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 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 MASTER 242 0 0 4 0 0 0 6 0 0 0 12 END