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 MASTER 288 0 7 2 0 0 2 6 0 0 0 4 END