HEADER DE NOVO PROTEIN 25-FEB-05 1YYX TITLE THE SOLUTION STRUCTURE OF A REDESIGNED APOCYTOCHROME B562 TITLE 2 (RD-APOCYT B562) AT 2.8M UREA COMPND MOL_ID: 1; COMPND 2 MOLECULE: REDESIGNED APO-CYTOCHROME B562; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SOURCE 4 SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS SOURCE 5 (HUMAN). KEYWDS RD-APOCYT B562, INTERMEDIATES, HYDROPHOBIC INTERACTIONS, KEYWDS 2 STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE INITIATIVE, KEYWDS 3 BERKELEY STRUCTURAL GENOMICS CENTER, BSGC, DE NOVO PROTEIN EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR H.FENG,N.VU,Y.BAI,BERKELEY STRUCTURAL GENOMICS CENTER (BSGC) REVDAT 2 24-FEB-09 1YYX 1 VERSN REVDAT 1 25-AUG-05 1YYX 0 JRNL AUTH H.FENG,N.VU,Y.BAI JRNL TITL DETECTION AND STRUCTURE DETERMINATION OF AN JRNL TITL 2 EQUILIBRIUM UNFOLDING INTERMEDIATES OF JRNL TITL 3 RD-APOCYTOCHROME B562: NATIVE FOLD WITH NON-NATIVE JRNL TITL 4 HYDROPHOBIC INTERACTIONS JRNL REF J.MOL.BIOL. V. 343 1477 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15491625 JRNL DOI 10.1016/J.JMB.2004.08.099 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH-2.9 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1YYX COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-MAR-05. REMARK 100 THE RCSB ID CODE IS RCSB032087. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.84 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : NULL; NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D HSQC, 3D_15N-SEPARATED_ REMARK 210 NOESY, 3D_13C-SEPARATED_NOESY, REMARK 210 HNHA, 3D HNCACB, 3D CBCACONH,, REMARK 210 3D HAHBCONH, 3D HNCO, 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 5.0.4, X-PLOR NIH-2.9 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING, MOLECULAR DYNAMICS, REMARK 210 MATRIX RELAXATION, TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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 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 ASP A 2 -159.13 -81.02 REMARK 500 1 ASP A 21 -32.95 66.42 REMARK 500 1 ALA A 37 -73.93 -66.82 REMARK 500 1 ALA A 43 68.02 -166.13 REMARK 500 1 LYS A 47 19.65 41.95 REMARK 500 1 LEU A 48 -84.20 43.20 REMARK 500 1 LYS A 51 -74.51 -165.67 REMARK 500 1 SER A 52 61.80 -175.41 REMARK 500 1 ASP A 54 -58.84 -138.70 REMARK 500 1 SER A 55 -43.67 115.17 REMARK 500 1 GLU A 57 -1.00 -58.76 REMARK 500 1 LYS A 83 66.72 -101.15 REMARK 500 1 ASN A 102 66.34 90.62 REMARK 500 1 LYS A 104 -95.03 63.21 REMARK 500 1 TYR A 105 20.60 -145.71 REMARK 500 2 ASP A 2 4.04 -157.37 REMARK 500 2 LEU A 3 -37.78 179.48 REMARK 500 2 ASP A 21 -35.62 66.59 REMARK 500 2 ALA A 43 93.12 -162.85 REMARK 500 2 LYS A 47 25.88 37.49 REMARK 500 2 LEU A 48 -88.88 40.93 REMARK 500 2 GLU A 49 97.68 -68.36 REMARK 500 2 LYS A 51 -85.96 -164.86 REMARK 500 2 SER A 52 70.28 -171.78 