PDB Short entry for 1LG4 HEADER PRION PROTEIN 15-APR-02 1LG4 TITLE NMR STRUCTURE OF THE HUMAN DOPPEL PROTEIN FRAGMENT 24-152 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRION-LIKE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HDPL(24-152); COMPND 5 SYNONYM: DOPPEL PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PRND; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21/DE3; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PRSETA KEYWDS PRION, DOPPEL, SCRAPIE, PRION PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.LUHRS,R.RIEK,P.GUNTERT,K.WUTHRICH REVDAT 3 23-FEB-22 1LG4 1 REMARK REVDAT 2 24-FEB-09 1LG4 1 VERSN REVDAT 1 25-FEB-03 1LG4 0 JRNL AUTH T.LUHRS,R.RIEK,P.GUNTERT,K.WUTHRICH JRNL TITL NMR STRUCTURE OF THE HUMAN DOPPEL PROTEIN JRNL REF J.MOL.BIOL. V. 326 1549 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 12595265 JRNL DOI 10.1016/S0022-2836(02)01471-7 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : OPALP 1.3 REMARK 3 AUTHORS : LUGINBUHL, P., GUNTERT, P., BILLETER, M., AND REMARK 3 WUTHRICH, K. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1LG4 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-APR-02. REMARK 100 THE DEPOSITION ID IS D_1000015919. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 4.5 REMARK 210 IONIC STRENGTH : 10 MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 13C,15N LABELED HDPL(24-152); REMARK 210 15N LABELED HDPL(24-152); 13C, REMARK 210 15N LABELED HDPL(24-152) REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XEASY 1.5, DYANA 1.65 REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 VAL A 24 REMARK 465 GLN A 25 REMARK 465 THR A 26 REMARK 465 ARG A 27 REMARK 465 GLY A 28 REMARK 465 ILE A 29 REMARK 465 LYS A 30 REMARK 465 HIS A 31 REMARK 465 ARG A 32 REMARK 465 ILE A 33 REMARK 465 LYS A 34 REMARK 465 TRP A 35 REMARK 465 ASN A 36 REMARK 465 ARG A 37 REMARK 465 LYS A 38 REMARK 465 ALA A 39 REMARK 465 LEU A 40 REMARK 465 PRO A 41 REMARK 465 SER A 42 REMARK 465 THR A 43 REMARK 465 ALA A 44 REMARK 465 GLN A 45 REMARK 465 ILE A 46 REMARK 465 THR A 47 REMARK 465 GLU A 48 REMARK 465 ALA A 49 REMARK 465 GLN A 50 REMARK 465 VAL A 51 REMARK 465 ARG A 151 REMARK 465 GLY A 152 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 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 ARG A 134 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 TYR A 91 CB - CG - CD2 ANGL. DEV. = -3.9 DEGREES REMARK 500 3 TYR A 78 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 6 VAL A 105 CA - CB - CG1 ANGL. DEV. = 9.0 DEGREES REMARK 500 8 TYR A 78 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 13 CYS A 108 CA - CB - SG ANGL. DEV. = 7.6 DEGREES REMARK 500 14 CYS A 108 CA - CB - SG ANGL. DEV. = 7.0 DEGREES REMARK 500 19 CYS A 145 CB - CA - C ANGL. DEV. = 7.3 DEGREES REMARK 500 19 CYS A 145 CA - CB - SG ANGL. DEV. = 8.4 DEGREES REMARK 500 20 ARG A 76 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES 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 ASN A 54 34.87 -80.08 REMARK 500 1 PRO A 56 24.50 -74.59 REMARK 500 1 LEU A 66 -167.11 48.36 REMARK 500 1 ALA A 72 -76.08 -49.28 REMARK 500 1 ASN A 81 41.22 -150.90 REMARK 500 1 TYR A 91 47.54 -80.43 REMARK 500 1 CYS A 94 110.50 125.95 REMARK 500 1 ASN A 98 69.91 -166.72 REMARK 500 1 PHE A 120 31.42 -68.99 REMARK 500 1 ASP A 124 -106.60 -143.21 REMARK 500 1 LYS A 126 -65.75 -26.25 REMARK 500 1 SER A 141 -66.06 -102.58 REMARK 500 1 LEU A 142 -163.91 45.91 REMARK 500 1 LYS A 143 -80.97 -29.02 REMARK 500 