENSOR REMARK 3 L11: 0.3308 L22: 0.4115 REMARK 3 L33: 0.1076 L12: 0.1346 REMARK 3 L13: 0.0157 L23: 0.0530 REMARK 3 S TENSOR REMARK 3 S11: 0.0317 S12: 0.1590 S13: 0.0498 REMARK 3 S21: 0.0109 S22: 0.0164 S23: -0.0871 REMARK 3 S31: 0.0282 S32: 0.2574 S33: 0.0004 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 5HKN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1000217135. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JAN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-D REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.542 REMARK 200 MONOCHROMATOR : NI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6255 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 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 (%) : 94.6 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 69.1 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : 0.30900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 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 (%): 53.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M N-(2-ACETAMIDO)IMINODIACETIC REMARK 280 ACID, N-(CARBAMOYLMETHYL)IMINODIACETIC ACID (ADA) BUFFER, PH 6.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 44.82000 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 22.41000 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 44.82000 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 22.41000 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: 5370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 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 20.85500 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -36.12192 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 NE2 GLN A 22 OE1 GLN B 11 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 B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5HKR RELATED DB: PDB DBREF 5HKN A 1 30 PDB 5HKN 5HKN 1 30 DBREF 5HKN B 1 30 PDB 5HKN 5HKN 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 B 101 60 HETNAM 60C (C_{60}-I_{H})[5,6]FULLERENE HETSYN 60C BUCKMINSTERFULLERENE, BUCKYBALL FORMUL 3 60C C60 FORMUL 4 HOH *20(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 12 GLU A 2 SER A 5 ALA A 6 TYR A 9 SITE 2 AC1 12 LEU A 19 ALA A 23 GLU B 2 SER B 5 SITE 3 AC1 12 ALA B 6 TYR B 9 LEU B 19 ALA B 23 CRYST1 41.710 41.710 67.230 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 0.023975 0.013842 0.000000 0.00000 SCALE2 0.000000 0.027684 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014874 0.00000