REMARK 500 2 PRO A 53 -76.70 -69.98 REMARK 500 2 ASP A 54 -54.42 -135.71 REMARK 500 2 SER A 55 -44.37 113.59 REMARK 500 2 GLU A 57 -7.32 -58.52 REMARK 500 2 LYS A 83 70.95 -101.20 REMARK 500 2 ASN A 102 66.20 91.25 REMARK 500 2 LYS A 104 -80.37 60.90 REMARK 500 3 ASP A 21 -31.66 64.50 REMARK 500 3 ALA A 37 -72.03 -66.63 REMARK 500 3 ALA A 43 55.14 -165.79 REMARK 500 3 LYS A 47 -2.35 66.85 REMARK 500 3 LEU A 48 -75.25 60.20 REMARK 500 3 LYS A 51 -70.04 -166.11 REMARK 500 3 SER A 52 65.62 -175.75 REMARK 500 3 PRO A 53 -77.36 -65.53 REMARK 500 3 ASP A 54 -57.68 -136.82 REMARK 500 3 SER A 55 -43.82 112.98 REMARK 500 3 GLU A 57 -4.45 -59.10 REMARK 500 3 LYS A 83 68.49 -103.61 REMARK 500 3 ASN A 102 64.90 90.59 REMARK 500 3 LYS A 104 -83.16 58.72 REMARK 500 3 TYR A 105 10.15 -145.64 REMARK 500 4 ASP A 2 -155.12 -77.73 REMARK 500 4 ASP A 21 -35.34 72.69 REMARK 500 4 ALA A 37 -70.41 -63.58 REMARK 500 4 LYS A 42 -78.76 -80.95 REMARK 500 4 LYS A 47 129.46 66.60 REMARK 500 4 LEU A 48 0.87 -66.97 REMARK 500 4 LYS A 51 -76.45 -166.63 REMARK 500 4 SER A 52 60.03 -171.64 REMARK 500 4 PRO A 53 -73.09 -60.09 REMARK 500 4 ASP A 54 -82.09 -142.56 REMARK 500 4 SER A 55 -46.88 109.38 REMARK 500 4 MET A 58 -81.05 17.52 REMARK 500 4 LYS A 83 66.38 -101.25 REMARK 500 4 ASN A 102 69.10 85.48 REMARK 500 4 LYS A 104 -70.16 60.19 REMARK 500 4 TYR A 105 -12.29 -142.53 REMARK 500 5 ASP A 21 -33.29 68.74 REMARK 500 5 ALA A 23 -9.93 -52.69 REMARK 500 5 ALA A 37 -71.23 -65.28 REMARK 500 5 ALA A 43 90.06 -162.42 REMARK 500 5 LYS A 47 30.74 34.25 REMARK 500 5 LEU A 48 94.94 52.46 REMARK 500 5 GLU A 49 -165.69 59.69 REMARK 500 5 ASP A 50 49.79 -146.54 REMARK 500 5 LYS A 51 -19.74 -164.55 REMARK 500 5 SER A 52 76.13 85.22 REMARK 500 5 PRO A 53 -82.13 -52.36 REMARK 500 5 SER A 55 -42.91 113.49 REMARK 500 5 ASN A 102 63.97 89.62 REMARK 500 5 LYS A 104 -84.63 60.61 REMARK 500 5 TYR A 105 11.32 -143.88 REMARK 500 6 ASP A 2 166.40 51.47 REMARK 500 6 ASP A 21 -33.80 71.59 REMARK 500 6 ALA A 37 -73.57 -66.61 REMARK 500 6 ALA A 43 87.83 -168.66 REMARK 500 6 LYS A 47 25.96 37.98 REMARK 500 6 LEU A 48 -89.32 39.82 REMARK 500 6 LYS A 51 -70.74 -164.93 REMARK 500 6 SER A 52 70.46 -177.26 REMARK 500 6 PRO A 53 -78.90 -64.41 REMARK 500 6 ASP A 54 -54.33 -132.47 REMARK 500 6 SER A 55 -44.70 112.94 REMARK 500 6 GLU A 57 -8.50 -58.96 REMARK 500 6 LYS A 83 62.12 -100.30 REMARK 500 6 ASN A 102 65.35 88.19 REMARK 500 6 LYS A 104 -84.49 59.00 REMARK 500 6 TYR A 105 15.98 -147.72 REMARK 500 7 LEU A 3 92.43 -51.98 REMARK 500 7 GLU A 4 -35.22 -173.72 REMARK 500 7 ASP A 21 -32.25 72.11 REMARK 500 7 ALA A 43 75.68 -165.79 REMARK 500 7 LYS A 47 22.85 41.28 REMARK 500 7 LEU A 48 -89.64 45.69 REMARK 500 7 LYS A 51 -78.71 -166.10 REMARK 500 7 SER A 52 71.54 -172.32 REMARK 500 7 PRO A 53 -73.05 -66.92 REMARK 500 7 ASP A 54 -50.45 -136.69 