HEADER DE NOVO PROTEIN 23-SEP-12 4H8O TITLE CRYSTAL STRUCTURE OF A PARALLEL 6-HELIX COILED COIL CC-HEX-N24 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CC-HEX-N24; COMPND 3 CHAIN: A, B, C, D, E, F; 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: STANDARD F-MOC SOLID PHASE PEPTIDE SYNTHESIS KEYWDS CC-HEX, PARALLEL, HEXAMERIC COILED COIL, N-TERMINAL ACETYLATION, C- KEYWDS 2 TERMINAL AMIDATION, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.CHI,N.R.ZACCAI,R.L.BRADY,D.N.WOOLFSON REVDAT 2 20-SEP-23 4H8O 1 LINK REVDAT 1 05-FEB-14 4H8O 0 JRNL AUTH B.CHI,N.R.ZACCAI,R.L.BRADY,D.N.WOOLFSON JRNL TITL TBA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.040 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 50075 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 2501 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 46.2754 - 4.1869 0.99 2737 134 0.2081 0.2326 REMARK 3 2 4.1869 - 3.3235 1.00 2764 156 0.1582 0.1681 REMARK 3 3 3.3235 - 2.9035 1.00 2732 152 0.1745 0.2169 REMARK 3 4 2.9035 - 2.6380 1.00 2743 150 0.1848 0.2499 REMARK 3 5 2.6380 - 2.4490 1.00 2755 128 0.1572 0.2201 REMARK 3 6 2.4490 - 2.3046 0.99 2732 161 0.1682 0.1957 REMARK 3 7 2.3046 - 2.1892 0.98 2740 132 0.1835 0.2582 REMARK 3 8 2.1892 - 2.0939 0.97 2620 139 0.2139 0.2557 REMARK 3 9 2.0939 - 2.0133 0.98 2681 172 0.2169 0.2767 REMARK 3 10 2.0133 - 1.9438 0.96 2669 131 0.2428 0.3072 REMARK 3 11 1.9438 - 1.8830 0.97 2648 139 0.3054 0.3081 REMARK 3 12 1.8830 - 1.8292 0.93 2580 132 0.3290 0.3882 REMARK 3 13 1.8292 - 1.7810 0.94 2602 138 0.3398 0.4019 REMARK 3 14 1.7810 - 1.7376 0.94 2585 138 0.3643 0.3566 REMARK 3 15 1.7376 - 1.6981 0.94 2560 136 0.3797 0.3585 REMARK 3 16 1.6981 - 1.6619 0.92 2611 137 0.4142 0.4367 REMARK 3 17 1.6619 - 1.6287 0.91 2470 107 0.4334 0.4764 REMARK 3 18 1.6287 - 1.5980 0.84 2345 119 0.4469 0.5182 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 : 0.37 REMARK 3 B_SOL : 50.06 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.050 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) : -1.79340 REMARK 3 B22 (A**2) : 1.01090 REMARK 3 B33 (A**2) : 0.78240 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 : 0.016 1363 REMARK 3 ANGLE : 1.465 1812 REMARK 3 CHIRALITY : 0.094 210 REMARK 3 PLANARITY : 0.005 234 REMARK 3 DIHEDRAL : 14.560 522 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 4H8O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000075158. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27487 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.598 REMARK 200 RESOLUTION RANGE LOW (A) : 50.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3R46 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3% D-SORBITOL, 20 MM SODIUM FORMATE, REMARK 280 20 MM AMMONIUM ACETATE, 20 MM TRISODIUM CITRATE, 20 MM SODIUM REMARK 280 POTASSIUM L-TARTRATE, 20 MM SODIUM OXAMATE; 100 MM MES/IMIDAZOLE REMARK 280 PH 6.5; AND 10 % PEG 20K, 20 % PEG MME 550, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 25.44000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.52500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.44000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.52500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -90.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 123 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 125 LIES ON A SPECIAL POSITION. 