Header list of 1ohm.pdb file
Complete list - 25 20 Bytes
HEADER ANTIBIOTIC 28-MAY-03 1OHM TITLE SAKACIN P VARIANT THAT IS STRUCTURALLY STABILIZED BY AN TITLE 2 INSERTED C-TERMINAL DISULFIDE BRIDGE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACTERIOCIN SAKACIN P; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SAKACIN 674; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: SAKACIN P VARIANT THAT IS STRUCTURALLY COMPND 8 STABILIZED BY AN INSERTED C-TERMINAL DISULFIDE BRIDGE. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOBACILLUS SAKE; SOURCE 3 ORGANISM_TAXID: 1599; SOURCE 4 STRAIN: LB790; SOURCE 5 VARIANT: LB790/PGF10; SOURCE 6 EXPRESSION_SYSTEM: LACTOBACILLUS SAKE; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 1599; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: LB790; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: LB790/PGF10; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PMG36E; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PGF10 KEYWDS ANTIBIOTIC, PEDIOCIN-LIKE BACTERIOCINS, ANTIMICROBIAL KEYWDS 2 PEPTIDES, SAKACIN ANTIBIOTIC, BACTERIOCIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.UTENG,H.H.HAUGE,P.R.MARKWICK,G.FIMLAND,D.MANTZILAS, AUTHOR 2 J.NISSEN-MEYER,C.MUHLE-GOLL REVDAT 3 24-FEB-09 1OHM 1 VERSN REVDAT 2 02-OCT-03 1OHM 1 JRNL REVDAT 1 22-SEP-03 1OHM 0 JRNL AUTH M.UTENG,H.H.HAUGE,P.R.MARKWICK,G.FIMLAND, JRNL AUTH 2 D.MANTZILAS,J.NISSEN-MEYER,C.MUHLE-GOLL JRNL TITL THREE-DIMENSIONAL STRUCTURE IN LIPID MICELLES OF JRNL TITL 2 THE PEDIOCIN-LIKE ANTIMICROBIAL PEPTIDE SAKACIN P JRNL TITL 3 AND A SAKACIN P VARIANT THAT IS STRUCTURALLY JRNL TITL 4 STABILIZED BY AN INSERTED C-TERMINAL DISULFIDE JRNL TITL 5 BRIDGE JRNL REF BIOCHEMISTRY V. 42 11417 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 14516192 JRNL DOI 10.1021/BI034572I REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 6 REMARK 3 AUTHORS : CASE, D.A., PEARLMAN, D.A., CALDWELL, III, REMARK 3 J.C., ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: AMBER 6, SAN FRANCISCO, UNIVERSITY REMARK 3 OF CALIFORNIA, 1999. REMARK 4 REMARK 4 1OHM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-MAY-03. REMARK 100 THE PDBE ID CODE IS EBI-12621. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 2.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 250 MM DPC/10% D2O/ REMARK 210 0.1% TFA/1MM PEPTIDE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 REMARK 210 SPECTROMETER MODEL : DRX500 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ARIA, AMBER REMARK 210 METHOD USED : MOLECULAR DYNAMICS/ REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAIN VIOLATION REMARK 210 AND OVERALL ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURES WERE DETERMINED USING A COMBINATION REMARK 210 OF 1H NMR SPECTROSCOPIC METHODS FOLLOWED BY DISTANCE REMARK 210 GEOMETRY/SIMULATED ANNEALING CALCULATIONS. 