PDB Short entry for 1QP6 HEADER DE NOVO PROTEIN 01-JUN-99 1QP6 TITLE SOLUTION STRUCTURE OF ALPHA2D COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (ALPHA2D); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THIS SEQUENCE SOURCE 4 WAS DESIGNED TO FOLD INTO A HELIX-TURN-HELIX PEPTIDE THAT DIMERIZES SOURCE 5 TO FORM A FOUR-HELIX BUNDLE. KEYWDS DE NOVO DESIGN, PROTEIN DESIGN, PROTEIN FOLDING, BISECTING U MOTIF, KEYWDS 2 FOUR-HELIX BUNDLE, HELIX-TURN-HELIX, DE NOVO PROTEIN EXPDTA SOLUTION NMR NUMMDL 16 AUTHOR R.B.HILL,W.F.DEGRADO REVDAT 3 02-MAR-22 1QP6 1 REMARK REVDAT 2 24-FEB-09 1QP6 1 VERSN REVDAT 1 09-JUN-99 1QP6 0 JRNL AUTH R.B.HILL,W.F.DEGRADO JRNL TITL SOLUTION STRUCTURE OF ALPHA2D, A NATIVELIKE DE NOVO DESIGNED JRNL TITL 2 PROTEIN JRNL REF J.AM.CHEM.SOC. V. 120 1138 1998 JRNL REFN ISSN 0002-7863 JRNL DOI 10.1021/JA9733649 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.P.RALEIGH,S.F.BETZ,W.F.DEGRADO REMARK 1 TITL A DE NOVO DESIGNED PROTEIN MIMICS THE NATIVE STATE OF REMARK 1 TITL 2 NATURAL PROTEINS REMARK 1 REF J.AM.CHEM.SOC. V. 117 7558 1995 REMARK 1 REFN ISSN 0002-7863 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 STRUCTURE BASED ON 834 RESTRAINTS: 140 LONG-RANGE RESTRAINTS, 30 REMARK 3 PHI ANGLE REMARK 3 RESTRAINTS, AND 14 CHI-1 ANGLE RESTRAINTS. 83 OF THE LONG-RANGE REMARK 3 NOES (59%) REMARK 3 WERE DETERMINED TO ARISE FROM INTER-MONOMER CORRELATIONS BY REMARK 3 COMPUTATIONAL REMARK 3 METHODS. THE OTHER NOES WERE TREATED USING A WEIGHTING FUNCTION REMARK 3 DEVELOPED FOR REMARK 3 SYMMMETRIC HOMODIMERS THAT ALLOWS EACH NOE TO ARISE FROM EITHER AN REMARK 3 INTRA- OR REMARK 3 INTER- MONOMER CORRELATIONS AS DESCRIBED BY NILGES, M. PROTEINS REMARK 3 (1993) 17:297- REMARK 3 309. SYMMETRY TERMS WERE EMPLOYED FOR C-ALPHA CARBONS ONLY. SEE REMARK 3 JACS(1998)120: REMARK 3 1138-1145 FOR MORE DETAILS. REMARK 4 REMARK 4 1QP6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUN-99. REMARK 100 THE DEPOSITION ID IS D_1000009135. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.0 REMARK 210 PH : 7.3 REMARK 210 IONIC STRENGTH : 52 MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2 MM ALPHA2D TRIS, PH 7.3, 25 C REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; E-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.1 REMARK 210 METHOD USED : SIMULATED ANNEALING FOR 48 PS AT REMARK 210 2000K FOLLOWED BY A SLOW COOL TO REMARK 210 50K REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 60 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 16 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 