HEADER DE NOVO PROTEIN 13-JUL-12 4G3B TITLE CRYSTAL STRUCTURE OF THE DE NOVO DESIGNED FLUORINATED PEPTIDE TITLE 2 ALPHA4F3D COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA4F3D; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHESIZED KEYWDS ALPHA HELIX, DE NOVO DESIGNED, FLUORINATED PROTEIN, COILED-COIL, DE KEYWDS 2 NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.C.BUER,J.L.MEAGHER,J.A.STUCKEY,E.N.G.MARSH REVDAT 3 15-NOV-17 4G3B 1 REMARK REVDAT 2 21-NOV-12 4G3B 1 JRNL REVDAT 1 31-OCT-12 4G3B 0 JRNL AUTH B.C.BUER,J.L.MEAGHER,J.A.STUCKEY,E.N.MARSH JRNL TITL COMPARISON OF THE STRUCTURES AND STABILITIES OF COILED-COIL JRNL TITL 2 PROTEINS CONTAINING HEXAFLUOROLEUCINE AND T-BUTYLALANINE JRNL TITL 3 PROVIDES INSIGHT INTO THE STABILIZING EFFECTS OF HIGHLY JRNL TITL 4 FLUORINATED AMINO ACID SIDE-CHAINS. JRNL REF PROTEIN SCI. V. 21 1705 2012 JRNL REFN ISSN 0961-8368 JRNL PMID 22930450 JRNL DOI 10.1002/PRO.2150 REMARK 2 REMARK 2 RESOLUTION. 1.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER-TNT BUSTER 2.8.0 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 11.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 16392 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 831 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.19 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.27 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2857 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.1388 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2696 REMARK 3 BIN R VALUE (WORKING SET) : 0.1376 REMARK 3 BIN FREE R VALUE : 0.1587 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.64 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 161 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 482 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 49 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.50630 REMARK 3 B22 (A**2) : 1.01220 REMARK 3 B33 (A**2) : 0.49400 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.127 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 520 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 717 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 193 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 18 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 68 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 520 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 12 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 46 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 575 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.08 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.27 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 12.40 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|1 - A|26 } REMARK 3 ORIGIN FOR THE GROUP (A): -8.0006 -0.6372 14.9524 REMARK 3 T TENSOR REMARK 3 T11: -0.0256 T22: -0.0330 REMARK 3 T33: -0.0044 T12: 0.0043 REMARK 3 T13: -0.0040 T23: 0.0044 REMARK 3 L TENSOR REMARK 3 L11: 1.3839 L22: 2.3805 REMARK 3 L33: 3.1191 L12: -0.0467 REMARK 3 L13: 0.1573 L23: -1.3718 REMARK 3 S TENSOR REMARK 3 S11: -0.0067 S12: 0.0666 S13: 0.0591 REMARK 3 S21: -0.0726 S22: -0.0439 S23: -0.0590 REMARK 3 S31: 0.0042 S32: 0.0884 S33: 0.0506 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|1 - B|26 } REMARK 3 ORIGIN FOR THE GROUP (A): -14.8816 -7.2778 17.4940 REMARK 3 T TENSOR REMARK 3 T11: -0.0234 T22: -0.0278 REMARK 3 T33: -0.0005 T12: 0.0044 REMARK 3 T13: 0.0003 T23: -0.0065 REMARK 3 L TENSOR REMARK 3 L11: 1.3224 L22: 1.2428 REMARK 3 L33: 4.1336 L12: 0.3657 REMARK 3 L13: -0.6992 L23: -0.3640 REMARK 3 S TENSOR REMARK 3 S11: -0.0159 S12: 0.0531 S13: -0.0121 REMARK 3 S21: -0.0365 S22: -0.0183 S23: 0.0126 REMARK 3 S31: 0.0946 S32: -0.0103 S33: 0.0342 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4G3B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000073684. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : DIAMOND [111] REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16392 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.190 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 (%) : 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 55% PEG400, 0.1M TRIS PH 7.8, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293.15K 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 15.40950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.62550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.40950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.62550 REMARK 290 SMTRY3 4 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A TETRAMER GENERATED FROM THE REMARK 300 DIMER IN THE ASYMMETRIC UNIT BY THE OPERATIONSI: -X-1, -Y, Z 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 APPLY THE FOLLOWING TO CHAINS: A, 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 -1.000000 0.000000 0.000000 -30.81900 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 LYS A 23 CE NZ 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 N GLY B 1 C ACE B 101 1.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACE B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3TWE RELATED DB: PDB REMARK 900 RELATED ID: 3TWF RELATED DB: PDB REMARK 900 RELATED ID: 3TWG RELATED DB: PDB REMARK 900 RELATED ID: 4G4L RELATED DB: PDB REMARK 900 RELATED ID: 4G4M RELATED DB: PDB DBREF 4G3B A 1 26 PDB 4G3B 4G3B 1 26 DBREF 4G3B B 1 26 PDB 4G3B 4G3B 1 26 SEQRES 1 A 26 GLY ASN ALA ASP GLU 6FL TYR LYS GLU LEU GLU ASP 6FL SEQRES 2 A 26 GLN GLU ARG LEU ARG LYS 6FL ARG LYS LYS LEU ARG SER SEQRES 1 B 26 GLY ASN ALA ASP GLU 6FL TYR LYS GLU LEU GLU ASP 6FL SEQRES 2 B 26 GLN GLU ARG LEU ARG LYS 6FL ARG LYS LYS LEU ARG SER HET 6FL A 6 14 HET 6FL A 13 14 HET 6FL A 20 14 HET 6FL B 6 28 HET 6FL B 13 14 HET 6FL B 20 14 HET ACE B 101 3 HETNAM 6FL 5,5,5,5',5',5'-HEXAFLUORO-L-LEUCINE HETNAM ACE ACETYL GROUP FORMUL 1 6FL 6(C6 H7 F6 N O2) FORMUL 3 ACE C2 H4 O FORMUL 4 HOH *49(H2 O) HELIX 1 1 ASN A 2 SER A 26 1 25 HELIX 2 2 ASN B 2 SER B 26 1 25 LINK C GLU A 5 N 6FL A 6 1555 1555 1.34 LINK C 6FL A 6 N TYR A 7 1555 1555 1.32 LINK C ASP A 12 N 6FL A 13 1555 1555 1.34 LINK C 6FL A 13 N GLN A 14 1555 1555 1.34 LINK C ALYS A 19 N 6FL A 20 1555 1555 1.33 LINK C BLYS A 19 N 6FL A 20 1555 1555 1.34 LINK C 6FL A 20 N ARG A 21 1555 1555 1.34 LINK C GLU B 5 N A6FL B 6 1555 1555 1.32 LINK C GLU B 5 N B6FL B 6 1555 1555 1.35 LINK C A6FL B 6 N TYR B 7 1555 1555 1.35 LINK C B6FL B 6 N TYR B 7 1555 1555 1.32 LINK C ASP B 12 N 6FL B 13 1555 1555 1.34 LINK C 6FL B 13 N GLN B 14 1555 1555 1.33 LINK C LYS B 19 N 6FL B 20 1555 1555 1.34 LINK C 6FL B 20 N ARG B 21 1555 1555 1.34 SITE 1 AC1 7 ASN A 2 TYR A 7 GLY B 1 ASN B 2 SITE 2 AC1 7 LYS B 22 ARG B 25 HOH B 223 CRYST1 30.819 39.251 41.233 90.00 90.00 90.00 P 21 21 2 8 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 0.032448 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025477 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024252 0.00000