HEADER DE NOVO PROTEIN 08-MAY-19 6OVS TITLE COILED-COIL TRIMER WITH GLU:TYR:LYS TRIAD COMPND MOL_ID: 1; COMPND 2 MOLECULE: COILED-COIL TRIMER WITH GLU:TYR:LYS TRIAD; 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 TRIMER, HELIX, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.S.SMITH,K.L.STERN,W.M.BILLINGS,J.L.PRICE REVDAT 2 20-MAY-20 6OVS 1 JRNL REVDAT 1 29-APR-20 6OVS 0 JRNL AUTH K.L.STERN,M.S.SMITH,W.M.BILLINGS,T.J.LOFTUS,B.M.CONOVER, JRNL AUTH 2 D.DELLA CORTE,J.L.PRICE JRNL TITL CONTEXT-DEPENDENT STABILIZING INTERACTIONS AMONG JRNL TITL 2 SOLVENT-EXPOSED RESIDUES ALONG THE SURFACE OF A TRIMERIC JRNL TITL 3 HELIX BUNDLE. JRNL REF BIOCHEMISTRY V. 59 1672 2020 JRNL REFN ISSN 0006-2960 JRNL PMID 32270676 JRNL DOI 10.1021/ACS.BIOCHEM.0C00045 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_2906 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 5310 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.710 REMARK 3 FREE R VALUE TEST SET COUNT : 1001 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 20.1205 - 3.4389 0.99 1362 155 0.1510 0.1574 REMARK 3 2 3.4389 - 2.7317 1.00 1374 142 0.1457 0.1646 REMARK 3 3 2.7317 - 2.3870 1.00 1402 130 0.1403 0.1742 REMARK 3 4 2.3870 - 2.1691 0.98 1341 148 0.1230 0.1792 REMARK 3 5 2.1691 - 2.0138 0.96 1284 152 0.1354 0.1811 REMARK 3 6 2.0138 - 1.8951 0.94 1331 129 0.1565 0.1948 REMARK 3 7 1.8951 - 1.8003 0.91 1210 145 0.1969 0.2326 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.390 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.88 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6OVS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1000241398. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-AUG-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 : ENRAF-NONIUS FR591 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5406 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : APEX II CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROTEUM PLUS REMARK 200 DATA SCALING SOFTWARE : PROTEUM PLUS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5310 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 16.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.87 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.31800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG600, 10% GLYCEROL, 100 MM HEPES REMARK 280 -NAOH, PH 7.5, 50 MM LITHIUM SULFATE, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.63300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 11.33512 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 33.27433 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 19.63300 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 11.33512 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 33.27433 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 19.63300 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 11.33512 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 33.27433 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 22.67024 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 66.54867 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 22.67024 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 66.54867 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 22.67024 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 66.54867 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 -0.500000 -0.866025 0.000000 19.63300 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -34.00535 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 39.26600 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 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 A 144 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 119 O HOH A 140 1.92 REMARK 500 OE1 GLU A 1 O HOH A 101 1.94 REMARK 500 O HOH B 238 O HOH B 243 2.07 REMARK 500 NH2 ARG B 33 O HOH B 201 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 247 O HOH B 253 5445 1.89 REMARK 500 O HOH B 235 O HOH B 236 9544 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 1PE B 101 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 1PE B 101 DBREF 6OVS A 0 33 PDB 6OVS 6OVS 0 33 DBREF 6OVS B 0 33 PDB 6OVS 6OVS 0 33 SEQRES 1 A 34 ACE GLU VAL GLU ALA LEU GLU LYS LYS VAL GLU ALA LEU SEQRES 2 A 34 GLU TYR LYS VAL GLN LYS LEU GLU LYS LYS VAL GLU ALA SEQRES 3 A 34 LEU GLU HIS GLY TRP ASP GLY ARG SEQRES 1 B 34 ACE GLU VAL GLU ALA LEU GLU LYS LYS VAL GLU ALA LEU SEQRES 2 B 34 GLU TYR LYS VAL GLN LYS LEU GLU LYS LYS VAL GLU ALA SEQRES 3 B 34 LEU GLU HIS GLY TRP ASP GLY ARG HET ACE A 0 6 HET ACE B 0 6 HET 1PE B 101 25 HETNAM ACE ACETYL GROUP HETNAM 1PE PENTAETHYLENE GLYCOL HETSYN 1PE PEG400 FORMUL 1 ACE 2(C2 H4 O) FORMUL 3 1PE C10 H22 O6 FORMUL 4 HOH *99(H2 O) HELIX 1 AA1 GLU A 1 GLY A 29 1 29 HELIX 2 AA2 TRP A 30 ARG A 33 5 4 HELIX 3 AA3 GLU B 1 GLY B 29 1 29 HELIX 4 AA4 TRP B 30 ARG B 33 5 4 LINK C ACE A 0 N GLU A 1 1555 1555 1.34 LINK C ACE B 0 N GLU B 1 1555 1555 1.34 SITE 1 AC1 2 LYS B 15 HOH B 211 CRYST1 39.266 39.266 99.823 90.00 90.00 120.00 H 3 18 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 0.025467 0.014704 0.000000 0.00000 SCALE2 0.000000 0.029407 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010018 0.00000 HETATM 1 C ACE A 0 12.751 -15.500 -32.159 1.00 21.37 C HETATM 2 O ACE A 0 12.412 -15.397 -30.967 1.00 18.19 O HETATM 3 CH3 ACE A 0 11.755 -15.381 -33.278 1.00 20.04 C HETATM 4 H1 ACE A 0 11.978 -14.498 -33.874 1.00 24.07 H HETATM 5 H2 ACE A 0 11.809 -16.266 -33.912 1.00 24.07 H HETATM 6 H3 ACE A 0 10.751 -15.305 -32.864 1.00 24.07 H