11 REMARK 210 REMARK 210 REMARK: REMARK 210 THE STRUCTURE WAS DETERMINED USING 2D HOMONUCLEAR TECHNIQUES. REMARK 210 BECAUSE ALPHA2D REMARK 210 EXISTS AS A SYMMETRIC HOMODIMER, THERE EXISTS A PROBLEM OF REMARK 210 DETERMINING WHETHER REMARK 210 AN OBSERVED NOE ARISES FROM AN INTER- OR INTRA- MONOMER REMARK 210 CORRELATION. THIS REMARK 210 PROBLEM WAS DEALT WITH AS DESCRIBED REMARK 3. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 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: DIMERIC 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 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 1 GLU A 2 -97.58 -133.01 REMARK 500 1 PRO A 17 -157.17 -78.60 REMARK 500 1 ARG A 18 -175.06 -53.32 REMARK 500 1 ARG A 19 -49.64 -147.60 REMARK 500 1 LYS A 34 -174.06 52.21 REMARK 500 1 GLU B 2 -97.62 -132.99 REMARK 500 1 PRO B 17 -157.16 -78.69 REMARK 500 1 ARG B 18 -174.97 -53.26 REMARK 500 1 ARG B 19 -49.61 -147.67 REMARK 500 1 LYS B 34 -174.17 52.11 REMARK 500 2 PRO A 17 -154.78 -76.43 REMARK 500 2 ARG A 18 -175.06 -53.74 REMARK 500 2 ARG A 19 -41.55 -149.92 REMARK 500 2 LYS A 34 95.38 53.18 REMARK 500 2 PRO B 17 -154.86 -76.29 REMARK 500 2 ARG B 18 -174.99 -53.65 REMARK 500 2 ARG B 19 -41.60 -150.06 REMARK 500 2 LYS B 34 95.46 53.23 REMARK 500 3 PRO A 17 -157.78 -77.31 REMARK 500 3 ARG A 18 177.15 -49.62 REMARK 500 3 ARG A 19 -39.38 -143.95 REMARK 500 3 LYS A 34 88.99 52.15 REMARK 500 3 PRO B 17 -157.82 -77.21 REMARK 500 3 ARG B 18 177.26 -49.60 REMARK 500 3 ARG B 19 -39.30 -144.05 REMARK 500 3 LYS B 34 88.95 52.12 REMARK 500 4 LYS A 15 74.55 -102.23 REMARK 500 4 PRO A 17 -159.13 -77.08 REMARK 500 4 ARG A 18 171.80 -47.91 REMARK 500 4 ARG A 19 -43.22 -139.06 REMARK 500 4 LYS A 34 74.83 54.12 REMARK 500 4 LYS B 15 74.61 -102.51 REMARK 500 4 PRO B 17 -159.08 -77.07 REMARK 500 4 ARG B 18 171.74 -47.82 REMARK 500 4 ARG B 19 -43.25 -139.11 REMARK 500 4 LYS B 34 74.63 54.42 REMARK 500 5 LYS A 15 76.44 -102.56 REMARK 500 5 PRO A 17 -158.21 -77.19 REMARK 500 5 ARG A 18 174.24 -48.82 REMARK 500 5 ARG A 19 -40.04 -139.43 REMARK 500 5 LYS B 15 76.44 -102.52 REMARK 500 5 PRO B 17 -158.16 -77.24 REMARK 500 5 ARG B 18 174.20 -48.88 REMARK 500 5 ARG B 19 -40.09 -139.41 REMARK 500 6 LYS A 15 61.82 -103.35 REMARK 500 6 PRO A 17 -90.47 -74.40 REMARK 500 6 LYS A 34 87.58 55.11 REMARK 500 6 LYS B 15 62.01 -103.26 REMARK 500 6 PRO B 17 -90.43 -74.36 REMARK 500 6 LYS B 34 87.45 55.08 REMARK 500 REMARK 500 THIS ENTRY HAS 138 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 18 0.10 SIDE CHAIN REMARK 500 1 ARG A 19 0.31 SIDE