1 CYS A 145 -89.68 -86.82 REMARK 500 1 GLU A 146 -69.49 -144.45 REMARK 500 2 LYS A 61 70.64 27.29 REMARK 500 2 ASP A 67 77.04 -106.53 REMARK 500 2 PHE A 70 -10.25 -146.97 REMARK 500 2 HIS A 90 -101.40 -77.53 REMARK 500 2 TYR A 91 -9.18 72.15 REMARK 500 2 ASN A 92 151.76 68.61 REMARK 500 2 CYS A 94 166.66 72.95 REMARK 500 2 SER A 95 -30.33 -164.82 REMARK 500 2 ASN A 116 55.34 -110.62 REMARK 500 2 ASP A 124 -56.82 -134.43 REMARK 500 2 ASN A 125 93.04 36.86 REMARK 500 2 LYS A 126 -87.46 -104.02 REMARK 500 2 CYS A 145 -86.27 -73.25 REMARK 500 2 GLU A 146 -70.62 -142.73 REMARK 500 2 TRP A 148 39.44 -95.47 REMARK 500 3 GLN A 62 5.14 -61.11 REMARK 500 3 ASP A 67 44.38 -85.30 REMARK 500 3 ALA A 72 -86.05 -120.16 REMARK 500 3 ASN A 81 30.78 -154.52 REMARK 500 3 ASP A 87 -45.28 -135.62 REMARK 500 3 ALA A 103 -63.04 -101.44 REMARK 500 3 ASN A 125 44.43 -99.71 REMARK 500 3 LYS A 126 -98.66 -100.90 REMARK 500 3 SER A 141 -91.27 -62.35 REMARK 500 3 LEU A 142 31.97 26.04 REMARK 500 3 LYS A 143 -49.74 179.75 REMARK 500 3 HIS A 144 -175.02 58.65 REMARK 500 3 CYS A 145 -8.28 -147.50 REMARK 500 3 GLU A 146 -90.14 -109.49 REMARK 500 3 TRP A 148 42.56 -86.47 REMARK 500 4 ALA A 58 -156.05 45.46 REMARK 500 4 LYS A 61 85.72 26.36 REMARK 500 4 ASP A 67 76.95 -106.32 REMARK 500 4 ALA A 72 -74.69 -107.60 REMARK 500 REMARK 500 THIS ENTRY HAS 322 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLN A 121 LYS A 122 2 148.36 REMARK 500 ASN A 92 GLY A 93 6 143.25 REMARK 500 TRP A 148 LEU A 149 6 149.95 REMARK 500 LEU A 66 ASP A 67 11 149.82 REMARK 500 ASP A 124 ASN A 125 11 -148.65 REMARK 500 ASP A 87 GLY A 88 15 149.38 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 3 ARG A 55 0.09 SIDE CHAIN REMARK 500 3 ARG A 134 0.11 SIDE CHAIN REMARK 500 4 TYR A 82 0.07 SIDE CHAIN REMARK 500 5 ARG A 76 0.11 SIDE CHAIN REMARK 500 5 TYR A 78 0.08 SIDE CHAIN REMARK 500 6 ARG A 134 0.12 SIDE CHAIN REMARK 500 7 TYR A 78 0.09 SIDE CHAIN REMARK 500 8 TYR A 78 0.08 SIDE CHAIN REMARK 500 10 TYR A 78 0.10 SIDE CHAIN REMARK 500 12 ARG A 64 0.12 SIDE CHAIN REMARK 500 12 TYR A 78 0.08 SIDE CHAIN REMARK 500 13 ARG A 76 0.10 SIDE CHAIN REMARK 500 16 ARG A 76 0.08 SIDE CHAIN REMARK 500 17 ARG A 55 0.09 SIDE CHAIN REMARK 500 18 ARG A 55 0.10 SIDE CHAIN REMARK 500 18 ARG A 76 0.08 SIDE CHAIN REMARK 500 19 TYR A 82 0.07 SIDE CHAIN REMARK 500 20 ARG A 55 0.08 SIDE CHAIN REMARK 500 20 ARG A 76 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1I17 RELATED DB: PDB REMARK 900 NMR STRUCTURE OF THE MURINE DOPPEL PROTEIN DBREF 1LG4 A 24 152 UNP Q9UKY0 PRND_HUMAN 24 152 SEQRES 1 A 129 VAL GLN THR ARG GLY ILE LYS HIS ARG ILE LYS TRP ASN SEQRES 2 A 129 ARG LYS ALA LEU PRO SER THR ALA GLN ILE THR GLU ALA SEQRES 3 A 129 GLN VAL ALA GLU ASN ARG PRO GLY ALA PHE ILE LYS GLN SEQRES 4 A 129 GLY ARG LYS LEU ASP ILE ASP PHE GLY ALA GLU GLY ASN SEQRES 5 A 129 ARG TYR TYR GLU ALA ASN TYR TRP GLN PHE PRO ASP GLY SEQRES 6 A 129 ILE HIS TYR ASN GLY CYS SER GLU ALA ASN VAL THR LYS SEQRES 7 A 129 GLU ALA PHE VAL THR GLY CYS ILE ASN ALA THR GLN ALA SEQRES 8 A 129 ALA ASN GLN GLY GLU PHE GLN LYS PRO ASP ASN LYS LEU SEQRES 9 A 129 HIS GLN GLN VAL LEU TRP ARG LEU VAL GLN GLU LEU CYS SEQRES 10 A 129 SER LEU LYS HIS CYS GLU PHE TRP LEU GLU ARG GLY HELIX 1 1 GLY A 71 TYR A 82 1 12 HELIX 2 2 TRP A 83 PHE A 85 5 3 HELIX 3 3 THR A 100 ASN A 116 1 17 HELIX 4 4 ASN A 125 LEU A 142 1 18 SSBOND 1 CYS A 94 CYS A 145 1555 1555 2.02 SSBOND 2 CYS A 108 CYS A 140 1555 1555 2.02 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