HEADER DE NOVO PROTEIN 17-MAR-11 3R4A TITLE CRYSTAL STRUCTURE OF THE 4-HELIX COILED COIL CC-TET COMPND MOL_ID: 1; COMPND 2 MOLECULE: COILED COIL HELIX CC-TET; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 OTHER_DETAILS: PEPTIDE SYNTHESIS WAS CARRIED OUT ACCORDING TO SOURCE 6 STANDARD FMOC SPPS PROTOCOLS KEYWDS COILED COIL DOMAIN, TETRAMER, KIH INTERACTIONS, SYNTHETIC BIOLOGY, DE KEYWDS 2 NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.R.ZACCAI,B.H.C.CHI,D.N.WOOLFSON,R.L.BRADY REVDAT 5 13-SEP-23 3R4A 1 REMARK REVDAT 4 17-JUL-19 3R4A 1 SOURCE REMARK REVDAT 3 25-OCT-17 3R4A 1 REMARK REVDAT 2 30-NOV-11 3R4A 1 JRNL REVDAT 1 16-NOV-11 3R4A 0 JRNL AUTH N.R.ZACCAI,B.CHI,A.R.THOMSON,A.L.BOYLE,G.J.BARTLETT, JRNL AUTH 2 M.BRUNING,N.LINDEN,R.B.SESSIONS,P.J.BOOTH,R.L.BRADY, JRNL AUTH 3 D.N.WOOLFSON JRNL TITL A DE NOVO PEPTIDE HEXAMER WITH A MUTABLE CHANNEL. JRNL REF NAT.CHEM.BIOL. V. 7 935 2011 JRNL REFN ISSN 1552-4450 JRNL PMID 22037471 JRNL DOI 10.1038/NCHEMBIO.692 REMARK 2 REMARK 2 RESOLUTION. 2.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7_650 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) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 7271 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 362 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 22.8201 - 2.9841 1.00 2445 121 0.2142 0.2468 REMARK 3 2 2.9841 - 2.3693 0.98 2281 127 0.1962 0.3031 REMARK 3 3 2.3693 - 2.0701 0.94 2183 114 0.2144 0.2923 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 36.02 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.610 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.10440 REMARK 3 B22 (A**2) : 8.98860 REMARK 3 B33 (A**2) : -9.09290 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: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 887 REMARK 3 ANGLE : 0.773 1182 REMARK 3 CHIRALITY : 0.043 143 REMARK 3 PLANARITY : 0.003 140 REMARK 3 DIHEDRAL : 18.106 334 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 3R4A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAR-11. REMARK 100 THE DEPOSITION ID IS D_1000064470. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-AUG-09 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 : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7490 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.070 REMARK 200 RESOLUTION RANGE LOW (A) : 41.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.62400 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 REMARK 200 STARTING MODEL: PDB ENTRY 3R4H WITH IODOPHENYL GROUPS CHANGED TO REMARK 200 TYROSINE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M LITHIUM SULFATE, 0.1M TRIS PH REMARK 280 8.5, 1.26M AMMONIUM SULFATE, SUPPLEMENTED WITH 25% GLYCEROL FOR REMARK 280 CRYO-PROTECTION , VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 1.000000 0.000000 0.000000 22.36500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.45000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 51.53000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 22.36500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.45000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.53000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 22.36500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 25.45000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.53000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 22.36500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 25.45000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 51.53000 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 300 REMARK: TETRAMER CONFIRMED BY ANALYTICAL ULTRACENTRIFUGATION 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: 5000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 ACE A 0 REMARK 465 GLN A 29 REMARK 465 GLY A 30 REMARK 465 ALA A 31 REMARK 465 GLY A 32 REMARK 465 NH2 A 33 REMARK 465 ACE B 0 REMARK 465 ALA B 31 REMARK 465 GLY B 32 REMARK 465 NH2 B 33 REMARK 465 ACE C 0 REMARK 465 ALA C 31 REMARK 465 GLY C 32 REMARK 465 NH2 C 33 REMARK 465 ACE D 0 REMARK 465 GLY D 30 REMARK 465 ALA D 31 REMARK 465 GLY D 32 REMARK 465 NH2 D 33 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3R4H RELATED DB: PDB DBREF 3R4A A 0 33 PDB 3R4A 3R4A 0 33 DBREF 3R4A B 0 33 PDB 3R4A 3R4A 0 33 DBREF 3R4A C 0 33 PDB 3R4A 3R4A 0 33 DBREF 3R4A D 0 33 PDB 3R4A 3R4A 0 33 SEQRES 1 A 34 ACE GLY GLU LEU ALA ALA ILE LYS GLN GLU LEU ALA ALA SEQRES 2 A 34 ILE LYS LYS GLU LEU ALA ALA ILE LYS TRP GLU LEU ALA SEQRES 3 A 34 ALA ILE LYS GLN GLY ALA GLY NH2 SEQRES 1 B 34 ACE GLY GLU LEU ALA ALA ILE LYS GLN GLU LEU ALA ALA SEQRES 2 B 34 ILE LYS LYS GLU LEU ALA ALA ILE LYS TRP GLU LEU ALA SEQRES 3 B 34 ALA ILE LYS GLN GLY ALA GLY NH2 SEQRES 1 C 34 ACE GLY GLU LEU ALA ALA ILE LYS GLN GLU LEU ALA ALA SEQRES 2 C 34 ILE LYS LYS GLU LEU ALA ALA ILE LYS TRP GLU LEU ALA SEQRES 3 C 34 ALA ILE LYS GLN GLY ALA GLY NH2 SEQRES 1 D 34 ACE GLY GLU LEU ALA ALA ILE LYS GLN GLU LEU ALA ALA SEQRES 2 D 34 ILE LYS LYS GLU LEU ALA ALA ILE LYS TRP GLU LEU ALA SEQRES 3 D 34 ALA ILE LYS GLN GLY ALA GLY NH2 FORMUL 5 HOH *63(H2 O) HELIX 1 1 GLY A 1 ALA A 26 1 26 HELIX 2 2 GLY B 1 GLY B 30 1 30 HELIX 3 3 GLU C 2 GLN C 29 1 28 HELIX 4 4 GLU D 2 GLN D 29 1 28 CISPEP 1 GLY D 1 GLU D 2 0 8.43 CRYST1 44.730 50.900 103.060 90.00 90.00 90.00 I 2 2 2 32 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 0.022356 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019646 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009703 0.00000