HEADER ELECTRON TRANSPORT 28-FEB-05 1YZC TITLE THE SOLUTION STRUCTURE OF A REDESIGNED APOCYTOCHROME B562 (RD-APOCYT TITLE 2 B562) WITH THE N- AND A PART OF THE C-TERMINAL HELICES UNFOLDED COMPND MOL_ID: 1; COMPND 2 MOLECULE: EDESIGNED APO-CYTOCHROME B562; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) PLYSS CELLS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: ET17B KEYWDS FOLDING INTERMEDIATES, NATIVE-STATE HYDROGEN EXCHANGE, PROTEIN KEYWDS 2 ENGINEERING, PROTEIN STRUCTURE, STRUCTURAL GENOMICS, PSI, PROTEIN KEYWDS 3 STRUCTURE INITIATIVE, BERKELEY STRUCTURAL GENOMICS CENTER, BSGC, KEYWDS 4 ELECTRON TRANSPORT EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR H.FENG,Z.ZHOU,Y.BAI,BERKELEY STRUCTURAL GENOMICS CENTER (BSGC) REVDAT 4 29-MAY-24 1YZC 1 REMARK REVDAT 3 02-MAR-22 1YZC 1 REMARK REVDAT 2 24-FEB-09 1YZC 1 VERSN REVDAT 1 28-MAR-06 1YZC 0 JRNL AUTH H.FENG,Z.ZHOU,Y.BAI JRNL TITL A PROTEIN FOLDING PATHWAY WITH MULTIPLE FOLDING JRNL TITL 2 INTERMEDIATES AT ATOMIC RESOLUTION JRNL REF PROC.NATL.ACAD.SCI.USA V. 102 5026 2005 JRNL REFN ISSN 0027-8424 JRNL PMID 15793003 JRNL DOI 10.1073/PNAS.0501372102 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 5.0.4, X-PLOR NIH-2.9 REMARK 3 AUTHORS : DELAGLIO, F. (NMRPIPE), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1YZC COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1000032101. 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 : 50MM SODIUM ACETATE; 92.5% H2O, REMARK 210 7.5% D2O; 50MM SODIUM ACETATE; REMARK 210 99% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D HSQC; 3D_15N-SEPARATED_NOESY; REMARK 210 3D_13C-SEPARATED_NOESY; HNHA; 3D REMARK 210 HNCACB, 3D CBCACONH; 3D HAHBCONH, REMARK 210 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 : X-PLOR NIH-2.9 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: 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 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 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 LYS A 59 H HIS A 63 1.47 REMARK 500 O SER A 52 H ASP A 54 1.50 REMARK 500 O GLY A 101 H GLN A 103 1.53 REMARK 500 O ASP A 66 H GLY A 70 1.58 REMARK 500 O GLN A 41 H ALA A 43 1.58 REMARK 500 O ALA A 35 H ASP A 39 1.59 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 LEU A 3 -80.42 -89.84 REMARK 500 1 GLU A 4 -157.21 59.99 REMARK 500 1 ASP A 5 23.89 49.87 REMARK 500 1 ASP A 7 -37.44 -150.62 REMARK 500 1 THR A 9 34.23 -89.12 REMARK 500 1 ASN A 13 -33.56 -156.12 REMARK 500 1 LYS A 15 -81.34 -156.98 REMARK 500 1 LYS A 19 -85.40 47.18 REMARK 500 1 ASP A 21 -83.57 -85.65 REMARK 500 1 ASN A 22 95.61 -161.87 REMARK 500 1 ALA A 23 -23.34 79.21 REMARK 500 1 GLN A 41 -148.65 -69.41 REMARK 500 1 ALA A 43 -51.82 -141.89 REMARK 500 1 PRO A 45 97.47 -33.27 REMARK 500 1 LYS A 47 25.27 -148.89 REMARK 500 1 LEU A 48 -91.94 -73.30 REMARK 500 1 GLU A 49 26.45 44.67 REMARK 500 1 ASP A 50 26.86 -172.35 REMARK 500 1 LYS A 51 -61.35 -146.62 REMARK 500 1 SER A 52 -174.20 55.20 REMARK 500 1 PRO A 53 58.65 -59.14 REMARK 500 1 SER A 55 -172.46 82.03 REMARK 500 1 PRO A 56 2.55 -53.63 REMARK 500 1 LYS A 83 -162.30 -78.61 REMARK 500 1 THR A 97 -78.97 -87.18 REMARK 500 1 ALA A 100 -62.00 -162.91 REMARK 500 1 ASN A 102 -40.70 65.86 REMARK 500 1 GLN A 103 -152.05 -97.66 REMARK 500 1 LYS A 104 120.01 52.80 REMARK 500 2 GLU A 4 -70.15 -85.08 REMARK 500 2 ASN A 6 43.30 -146.63 REMARK 500 2 GLU A 8 -16.48 58.82 REMARK 500 2 THR A 9 25.39 38.48 REMARK 500 2 ASN A 13 -6.43 60.53 REMARK 500 2 GLU A 18 17.32 -147.75 REMARK 500 2 LYS A 19 -88.83 53.41 REMARK 500 2 ALA A 20 88.79 52.01 REMARK 500 2 ASP A 21 -56.87 -148.55 REMARK 500 2 ASN A 22 65.18 -155.28 REMARK 500 2 ALA A 23 -3.17 65.37 REMARK 500 2 GLN A 41 -137.30 -73.73 REMARK 500 2 ALA A 43 -52.02 -139.18 REMARK 500 2 PRO A 45 88.28 -25.76 REMARK 500 2 PRO A 46 -62.42 -90.92 REMARK 500 2 ASP A 50 51.04 -170.26 REMARK 500 2 LYS A 51 -65.54 -140.87 REMARK 500 2 SER A 52 -174.48 52.72 REMARK 500 2 PRO A 53 49.64 -58.22 REMARK 500 2 ASP A 54 -74.73 -107.80 REMARK 500 2 PRO A 56 -0.05 -57.61 REMARK 500 REMARK 500 THIS ENTRY HAS 248 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YZA RELATED DB: PDB REMARK 900 REDESIGNED APOCYTOCHROME B562 (RD-APOCYT B562) WITH THE N-TERMINAL REMARK 900 HELIX UNFOLDED DBREF 1YZC A 1 106 PDB 1YZC 1YZC 1 106 SEQRES 1 A 106 ALA ASP LEU GLU ASP ASN ASP GLU THR GLY ASN ASP ASN SEQRES 2 A 106 GLY LYS GLY GLY 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 GLY ARG ALA GLY ASN GLN LYS SEQRES 9 A 106 GLY GLY HELIX 1 1 ALA A 23 GLN A 41 1 19 HELIX 2 2 PRO A 56 GLY A 82 1 27 HELIX 3 3 LYS A 83 GLY A 98 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 MODEL 1