HEADER DE NOVO PROTEIN 25-FEB-05 1YYJ TITLE THE NMR SOLUTION STRUCTURE OF A REDESIGNED APOCYTOCHROME B562:RD- TITLE 2 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 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS FOUR HELIX PROTEIN, STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, BERKELEY STRUCTURAL GENOMICS CENTER, BSGC, DE NOVO KEYWDS 3 PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR H.FENG,J.TAKEI,R.LIPSITZ,N.TJANDRA,Y.BAI,BERKELEY STRUCTURAL GENOMICS AUTHOR 2 CENTER (BSGC) REVDAT 4 27-SEP-23 1YYJ 1 SOURCE REVDAT 3 02-MAR-22 1YYJ 1 REMARK 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 HIDDEN JRNL TITL 2 FOLDING INTERMEDIATE: IMPLICATIONS FOR PROTEIN FOLDING JRNL REF BIOCHEMISTRY V. 42 12461 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 14580191 JRNL DOI 10.1021/BI035561S REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH-2.9, X-PLOR NIH-2.9 REMARK 3 AUTHORS : BRUNGER (X-PLOR), BRUNGER (X-PLOR) 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 DEPOSITION ID IS D_1000032073. 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, 15N REMARK 210 AND/OR 13C UNIFORMLY LABELED REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D HSQC; 3D_13C-SEPARATED_NOESY; REMARK 210 3D_15N-SEPARATED_NOESY; HNHA; 3D REMARK 210 HNCACB, 3D CBCA(CO)NH; 3D REMARK 210 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 : NMRPIPE REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING, MOLECULAR DYNAMICS, REMARK 210 MATRIX RELAXATION, TORSION ANGLE REMARK 210 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 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-10 REMARK 470 RES CSSEQI ATOMS REMARK 470 GLU A 4 CG REMARK 470 ASN A 80 C O REMARK 470 GLU A 81 N CA CB REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 O SER A 55 H GLU A 57 1.39 REMARK 500 O LYS A 27 HG1 THR A 31 1.44 REMARK 500 O VAL A 84 H GLN A 88 1.46 REMARK 500 O GLU A 8 H ASP A 12 1.47 REMARK 500 O HIS A 63 H ILE A 67 1.47 REMARK 500 O ILE A 17 H ALA A 20 1.48 REMARK 500 O ARG A 62 H ASP A 66 1.50 REMARK 500 O MET A 58 H PHE A 61 1.57 REMARK 500 O ALA A 36 H ALA A 40 1.59 REMARK 500 O LYS A 27 H THR A 31 1.59 REMARK 500 O ASN A 6 H LEU A 10 1.60 REMARK 500 REMARK 500 REMARK: NULL 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 REMARK 500 THIS ENTRY HAS 128 RAMACHANDRAN OUTLIERS. 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 MODEL 1