HEADER DE NOVO PROTEIN 11-JUN-14 4TQL TITLE COMPUTATIONALLY DESIGNED THREE HELIX BUNDLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THREE HELIX BUNDLE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HELICAL BUNDLE, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.L.NANNENGA,G.OBERDORFER,F.DIMAIO,D.BAKER,T.GONEN REVDAT 5 27-DEC-23 4TQL 1 REMARK REVDAT 4 06-SEP-17 4TQL 1 REMARK REVDAT 3 26-AUG-15 4TQL 1 REMARK REVDAT 2 05-NOV-14 4TQL 1 JRNL REVDAT 1 15-OCT-14 4TQL 0 JRNL AUTH P.S.HUANG,G.OBERDORFER,C.XU,X.Y.PEI,B.L.NANNENGA,J.M.ROGERS, JRNL AUTH 2 F.DIMAIO,T.GONEN,B.LUISI,D.BAKER JRNL TITL HIGH THERMODYNAMIC STABILITY OF PARAMETRICALLY DESIGNED JRNL TITL 2 HELICAL BUNDLES. JRNL REF SCIENCE V. 346 481 2014 JRNL REFN ESSN 1095-9203 JRNL PMID 25342806 JRNL DOI 10.1126/SCIENCE.1257481 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 12173 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.264 REMARK 3 FREE R VALUE : 0.310 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.450 REMARK 3 FREE R VALUE TEST SET COUNT : 663 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 20.5728 - 4.4395 0.92 2965 150 0.3093 0.3463 REMARK 3 2 4.4395 - 3.5295 0.92 2934 149 0.2151 0.2535 REMARK 3 3 3.5295 - 3.0851 0.88 2811 151 0.2294 0.3178 REMARK 3 4 3.0851 - 2.8000 0.86 2776 168 0.2422 0.3040 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.010 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) : 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: 0.5000 REMARK 3 OPERATOR: -H,K,-K-L REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.013 3886 REMARK 3 ANGLE : 1.569 5084 REMARK 3 CHIRALITY : 0.064 564 REMARK 3 PLANARITY : 0.006 623 REMARK 3 DIHEDRAL : 19.094 1736 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 4TQL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000202085. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999 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 : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12173 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3000 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: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS HCL, 30% JEFFAMINE M-600, REMARK 280 PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 ASN A 1 REMARK 465 GLU A 2 REMARK 465 ASP A 3 REMARK 465 ASP A 4 REMARK 465 MET A 5 REMARK 465 LYS A 6 REMARK 465 LYS A 7 REMARK 465 LEU A 8 REMARK 465 GLY A 160 REMARK 465 ASP A 161 REMARK 465 LEU A 240 REMARK 465 GLU A 241 REMARK 465 HIS A 242 REMARK 465 HIS A 243 REMARK 465 HIS A 244 REMARK 465 HIS A 245 REMARK 465 HIS A 246 REMARK 465 HIS A 247 REMARK 465 ASN B 1 REMARK 465 GLU B 2 REMARK 465 ASP B 3 REMARK 465 ASP B 4 REMARK 465 LEU B 240 REMARK 465 GLU B 241 REMARK 465 HIS B 242 REMARK 465 HIS B 243 REMARK 465 HIS B 244 REMARK 465 HIS B 245 REMARK 465 HIS B 246 REMARK 465 HIS B 247 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP B 159 CG OD1 OD2 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 LYS B 167 ND2 ASN B 171 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 82 143.00 137.60 REMARK 500 LYS A 157 -75.94 -102.92 REMARK 500 ARG A 203 -9.27 -57.92 REMARK 500 LYS B 157 -76.30 -105.60 REMARK 500 ASP B 161 103.13 -171.58 REMARK 500 REMARK 