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 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 ENGINEERED MUTATION IN CHAIN A: CYS 42 TO ASN 42 REMARK 400 REMARK 400 SAKACIN P VARIANT THAT IS STRUCTURALLY STABILIZED BY AN REMARK 400 INSERTED C-TERMINAL DISULFIDE BRIDGE. 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 CYS A 9 CA - CB - SG ANGL. DEV. = 8.4 DEGREES REMARK 500 2 CYS A 9 CB - CA - C ANGL. DEV. = 7.5 DEGREES REMARK 500 5 VAL A 16 C - N - CA ANGL. DEV. = 15.9 DEGREES REMARK 500 9 ASN A 38 C - N - CA ANGL. DEV. = 15.3 DEGREES REMARK 500 10 SER A 13 C - N - CA ANGL. DEV. = 15.4 DEGREES REMARK 500 10 VAL A 16 CA - CB - CG1 ANGL. DEV. = 10.4 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 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 VAL A 7 150.04 51.39 REMARK 500 1 SER A 13 -44.97 172.62 REMARK 500 1 CYS A 14 -74.01 -74.42 REMARK 500 1 THR A 15 -127.44 52.89 REMARK 500 1 VAL A 16 95.51 48.82 REMARK 500 1 ALA A 29 -72.97 -56.79 REMARK 500 1 TRP A 33 -126.04 -178.63 REMARK 500 1 ASN A 38 7.30 -153.62 REMARK 500 1 ASN A 42 3.72 -164.52 REMARK 500 2 LYS A 11 -5.24 -56.53 REMARK 500 2 CYS A 24 -73.45 -52.96 REMARK 500 2 TRP A 33 -135.24 175.59 REMARK 500 2 ASN A 42 -2.24 -53.25 REMARK 500 3 CYS A 14 81.82 61.41 REMARK 500 3 VAL A 16 112.11 -14.31 REMARK 500 3 TRP A 33 -122.30 172.92 REMARK 500 3 ALA A 34 -34.15 -145.13 REMARK 500 3 ASN A 42 2.25 -57.14 REMARK 500 4 VAL A 7 -95.96 49.60 REMARK 500 4 HIS A 8 99.11 97.07 REMARK 500 4 LYS A 11 -26.33 61.46 REMARK 500 4 SER A 13 -169.67 172.47 REMARK 500 4 THR A 15 -133.81 -142.86 REMARK 500 4 VAL A 16 -1.19 -146.19 REMARK 500 4 ASP A 17 -18.23 102.34 REMARK 500 4 CYS A 24 -74.08 -55.74 REMARK 500 4 TRP A 33 -101.61 146.04 REMARK 500 4 ALA A 34 43.49 -154.84 REMARK 500 4 ASN A 42 8.26 147.49 REMARK 500 4 LYS A 43 82.38 1.28 REMARK 500 5 HIS A 8 89.11 -156.89 REMARK 500 5 HIS A 12 -124.69 -116.13 REMARK 500 5 CYS A 14 -66.39 -128.32 REMARK 500 5 THR A 15 -174.78 54.04 REMARK 500 5 ALA A 29 -72.67 -55.61 REMARK 500 5 TRP A 33 -55.46 -153.35 REMARK 500 5 ASN A 38 -48.62 -144.05 REMARK 500 5 ASN A 42 0.18 -162.77 REMARK 500 5 LYS A 43 138.95 -27.81 REMARK 500 6 TYR A 2 95.06 85.46 REMARK 500 6 VAL A 7 136.20 -20.84 REMARK 500 6 HIS A 12 -82.91 -102.35 REMARK 500 6 CYS A 14 92.68 54.28 REMARK 500 6 THR A 15 -55.78 -121.64 REMARK 500 6 TRP A 33 -118.05 157.86 REMARK 500 6 ASN A 42 25.34 149.66 REMARK 500 6 LYS A 43 108.21 -24.34 REMARK 500 7 HIS A 8 77.64 33.57 REMARK 500 7 CYS A 14 -87.00 -66.12 REMARK 500 7 THR A 15 -60.25 61.01 REMARK 500 7 TRP A 33 -106.33 147.26 REMARK 500 7 ALA A 34 -33.99 -165.00 REMARK 500 7 ASN A 42 12.29 -152.51 REMARK 500 7 LYS A 43 173.13 46.77 REMARK 500 8 LYS A 11 40.97 -72.01 REMARK 500 8 HIS A 12 -118.20 -131.32 REMARK 500 8 CYS A 14 86.71 62.95 REMARK 500 8 CYS A 24 -70.20 -56.48 REMARK 500 8 TRP A 33 -113.43 170.80 REMARK 500 8 ALA A 34 -39.04 -154.19 REMARK 500 8 ASN A 42 20.28 153.13 REMARK 500 8 LYS A 43 94.50 -15.05 REMARK 500 9 HIS A 12 -87.70 -116.33 REMARK 500 9 CYS A 14 158.97 65.66 REMARK 500 9 TRP A 33 -123.83 175.51 REMARK 500 9 ASN A 38 -32.30 127.63 REMARK 500 9 ASN