HEADER ANTIMICROBIAL PROTEIN 06-APR-06 2GMD TITLE STRUCTURE OF C12-LF11 BOUND TO THE SDS MICELLES COMPND MOL_ID: 1; COMPND 2 MOLECULE: LACTOFERRIN-BASED SYNTHETIC PEPTIDE C12-LF11; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS ANTIMICROBIAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.JAPELJ REVDAT 3 24-JUN-20 2GMD 1 SOURCE REMARK DBREF LINK REVDAT 2 24-FEB-09 2GMD 1 VERSN REVDAT 1 13-FEB-07 2GMD 0 JRNL AUTH B.JAPELJ,M.ZORKO,A.MAJERLE,P.PRISTOVSEK,S.SANCHEZ-GOMEZ, JRNL AUTH 2 G.M.TEJADA,I.MORIYON,S.E.BLONDELLE,K.BRANDENBURG,J.ANDRA, JRNL AUTH 3 K.LOHNER,R.JERALA JRNL TITL THE ACYL GROUP AS THE CENTRAL ELEMENT OF THE STRUCTURAL JRNL TITL 2 ORGANIZATION OF ANTIMICROBIAL LIPOPEPTIDE. JRNL REF J.AM.CHEM.SOC. V. 129 1022 2007 JRNL REFN ISSN 0002-7863 JRNL PMID 17263370 JRNL DOI 10.1021/JA067419V REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5, DISCOVER, DYANA 1.5 REMARK 3 AUTHORS : GUENTERT, P., MUMENTHALER, C. & WUETHRICH, K. REMARK 3 (DYANA), MOLECULAR SIMULATIONS INC. (DISCOVER), REMARK 3 GUENTERT, P., MUMENTHALER, C. & WUETHRICH, K. REMARK 3 (DYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2GMD COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000037292. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 0.247 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.3 MM C12-LF11, 227.1 MM D25 REMARK 210 -SDS (SODIUMDODECYLSULPHATE), 20 REMARK 210 MM PHOSPHATE BUFFER NA, 7% D20, REMARK 210 93 % H20 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D TOCSY; 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITY REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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: 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 TRP A 3 CD1 - NE1 - CE2 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 3 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 4 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 4 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 4 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 5 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 5 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 6 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 6 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 6 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 7 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 7 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 7 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 8 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 8 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 8 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 9 TRP A 3 CD1 - NE1 - CE2 ANGL. DEV. = -5.6 DEGREES REMARK 500 9 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 9 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 9 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 10 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 11 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 11 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 11 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 12 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 12 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 12 ARG A 8 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 12 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 13 TRP A 3 CD1 - NE1 - CE2 ANGL. DEV. = -5.6 DEGREES REMARK 500 13 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 13 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 13 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 14 TRP A 3 CB - CG - CD2 ANGL. DEV. = 8.3 DEGREES REMARK 500 14 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 14 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 14 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 15 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 15 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 15 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 68 ANGLE DEVIATIONS. 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 GLN A 4 -97.61 -106.80 REMARK 500 1 ASN A 6 96.29 -164.48 REMARK 500 1 VAL A 10 -34.96 -132.99 REMARK 500 2 GLN A 4 -108.99 -76.40 REMARK 500 2 ASN A 6 94.28 -171.85 REMARK 500 2 ILE A 7 -79.92 -79.06 REMARK 500 2 ARG A 8 -123.46 65.51 REMARK 500 2 VAL A 10 115.01 -18.57 REMARK 500 3 GLN A 4 -111.32 -78.78 REMARK 500 3 ASN A 6 102.87 -170.30 REMARK 500 4 GLN A 4 -105.64 -71.18 REMARK 500 4 ARG A 5 18.70 -144.53 REMARK 500 4 ILE A 7 -73.16 -78.97 REMARK 500 4 ARG A 8 83.80 10.18 REMARK 500 4 VAL A 10 -65.78 -157.23 REMARK 500 5 GLN A 2 28.31 -145.28 REMARK 500 5 TRP A 3 -179.31 -57.01 REMARK 500 5 GLN A 4 -99.77 -80.30 REMARK 500 5 ARG A 5 69.51 -151.71 REMARK 500 5 ASN A 6 82.76 -158.55 REMARK 500 5 ILE A 7 -68.79 -93.00 REMARK 500 5 VAL A 10 -66.15 -141.42 REMARK 500 6 GLN A 4 -57.97 -126.50 REMARK 500 6 ASN A 6 98.30 -167.51 REMARK 500 6 ILE A 7 -69.49 -90.60 REMARK 500 7 GLN A 4 -65.75 -126.03 REMARK 500 7 ASN A 6 84.84 -165.61 REMARK 500 7 VAL A 10 -173.86 56.19 REMARK 500 8 GLN A 2 17.32 -144.59 REMARK 500 8 TRP A 3 179.06 -48.92 REMARK 500 8 GLN A 4 -105.14 -77.34 REMARK 500 8 ASN A 6 85.54 -151.01 REMARK 500 9 ASN A 6 83.27 -177.55 REMARK 500 9 VAL A 10 -76.18 -127.63 REMARK 500 10 GLN A 4 -101.52 -81.59 REMARK 500 10 ARG A 5 57.10 -140.79 REMARK 500 10 ASN A 6 106.65 -165.89 REMARK 500 10 VAL A 10 -160.37 57.61 REMARK 500 11 GLN A 4 -118.20 -72.22 REMARK 500 11 ASN A 6 72.05 -170.70 REMARK 500 11 ARG A 8 105.34 -52.00 REMARK 500 11 VAL A 10 -36.62 -150.74 REMARK 500 12 GLN A 2 35.09 -143.72 REMARK 500 12 TRP A 3 -178.01 -60.74 REMARK 500 12 GLN A 4 -100.74 -79.05 REMARK 500 12 ARG A 5 71.54 -150.40 REMARK 500 12 ASN A 6 79.26 -154.62 REMARK 500 12 ILE A 7 -71.26 -101.39 REMARK 500 13 ARG A 5 -87.55 -91.92 REMARK 500 13 ILE A 7 -74.99 -55.86 REMARK 500 REMARK 500 THIS ENTRY HAS 82 RAMACHANDRAN OUTLIERS. 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 12 ARG A 8 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DAO A 13 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2GMC RELATED DB: PDB DBREF 2GMD A 1 12 PDB 2GMD 2GMD 1 12 SEQRES 1 A 12 PHE GLN TRP GLN ARG ASN ILE ARG LYS VAL ARG NH2 HET NH2 A 12 3 HET DAO A 13 36 HETNAM NH2 AMINO GROUP HETNAM DAO LAURIC ACID FORMUL 1 NH2 H2 N FORMUL 2 DAO C12 H24 O2 LINK N PHE A 1 C1 DAO A 13 1555 1555 1.73 LINK C ARG A 11 N NH2 A 12 1555 1555 1.32 SITE 1 AC1 2 PHE A 1 TRP A 3 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