REMARK 500 7 SER A 55 -59.94 99.30 REMARK 500 7 GLU A 57 -2.90 -56.73 REMARK 500 7 LYS A 95 -73.45 -54.46 REMARK 500 7 ASN A 102 61.77 89.82 REMARK 500 7 LYS A 104 -87.42 59.46 REMARK 500 7 TYR A 105 18.76 -144.26 REMARK 500 8 ASP A 21 -34.38 69.19 REMARK 500 8 ALA A 43 63.12 -165.82 REMARK 500 8 LYS A 47 -4.15 67.89 REMARK 500 8 LEU A 48 -56.47 65.13 REMARK 500 8 LYS A 51 -75.51 -167.06 REMARK 500 8 SER A 52 60.55 -171.88 REMARK 500 8 PRO A 53 -73.15 -51.95 REMARK 500 8 ASP A 54 -60.60 -139.18 REMARK 500 8 SER A 55 -43.48 114.69 REMARK 500 8 GLU A 57 -2.82 -58.90 REMARK 500 8 LYS A 83 68.78 -102.00 REMARK 500 8 ASN A 102 63.80 88.97 REMARK 500 8 LYS A 104 -80.75 58.27 REMARK 500 9 ASP A 21 -32.45 69.11 REMARK 500 9 ALA A 37 -71.68 -65.41 REMARK 500 9 ALA A 43 73.42 80.58 REMARK 500 9 LYS A 47 26.12 40.71 REMARK 500 9 LEU A 48 -86.47 39.61 REMARK 500 9 LYS A 51 -68.68 -164.95 REMARK 500 9 SER A 52 63.45 -179.22 REMARK 500 9 PRO A 53 -73.95 -52.85 REMARK 500 9 ASP A 54 -61.12 -140.11 REMARK 500 9 SER A 55 -43.61 111.00 REMARK 500 9 MET A 58 -77.17 8.23 REMARK 500 9 LYS A 83 68.96 -100.28 REMARK 500 9 ASN A 102 66.11 88.70 REMARK 500 9 LYS A 104 -81.76 60.06 REMARK 500 10 ASP A 21 -34.21 70.08 REMARK 500 10 ALA A 37 -75.24 -66.82 REMARK 500 10 LYS A 47 113.61 55.86 REMARK 500 10 GLU A 49 -71.94 -101.71 REMARK 500 10 ASP A 50 -32.01 65.54 REMARK 500 10 LYS A 51 -83.42 -164.23 REMARK 500 10 SER A 52 65.08 -172.86 REMARK 500 10 PRO A 53 -73.62 -54.21 REMARK 500 10 ASP A 54 -70.14 -138.07 REMARK 500 10 SER A 55 -41.76 111.90 REMARK 500 10 MET A 58 -80.02 12.84 REMARK 500 10 LYS A 83 59.52 -101.42 REMARK 500 10 ASN A 102 65.32 88.46 REMARK 500 10 LYS A 104 -77.81 58.19 REMARK 500 11 ASP A 21 -34.51 70.94 REMARK 500 11 ALA A 37 -72.66 -67.82 REMARK 500 11 ALA A 43 92.28 -164.52 REMARK 500 11 LYS A 47 20.73 41.94 REMARK 500 11 LEU A 48 -83.14 39.08 REMARK 500 11 GLU A 49 93.01 -67.03 REMARK 500 11 LYS A 51 -71.64 -167.84 REMARK 500 11 SER A 52 67.83 -176.89 REMARK 500 11 PRO A 53 -71.84 -60.86 REMARK 500 11 ASP A 54 -64.91 -140.87 REMARK 500 11 SER A 55 -43.52 110.84 REMARK 500 11 GLU A 57 -71.45 -60.74 REMARK 500 11 MET A 58 -82.48 13.21 REMARK 500 11 ASN A 102 65.98 92.38 REMARK 500 11 LYS A 104 -86.61 62.19 REMARK 500 11 TYR A 105 15.59 -145.55 REMARK 500 12 LEU A 3 -19.06 -49.77 REMARK 500 12 ASP A 21 -33.26 69.29 REMARK 500 12 LYS A 42 -75.96 -90.62 REMARK 500 12 LYS A 47 -8.19 61.96 REMARK 500 12 LEU A 48 -66.87 63.76 REMARK 500 12 LYS A 51 -82.68 -166.34 REMARK 500 12 SER A 52 70.00 -171.46 REMARK 500 12 PRO A 53 -70.54 -63.87 REMARK 500 12 ASP A 54 -60.52 -132.72 REMARK 500 12 SER A 55 -47.46 115.12 REMARK 500 12 TYR A 101 0.91 -69.22 REMARK 500 12 ASN A 102 59.31 88.77 REMARK 500 12 LYS A 104 -72.06 63.89 REMARK 500 12 TYR A 105 -28.41 -145.31 REMARK 500 13 GLU A 4 -7.82 -59.04 REMARK 500 13 ASP A 21 -34.32 71.28 REMARK 500 13 ALA A 37 -70.03 -65.06 REMARK 500 13 ALA A 43 97.50 63.30 REMARK 500 13 LYS A 47 19.99 41.75 REMARK 500 13 LEU A 48 -79.44 37.73 REMARK 500 13 GLU A 49 81.02 -60.10 REMARK 500 13 LYS A 51 -10.06 105.25 REMARK 500 13 SER A 52 70.46 90.71 REMARK 500 13 PRO A 53 -74.91 -55.91 REMARK 500 13 ASP A 54 -56.89 -133.36 REMARK 500 13 SER A 55 -42.94 113.44 REMARK 500 13 LYS A 83 54.53 -100.11 REMARK 500 13 LYS A 95 -72.39 -56.24 REMARK 500 13 ASN A 102 61.03 89.56 REMARK 500 13 LYS A 104 -83.73 61.44 REMARK 500 13 TYR A 105 10.14 -147.88 REMARK 500 14 ASP A 2 -153.25 -82.21 REMARK 500 14 LEU A 3 91.73 -60.08 REMARK 500 14 GLU A 4 -35.92 -174.29 REMARK 500 14 ASP A 21 -36.15 67.16 REMARK 500 14 ALA A 37 -71.18 -66.71 REMARK 500 14 LYS A 42 -76.98 -84.58 REMARK 500 14 LEU A 48 -70.61 60.57 REMARK 500 14 GLU A 49 -166.88 -122.60 REMARK 500 14 LYS A 51 -94.62 -163.76 REMARK 500 14 SER A 52 78.28 -174.00 REMARK 500 14 PRO A 53 -76.69 -45.49 REMARK 500 14 SER A 55 -44.37 112.53 REMARK 500 14 LYS A 83 70.61 -101.50 REMARK 500 14 ASN A 102 68.25 89.16 REMARK 500 14 LYS A 104 -88.50 62.15 REMARK 500 14 TYR A 105 17.40 -143.10 REMARK 500 15 ASP A 2 -156.61 -77.94 REMARK 500 15 ASP A 21 -31.92 69.50 REMARK 500 15 ALA A 37 -73.10 -66.60 REMARK 500 15 ALA A 43 107.11 -164.06 REMARK 500 15 LYS A 47 111.83 36.32 REMARK 500 15 LEU A 48 174.81 -54.97 REMARK 500 15 GLU A 49 -72.12 67.45 REMARK 500 15 ASP A 50 -14.24 60.58 REMARK 500 15 LYS A 51 -87.92 -163.12 REMARK 500 15 SER A 52 68.58 -174.46 REMARK 500 15 PRO A 53 -73.31 -63.33 REMARK 500 15 ASP A 54 -54.55 -137.44 REMARK 500 15 SER A 55 -43.52 114.39 REMARK 500 15 GLU A 57 -9.11 -54.33 REMARK 500 15 ASN A 102 58.85 74.52 REMARK 500 15 LYS A 104 -70.72 66.10 REMARK 500 15 TYR A 105 27.59 -151.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RAC RELATED DB: PDB REMARK 900 REDESIGNED APOCYTOCHROME B562 REMARK 900 RELATED ID: 1YYJ RELATED DB: PDB REMARK 900 REDESIGNED APOCYTOCHROME B562 DBREF 1YYX A 1 106 PDB 1YYX 1YYX 1 106 SEQRES 1 A 106 ALA ASP LEU GLU ASP ASN TRP GLU THR LEU ASN ASP ASN SEQRES 2 A 106 LEU LYS VAL ILE GLU LYS ALA ASP ASN ALA ALA GLN VAL SEQRES 3 A 106 LYS ASP ALA LEU THR LYS MET ARG ALA ALA ALA LEU ASP SEQRES 4 A 106 ALA GLN LYS ALA THR PRO PRO LYS LEU GLU ASP LYS SER SEQRES 5 A 106 PRO ASP SER PRO GLU MET LYS ASP PHE ARG HIS GLY PHE SEQRES 6 A 106 ASP ILE LEU VAL GLY GLN ILE ASP ASP ALA LEU LYS LEU SEQRES 7 A 106 ALA ASN GLU GLY LYS VAL LYS GLU ALA GLN ALA ALA ALA SEQRES 8 A 106 GLU GLN LEU LYS THR THR ILE ARG ALA TYR ASN GLN LYS SEQRES 9 A 106 TYR GLY HELIX 1 1 ASP A 2 LYS A 19 1 18 HELIX 2 2 ASN A 22 LYS A 42 1 21 HELIX 3 3 PRO A 56 GLU A 81 1 26 HELIX 4 4 LYS A 83 TYR A 101 1 19 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 304 0 0 4 0 0 0 6 0 0 0 9 END