CHAIN REMARK 500 1 ARG B 18 0.10 SIDE CHAIN REMARK 500 1 ARG B 19 0.31 SIDE CHAIN REMARK 500 2 ARG A 18 0.24 SIDE CHAIN REMARK 500 2 ARG A 19 0.31 SIDE CHAIN REMARK 500 2 ARG B 18 0.24 SIDE CHAIN REMARK 500 2 ARG B 19 0.31 SIDE CHAIN REMARK 500 3 ARG A 18 0.27 SIDE CHAIN REMARK 500 3 ARG A 19 0.31 SIDE CHAIN REMARK 500 3 ARG B 18 0.27 SIDE CHAIN REMARK 500 3 ARG B 19 0.31 SIDE CHAIN REMARK 500 4 ARG A 18 0.17 SIDE CHAIN REMARK 500 4 ARG A 19 0.32 SIDE CHAIN REMARK 500 4 ARG B 18 0.17 SIDE CHAIN REMARK 500 4 ARG B 19 0.32 SIDE CHAIN REMARK 500 5 ARG A 18 0.26 SIDE CHAIN REMARK 500 5 ARG A 19 0.30 SIDE CHAIN REMARK 500 5 ARG B 18 0.26 SIDE CHAIN REMARK 500 5 ARG B 19 0.30 SIDE CHAIN REMARK 500 6 ARG A 18 0.23 SIDE CHAIN REMARK 500 6 ARG A 19 0.30 SIDE CHAIN REMARK 500 6 ARG B 18 0.23 SIDE CHAIN REMARK 500 6 ARG B 19 0.30 SIDE CHAIN REMARK 500 7 ARG A 18 0.25 SIDE CHAIN REMARK 500 7 ARG A 19 0.15 SIDE CHAIN REMARK 500 7 ARG B 18 0.25 SIDE CHAIN REMARK 500 7 ARG B 19 0.15 SIDE CHAIN REMARK 500 8 ARG A 18 0.24 SIDE CHAIN REMARK 500 8 ARG A 19 0.30 SIDE CHAIN REMARK 500 8 ARG B 18 0.24 SIDE CHAIN REMARK 500 8 ARG B 19 0.30 SIDE CHAIN REMARK 500 9 ARG A 18 0.26 SIDE CHAIN REMARK 500 9 ARG A 19 0.26 SIDE CHAIN REMARK 500 9 ARG B 18 0.26 SIDE CHAIN REMARK 500 9 ARG B 19 0.26 SIDE CHAIN REMARK 500 10 ARG A 18 0.26 SIDE CHAIN REMARK 500 10 ARG A 19 0.30 SIDE CHAIN REMARK 500 10 ARG B 18 0.26 SIDE CHAIN REMARK 500 10 ARG B 19 0.30 SIDE CHAIN REMARK 500 11 ARG A 18 0.19 SIDE CHAIN REMARK 500 11 ARG A 19 0.22 SIDE CHAIN REMARK 500 11 ARG B 18 0.19 SIDE CHAIN REMARK 500 11 ARG B 19 0.22 SIDE CHAIN REMARK 500 12 ARG A 18 0.32 SIDE CHAIN REMARK 500 12 ARG A 19 0.22 SIDE CHAIN REMARK 500 12 ARG B 18 0.32 SIDE CHAIN REMARK 500 12 ARG B 19 0.22 SIDE CHAIN REMARK 500 13 ARG A 18 0.14 SIDE CHAIN REMARK 500 13 ARG A 19 0.25 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 64 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1QP6 A 1 35 PDB 1QP6 1QP6 1 35 DBREF 1QP6 B 1 35 PDB 1QP6 1QP6 1 35 SEQRES 1 A 35 GLY GLU VAL GLU GLU LEU GLU LYS LYS PHE LYS GLU LEU SEQRES 2 A 35 TRP LYS GLY PRO ARG ARG GLY GLU ILE GLU GLU LEU HIS SEQRES 3 A 35 LYS LYS PHE HIS GLU LEU ILE LYS GLY SEQRES 1 B 35 GLY GLU VAL GLU GLU LEU GLU LYS LYS PHE LYS GLU LEU SEQRES 2 B 35 TRP LYS GLY PRO ARG ARG GLY GLU ILE GLU GLU LEU HIS SEQRES 3 B 35 LYS LYS PHE HIS GLU LEU ILE LYS GLY HELIX 1 1 VAL A 3 LYS A 15 1 13 HELIX 2 2 ARG A 19 LYS A 34 1 16 HELIX 3 3 VAL B 3 LYS B 15 1 13 HELIX 4 4 ARG B 19 LYS B 34 1 16 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000