500 REMARK: NULL DBREF 4TQL A 1 247 PDB 4TQL 4TQL 1 247 DBREF 4TQL B 1 247 PDB 4TQL 4TQL 1 247 SEQRES 1 A 247 ASN GLU ASP ASP MET LYS LYS LEU TYR LYS GLN MET VAL SEQRES 2 A 247 GLN GLU LEU GLU LYS ALA ARG ASP ARG MET GLU LYS LEU SEQRES 3 A 247 TYR LYS GLU MET VAL GLU LEU ILE GLN LYS ALA ILE GLU SEQRES 4 A 247 LEU MET ARG LYS ILE PHE GLN GLU VAL LYS GLN GLU VAL SEQRES 5 A 247 GLU LYS ALA ILE GLU GLU MET LYS LYS LEU TYR ASP GLU SEQRES 6 A 247 ALA LYS LYS LYS ILE GLU GLN MET ILE GLN GLN ILE LYS SEQRES 7 A 247 GLN GLY GLY ASP LYS GLN LYS MET GLU GLU LEU LEU LYS SEQRES 8 A 247 ARG ALA LYS GLU GLU MET LYS LYS VAL LYS ASP LYS MET SEQRES 9 A 247 GLU LYS LEU LEU GLU LYS LEU LYS GLN ILE MET GLN GLU SEQRES 10 A 247 ALA LYS GLN LYS MET GLU LYS LEU LEU LYS GLN LEU LYS SEQRES 11 A 247 GLU GLU MET LYS LYS MET LYS GLU LYS MET GLU LYS LEU SEQRES 12 A 247 LEU LYS GLU MET LYS GLN ARG MET GLU GLU VAL LYS LYS SEQRES 13 A 247 LYS MET ASP GLY ASP ASP GLU LEU LEU GLU LYS ILE LYS SEQRES 14 A 247 LYS ASN ILE ASP ASP LEU LYS LYS ILE ALA GLU ASP LEU SEQRES 15 A 247 ILE LYS LYS ALA GLU GLU ASN ILE LYS GLU ALA LYS LYS SEQRES 16 A 247 ILE ALA GLU GLN LEU VAL LYS ARG ALA LYS GLN LEU ILE SEQRES 17 A 247 GLU LYS ALA LYS GLN VAL ALA GLU GLU LEU ILE LYS LYS SEQRES 18 A 247 ILE LEU GLN LEU ILE GLU LYS ALA LYS GLU ILE ALA GLU SEQRES 19 A 247 LYS VAL LEU LYS GLY LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 247 ASN GLU ASP ASP MET LYS LYS LEU TYR LYS GLN MET VAL SEQRES 2 B 247 GLN GLU LEU GLU LYS ALA ARG ASP ARG MET GLU LYS LEU SEQRES 3 B 247 TYR LYS GLU MET VAL GLU LEU ILE GLN LYS ALA ILE GLU SEQRES 4 B 247 LEU MET ARG LYS ILE PHE GLN GLU VAL LYS GLN GLU VAL SEQRES 5 B 247 GLU LYS ALA ILE GLU GLU MET LYS LYS LEU TYR ASP GLU SEQRES 6 B 247 ALA LYS LYS LYS ILE GLU GLN MET ILE GLN GLN ILE LYS SEQRES 7 B 247 GLN GLY GLY ASP LYS GLN LYS MET GLU GLU LEU LEU LYS SEQRES 8 B 247 ARG ALA LYS GLU GLU MET LYS LYS VAL LYS ASP LYS MET SEQRES 9 B 247 GLU LYS LEU LEU GLU LYS LEU LYS GLN ILE MET GLN GLU SEQRES 10 B 247 ALA LYS GLN LYS MET GLU LYS LEU LEU LYS GLN LEU LYS SEQRES 11 B 247 GLU GLU MET LYS LYS MET LYS GLU LYS MET GLU LYS LEU SEQRES 12 B 247 LEU LYS GLU MET LYS GLN ARG MET GLU GLU VAL LYS LYS SEQRES 13 B 247 LYS MET ASP GLY ASP ASP GLU LEU LEU GLU LYS ILE LYS SEQRES 14 B 247 LYS ASN ILE ASP ASP LEU LYS LYS ILE ALA GLU ASP LEU SEQRES 15 B 247 ILE LYS LYS ALA GLU GLU ASN ILE LYS GLU ALA LYS LYS SEQRES 16 B 247 ILE ALA GLU GLN LEU VAL LYS ARG ALA LYS GLN LEU ILE SEQRES 17 B 247 GLU LYS ALA LYS GLN VAL ALA GLU GLU LEU ILE LYS LYS SEQRES 18 B 247 ILE LEU GLN LEU ILE GLU LYS ALA LYS GLU ILE ALA GLU SEQRES 19 B 247 LYS VAL LEU LYS GLY LEU GLU HIS HIS HIS HIS HIS HIS FORMUL 3 HOH *7(H2 O) HELIX 1 AA1 TYR A 9 MET A 12 5 4 HELIX 2 AA2 VAL A 13 GLN A 79 1 67 HELIX 3 AA3 ASP A 82 LYS A 157 1 76 HELIX 4 AA4 GLU A 163 LYS A 169 1 7 HELIX 5 AA5 ASP A 173 GLY A 239 1 67 HELIX 6 AA6 LYS B 6 GLN B 79 1 74 HELIX 7 AA7 ASP B 82 LYS B 157 1 76 HELIX 8 AA8 LEU B 164 LYS B 169 1 6 HELIX 9 AA9 ASP B 173 GLY B 239 1 67 CRYST1 24.877 41.547 133.202 98.94 92.25 90.06 P 1 2 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 0.040198 0.000042 0.001605 0.00000 SCALE2 0.000000 0.024069 0.003790 0.00000 SCALE3 0.000000 0.000000 0.007606 0.00000