A 42 21.70 170.57 REMARK 500 9 LYS A 43 103.13 -32.99 REMARK 500 10 VAL A 7 157.75 -46.50 REMARK 500 10 SER A 13 -71.46 -84.30 REMARK 500 10 ASP A 17 -47.23 132.36 REMARK 500 10 TRP A 33 -105.38 141.12 REMARK 500 10 ASN A 42 7.08 -152.20 REMARK 500 10 LYS A 43 -27.31 62.95 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 VAL A 16 ASP A 17 1 138.76 REMARK 500 ASN A 42 LYS A 43 1 -92.42 REMARK 500 THR A 35 GLY A 36 2 147.79 REMARK 500 ASN A 42 LYS A 43 2 139.93 REMARK 500 VAL A 16 ASP A 17 3 119.72 REMARK 500 ASN A 32 TRP A 33 3 -137.71 REMARK 500 THR A 35 GLY A 36 3 143.80 REMARK 500 ASN A 42 LYS A 43 3 141.24 REMARK 500 ASN A 42 LYS A 43 5 -114.84 REMARK 500 CYS A 14 THR A 15 6 -148.78 REMARK 500 VAL A 16 ASP A 17 6 143.77 REMARK 500 ASN A 32 TRP A 33 6 -129.59 REMARK 500 VAL A 16 ASP A 17 7 141.02 REMARK 500 GLY A 36 GLY A 37 7 142.57 REMARK 500 ASN A 42 LYS A 43 7 -141.74 REMARK 500 LYS A 43 CYS A 44 7 125.05 REMARK 500 VAL A 16 ASP A 17 8 118.74 REMARK 500 ASN A 32 TRP A 33 8 -147.90 REMARK 500 THR A 35 GLY A 36 8 148.21 REMARK 500 GLY A 36 GLY A 37 8 146.91 REMARK 500 THR A 35 GLY A 36 9 147.12 REMARK 500 ASN A 42 LYS A 43 9 -104.84 REMARK 500 CYS A 14 THR A 15 10 -138.72 REMARK 500 THR A 15 VAL A 16 10 -149.10 REMARK 500 LYS A 43 CYS A 44 10 -124.87 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 1 TRP A 41 0.10 SIDE CHAIN REMARK 500 2 HIS A 8 0.09 SIDE CHAIN REMARK 500 4 TRP A 18 0.07 SIDE CHAIN REMARK 500 4 TRP A 33 0.09 SIDE CHAIN REMARK 500 4 TRP A 41 0.08 SIDE CHAIN REMARK 500 5 TRP A 33 0.06 SIDE CHAIN REMARK 500 7 TRP A 41 0.08 SIDE CHAIN REMARK 500 10 TRP A 41 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 1 CYS A 9 19.1 L L OUTSIDE RANGE REMARK 500 2 CYS A 9 21.2 L L OUTSIDE RANGE REMARK 500 4 VAL A 7 22.4 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OG7 RELATED DB: PDB REMARK 900 THREE-DIMENSIONAL STRUCTURE IN LIPID MICELLES REMARK 900 OF THE PEDIOCIN-LIKE ANTIMICROBIAL PEPTIDE SAKACIN P. REMARK 900 RELATED ID: 1OHN RELATED DB: PDB REMARK 900 THREE-DIMENSIONAL STRUCTURE IN LIPID MICELLES OF THE REMARK 900 PEDIOCIN-LIKE ANTIMICROBIAL PEPTIDE SAKACIN P. REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE IS DESCRIBED IN J. BACTERIOL. 182, 2643-2648 DBREF 1OHM A 1 43 UNP P35618 SAKP_LACSK 19 61 DBREF 1OHM A 44 44 PDB 1OHM 1OHM 44 44 SEQADV 1OHM CYS A 24 UNP P35618 ASN 42 ENGINEERED MUTATION SEQADV 1OHM CYS A 44 PDB 1OHM INSERTION SEQRES 1 A 44 LYS TYR TYR GLY ASN GLY VAL HIS CYS GLY LYS HIS SER SEQRES 2 A 44 CYS THR VAL ASP TRP GLY THR ALA ILE GLY CYS ILE GLY SEQRES 3 A 44 ASN ASN ALA ALA ALA ASN TRP ALA THR GLY GLY ASN ALA SEQRES 4 A 44 GLY TRP ASN LYS CYS HELIX 1 1 TRP A 18 TRP A 33 1 16 SSBOND 1 CYS A 9 CYS A 14 1555 1555 2.01 SSBOND 2 CYS A 24 CYS A 44 1555 1555 2.05 CISPEP 1 CYS A 9 GLY A 10 2 10.04 CISPEP 2 THR A 15 VAL A 16 5 4.27 CISPEP 3 ASN A 32 TRP A 33 5 2.79 CISPEP 4 HIS A 12 SER A 13 10 5.93 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
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