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 A 139 O HOH F 125 1.85 REMARK 500 O HOH D 140 O HOH F 125 1.98 REMARK 500 O HOH A 125 O HOH F 125 2.12 REMARK 500 O HOH A 125 O HOH F 120 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3R3K RELATED DB: PDB REMARK 900 RELATED ID: 3R46 RELATED DB: PDB REMARK 900 RELATED ID: 3R47 RELATED DB: PDB REMARK 900 RELATED ID: 3R4A RELATED DB: PDB REMARK 900 RELATED ID: 4H7R RELATED DB: PDB REMARK 900 RELATED ID: 4H8F RELATED DB: PDB REMARK 900 RELATED ID: 4H8G RELATED DB: PDB REMARK 900 RELATED ID: 4H8L RELATED DB: PDB REMARK 900 RELATED ID: 4H8M RELATED DB: PDB DBREF 4H8O A 0 31 PDB 4H8O 4H8O 0 31 DBREF 4H8O B 0 31 PDB 4H8O 4H8O 0 31 DBREF 4H8O C 0 31 PDB 4H8O 4H8O 0 31 DBREF 4H8O D 0 31 PDB 4H8O 4H8O 0 31 DBREF 4H8O E 0 31 PDB 4H8O 4H8O 0 31 DBREF 4H8O F 0 31 PDB 4H8O 4H8O 0 31 SEQRES 1 A 32 ACE GLY GLU LEU LYS ALA ILE ALA GLN GLU LEU LYS ALA SEQRES 2 A 32 ILE ALA TYR GLU LEU LYS ALA ILE ALA LYS GLU ASN LYS SEQRES 3 A 32 ALA ILE ALA GLN GLY NH2 SEQRES 1 B 32 ACE GLY GLU LEU LYS ALA ILE ALA GLN GLU LEU LYS ALA SEQRES 2 B 32 ILE ALA TYR GLU LEU LYS ALA ILE ALA LYS GLU ASN LYS SEQRES 3 B 32 ALA ILE ALA GLN GLY NH2 SEQRES 1 C 32 ACE GLY GLU LEU LYS ALA ILE ALA GLN GLU LEU LYS ALA SEQRES 2 C 32 ILE ALA TYR GLU LEU LYS ALA ILE ALA LYS GLU ASN LYS SEQRES 3 C 32 ALA ILE ALA GLN GLY NH2 SEQRES 1 D 32 ACE GLY GLU LEU LYS ALA ILE ALA GLN GLU LEU LYS ALA SEQRES 2 D 32 ILE ALA TYR GLU LEU LYS ALA ILE ALA LYS GLU ASN LYS SEQRES 3 D 32 ALA ILE ALA GLN GLY NH2 SEQRES 1 E 32 ACE GLY GLU LEU LYS ALA ILE ALA GLN GLU LEU LYS ALA SEQRES 2 E 32 ILE ALA TYR GLU LEU LYS ALA ILE ALA LYS GLU ASN LYS SEQRES 3 E 32 ALA ILE ALA GLN GLY NH2 SEQRES 1 F 32 ACE GLY GLU LEU LYS ALA ILE ALA GLN GLU LEU LYS ALA SEQRES 2 F 32 ILE ALA TYR GLU LEU LYS ALA ILE ALA LYS GLU ASN LYS SEQRES 3 F 32 ALA ILE ALA GLN GLY NH2 HET ACE A 0 3 HET NH2 A 31 1 HET ACE B 0 3 HET NH2 B 31 1 HET ACE C 0 3 HET NH2 C 31 1 HET ACE D 0 3 HET NH2 D 31 1 HET ACE E 0 3 HET NH2 E 31 1 HET ACE F 0 3 HET NH2 F 31 1 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP FORMUL 1 ACE 6(C2 H4 O) FORMUL 1 NH2 6(H2 N) FORMUL 7 HOH *219(H2 O) HELIX 1 1 GLY A 1 GLY A 30 1 30 HELIX 2 2 GLY B 1 GLY B 30 1 30 HELIX 3 3 GLY C 1 GLY C 30 1 30 HELIX 4 4 GLY D 1 GLN D 29 1 29 HELIX 5 5 GLY E 1 GLY E 30 1 30 HELIX 6 6 GLY F 1 GLY F 30 1 30 LINK C ACE A 0 N GLY A 1 1555 1555 1.33 LINK C GLY A 30 N NH2 A 31 1555 1555 1.33 LINK C ACE B 0 N GLY B 1 1555 1555 1.33 LINK C GLY B 30 N NH2 B 31 1555 1555 1.33 LINK C ACE C 0 N GLY C 1 1555 1555 1.33 LINK C GLY C 30 N NH2 C 31 1555 1555 1.33 LINK C ACE D 0 N GLY D 1 1555 1555 1.33 LINK C GLY D 30 N NH2 D 31 1555 1555 1.33 LINK C ACE E 0 N GLY E 1 1555 1555 1.33 LINK C GLY E 30 N NH2 E 31 1555 1555 1.33 LINK C ACE F 0 N GLY F 1 1555 1555 1.33 LINK C GLY F 30 N NH2 F 31 1555 1555 1.33 CRYST1 50.880 111.050 35.980 90.00 90.00 90.00 P 21 21 2 24 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 0.019654 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009005 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027793 0.00000 HETATM 1 C ACE A 0 24.081 1.107 21.776 1.00 27.58 C HETATM 2 O ACE A 0 23.744 0.906 20.607 1.00 36.81 O HETATM 3 CH3 ACE A 0 23.369 0.411 22.914 1.00 31.81 C