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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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