10 20 30 40 50 60 70 80 1YYJ - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DE NOVO PROTEIN 25-FEB-05 1YYJ
TITLE THE NMR SOLUTION STRUCTURE OF A REDESIGNED APOCYTOCHROME TITLE 2 B562:RD-APOCYT B562
COMPND MOL_ID: 1; COMPND 2 MOLECULE: REDESIGNED APOCYTOCHROME 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 FOUR HELIX PROTEIN, STRUCTURAL GENOMICS, PSI, PROTEIN KEYWDS 2 STRUCTURE INITIATIVE, BERKELEY STRUCTURAL GENOMICS CENTER, KEYWDS 3 BSGC, DE NOVO PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR H.FENG,J.TAKEI,R.LIPSITZ,N.TJANDRA,Y.BAI,BERKELEY AUTHOR 2 STRUCTURAL GENOMICS CENTER (BSGC)
REVDAT 2 24-FEB-09 1YYJ 1 VERSN REVDAT 1 25-AUG-05 1YYJ 0
JRNL AUTH H.FENG,J.TAKEI,R.LIPSITZ,N.TJANDRA,Y.BAI JRNL TITL SPECIFIC NON-NATIVE HYDROPHOBIC INTERACTIONS IN A JRNL TITL 2 HIDDEN FOLDING INTERMEDIATE: IMPLICATIONS FOR JRNL TITL 3 PROTEIN FOLDING JRNL REF BIOCHEMISTRY V. 42 12461 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 14580191 JRNL DOI 10.1021/BI035561S
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 1YYJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-MAR-05. REMARK 100 THE RCSB ID CODE IS RCSB032073.
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 : 1.5MM RD APOCYTOCHROME B562, REMARK 210 15N AND/OR 13C UNIFORMLY REMARK 210 LABELED REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D HSQC, 3D_13C-SEPARATED_ REMARK 210 NOESY, 3D_15N-SEPARATED_NOESY, REMARK 210 HNHA, 3D HNCACB, 3D CBCA(CO) REMARK 210 NH, 3D HBHA(CO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 750 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR NIH-2.9, NMRPIPE 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 : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: RESIDUAL DIPOLAR COUPLING, 2D NOESY, 3D HNCA, ETC.
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 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 1 GLU A 4 CG REMARK 470 1 ASN A 80 C O REMARK 470 1 GLU A 81 N CA CB
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 ILE A 17 -72.19 -70.94 REMARK 500 1 ASP A 21 -13.51 67.13 REMARK 500 1 MET A 33 -73.15 -66.23 REMARK 500 1 LYS A 42 32.20 -74.32 REMARK 500 1 THR A 44 40.05 -156.91 REMARK 500 1 LYS A 47 105.93 82.89 REMARK 500 1 ASP A 50 42.59 -147.00 REMARK 500 1 LYS A 51 -143.07 -171.30 REMARK 500 1 ASP A 54 -126.73 65.89 REMARK 500 1 SER A 55 -37.44 -170.43 REMARK 500 1 PRO A 56 48.56 -54.02 REMARK 500 1 GLU A 57 29.71 45.58 REMARK 500 1 MET A 58 -6.59 63.73 REMARK 500 1 TYR A 105 30.86 -86.20 REMARK 500 2 ILE A 17 -72.99 -71.31 REMARK 500 2 ASP A 21 -11.00 59.13 REMARK 500 2 LYS A 42 4.00 -68.89 REMARK 500 2 THR A 44 69.61 -151.34 REMARK 500 2 PRO A 46 -94.33 -98.68 REMARK 500 2 LYS A 47 117.26 -171.57 REMARK 500 2 GLU A 49 30.59 -99.07 REMARK 500 2 ASP A 50 -53.72 -147.65 REMARK 500 2 LYS A 51 -161.03 -65.23 REMARK 500 2 ASP A 54 -137.72 64.63 REMARK 500 2 SER A 55 -38.92 -161.83 REMARK 500 2 PRO A 56 70.32 -49.21 REMARK 500 2 GLU A 57 32.22 39.47 REMARK 500 2 MET A 58 -8.70 64.73 REMARK 500 3 ILE A 17 -73.51 -70.16 REMARK 500 3 ASP A 21 -15.02 67.76 REMARK 500 3 THR A 44 69.18 -152.31 REMARK 500 3 LYS A 47 101.69 71.83 REMARK 500 3 ASP A 50 -59.50 -144.26 REMARK 500 3 LYS A 51 -162.96 -65.99 REMARK 500 3 ASP A 54 -143.99 76.27 REMARK 500 3 SER A 55 -26.62 -162.36 REMARK 500 3 PRO A 56 40.91 -56.43 REMARK 500 3 GLU A 57 25.56 49.87 REMARK 500 3 MET A 58 -5.08 63.95 REMARK 500 4 ILE A 17 -71.25 -71.23 REMARK 500 4 ASP A 21 -7.62 69.55 REMARK 500 4 LYS