HEADER DE NOVO PROTEIN 13-MAY-11 3S0R TITLE CRYSTAL STRUCTURE OF DE NOVO DESIGNED HELICAL ASSEMBLY PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGNED HELICAL ASSEMBLY; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HEXCOIL-ALA HELICAL ASSEMBLY; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: ARTIFICIAL GENE; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS INTERACTS WITH SINGLE WALLED NANOTUBE (SWNT), DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.ACHARYA,G.GRIGORYAN,Y.H.KIM,W.F.DEGRADO REVDAT 4 03-APR-24 3S0R 1 REMARK REVDAT 3 28-FEB-24 3S0R 1 REMARK REVDAT 2 17-AUG-11 3S0R 1 SOURCE VERSN REVDAT 1 15-JUN-11 3S0R 0 JRNL AUTH G.GRIGORYAN,Y.H.KIM,R.ACHARYA,K.AXELROD,R.M.JAIN,L.WILLIS, JRNL AUTH 2 M.DRNDIC,J.M.KIKKAWA,W.F.DEGRADO JRNL TITL COMPUTATIONAL DESIGN OF VIRUS-LIKE PROTEIN ASSEMBLIES ON JRNL TITL 2 CARBON NANOTUBE SURFACES. JRNL REF SCIENCE V. 332 1071 2011 JRNL REFN ISSN 0036-8075 JRNL PMID 21617073 JRNL DOI 10.1126/SCIENCE.1198841 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) 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 : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.070 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 3479 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.253 REMARK 3 R VALUE (WORKING SET) : 0.247 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.030 REMARK 3 FREE R VALUE TEST SET COUNT : 314 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 13.7564 - 3.0900 0.91 1585 156 0.2430 0.2859 REMARK 3 2 3.0900 - 2.4572 0.91 1556 158 0.2594 0.2676 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 : 0.50 REMARK 3 B_SOL : 78.95 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.26330 REMARK 3 B22 (A**2) : 2.26330 REMARK 3 B33 (A**2) : -4.52660 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: 0.4990 REMARK 3 OPERATOR: H,-K,-L REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 446 REMARK 3 ANGLE : 1.155 598 REMARK 3 CHIRALITY : 0.059 70 REMARK 3 PLANARITY : 0.003 80 REMARK 3 DIHEDRAL : 20.094 164 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 3S0R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAY-11. REMARK 100 THE DEPOSITION ID IS D_1000065615. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3479 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.440 REMARK 200 RESOLUTION RANGE LOW (A) : 18.888 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.5 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.16800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 10.80 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: 30-RESIDUE POLYALANINE ALPHA HELIX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE 2 UL DROP CONSISTED OF A 1:1 V/V REMARK 280 MIXTURE OF 5 MG/ML PROTEIN SOLUTION (IN 20 MM SODIUM PHOSPHATE, REMARK 280 PH 7.5, 100 MM NACL) AND RESERVOIR SOLUTION (75 MM HEPES SODIUM, REMARK 280 PH 7.5, 0.6 M SODIUM PHOSPHATE MONOBASIC MONOHYDRATE, 0.6 M REMARK 280 POTASSIUM PHOSPHATE MONOBASIC, 25% V/V GLYCEROL) , VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 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 22.76450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 22.76450 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.64650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 22.76450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 23.32325 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 22.76450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 69.96975 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 22.76450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 22.76450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 46.64650 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 22.76450 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 69.96975 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 22.76450 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 23.32325 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: 5020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 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 45.52900 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 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 GLU B 2 -80.68 -38.34 REMARK 500 REMARK 500 REMARK: NULL DBREF 3S0R A 1 30 PDB 3S0R 3S0R 1 30 DBREF 3S0R B 1 30 PDB 3S0R 3S0R 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 FORMUL 3 HOH *18(H2 O) HELIX 1 1 GLU A 2 ALA A 30 1 29 HELIX 2 2 ALA B 1 LYS B 29 1 29 CRYST1 45.529 45.529 93.293 90.00 90.00 90.00 I 41 16 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 0.021964 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021964 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010719 0.00000