A 42 1.05 -57.62 REMARK 500 4 PRO A 46 -90.60 -84.96 REMARK 500 4 LYS A 47 122.23 -176.60 REMARK 500 4 GLU A 49 18.83 50.74 REMARK 500 4 ASP A 50 -55.00 -148.61 REMARK 500 4 LYS A 51 -162.59 -65.69 REMARK 500 4 ASP A 54 164.22 75.40 REMARK 500 4 PRO A 56 62.58 -39.98 REMARK 500 4 GLU A 57 29.08 36.63 REMARK 500 4 MET A 58 -8.07 65.16 REMARK 500 5 ILE A 17 -74.87 -70.20 REMARK 500 5 ASP A 21 -17.60 63.57 REMARK 500 5 GLN A 41 -78.42 11.78 REMARK 500 5 LYS A 42 13.00 -56.26 REMARK 500 5 THR A 44 76.51 -153.58 REMARK 500 5 PRO A 46 -93.72 -93.10 REMARK 500 5 LYS A 47 103.06 -177.78 REMARK 500 5 ASP A 50 -61.33 -143.16 REMARK 500 5 LYS A 51 -146.98 -66.64 REMARK 500 5 ASP A 54 -128.20 69.02 REMARK 500 5 SER A 55 -28.45 -168.27 REMARK 500 5 PRO A 56 45.65 -54.75 REMARK 500 5 GLU A 57 27.94 46.98 REMARK 500 5 MET A 58 -8.25 65.40 REMARK 500 6 ILE A 17 -70.77 -70.41 REMARK 500 6 ASP A 21 -8.73 58.13 REMARK 500 6 LYS A 42 74.60 -63.22 REMARK 500 6 THR A 44 74.35 -154.91 REMARK 500 6 PRO A 46 -92.01 -96.90 REMARK 500 6 LYS A 47 102.40 -175.64 REMARK 500 6 ASP A 50 -56.80 -145.60 REMARK 500 6 LYS A 51 -163.79 -68.00 REMARK 500 6 ASP A 54 -24.37 63.14 REMARK 500 6 SER A 55 -26.44 102.47 REMARK 500 6 PRO A 56 36.86 -45.98 REMARK 500 6 MET A 58 -3.90 66.41 REMARK 500 7 ILE A 17 -72.48 -71.28 REMARK 500 7 ASP A 21 -0.92 66.11 REMARK 500 7 LYS A 42 3.99 -68.17 REMARK 500 7 THR A 44 67.90 -154.19 REMARK 500 7 LYS A 47 109.84 74.20 REMARK 500 7 GLU A 49 40.53 -68.34 REMARK 500 7 ASP A 50 -70.09 -146.55 REMARK 500 7 LYS A 51 -141.16 -64.28 REMARK 500 7 ASP A 54 -133.85 77.47 REMARK 500 7 SER A 55 -30.02 -167.97 REMARK 500 7 PRO A 56 41.74 -55.63 REMARK 500 7 MET A 58 -5.78 67.94 REMARK 500 8 ILE A 17 -72.25 -71.66 REMARK 500 8 ASP A 21 -13.28 57.25 REMARK 500 8 LYS A 42 10.11 -67.04 REMARK 500 8 THR A 44 61.93 -154.56 REMARK 500 8 LYS A 47 98.29 80.06 REMARK 500 8 ASP A 50 -50.33 -148.87 REMARK 500 8 LYS A 51 -160.55 -65.56 REMARK 500 8 ASP A 54 -114.48 72.59 REMARK 500 8 SER A 55 -32.45 -167.87 REMARK 500 8 PRO A 56 40.98 -56.44 REMARK 500 8 MET A 58 -3.51 66.38 REMARK 500 9 ILE A 17 -72.88 -71.53 REMARK 500 9 ASP A 21 -12.33 67.88 REMARK 500 9 LYS A 42 5.04 -53.96 REMARK 500 9 THR A 44 72.10 -152.18 REMARK 500 9 PRO A 46 -95.75 -97.63 REMARK 500 9 LYS A 47 116.57 -175.60 REMARK 500 9 GLU A 49 23.30 49.27 REMARK 500 9 ASP A 50 -70.50 -140.49 REMARK 500 9 LYS A 51 -121.69 -66.96 REMARK 500 9 ASP A 54 -131.60 65.05 REMARK 500 9 SER A 55 -33.84 -170.06 REMARK 500 9 PRO A 56 59.35 -51.52 REMARK 500 9 GLU A 57 29.51 42.42 REMARK 500 9 MET A 58 -8.17 65.27 REMARK 500 10 ILE A 17 -72.08 -71.28 REMARK 500 10 ASP A 21 -9.08 59.46 REMARK 500 10 LYS A 42 6.92 -65.35 REMARK 500 10 THR A 44 67.91 -152.05 REMARK 500 10 PRO A 46 -98.04 -103.07 REMARK 500 10 LYS A 47 102.78 -175.20 REMARK 500 10 LEU A 48 34.61 -82.05 REMARK 500 10 ASP A 50 -44.76 -151.75 REMARK 500 10 LYS A 51 -152.78 -66.89 REMARK 500 10 ASP A 54 -132.84 60.47 REMARK 500 10 SER A 55 -26.97 -165.60 REMARK 500 10 PRO A 56 47.29 -56.51 REMARK 500 10 GLU A 57 27.50 48.64 REMARK 500 10 MET A 58 -4.75 64.04 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: 1YYX RELATED DB: PDB REMARK 900 REDESIGNED APOCYTOCHROME B562
DBREF 1YYJ A 1 106 PDB 1YYJ 1YYJ 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 ALA A 1 LYS A 19 1 19 HELIX 2 2 ASN A 22 GLN A 41 1 20 HELIX 3 3 MET A 58 ASN A 80 1 23 HELIX 4 4 LYS A 83 TYR A 105 1 23
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