PDB Short entry for 2NDK HEADER HYDROLASE 29-JUN-16 2NDK TITLE 20 LOWEST ENERGY ENSEMBLE OF DERMCIDIN (DCD1L) NMR STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DERMCIDIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 63-110; COMPND 5 SYNONYM: PREPROTEOLYSIN, SURVIVAL-PROMOTING PEPTIDE, DCD-1; COMPND 6 EC: 3.4.-.-; COMPND 7 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: DCD, AIDD, DSEP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: N.A. KEYWDS DERMCIDIN, ANTIMICROBIAL, DCD1L, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.W.TAN,Y.K.MOK REVDAT 4 14-JUN-23 2NDK 1 REMARK REVDAT 3 16-OCT-19 2NDK 1 AUTHOR REMARK REVDAT 2 15-NOV-17 2NDK 1 JRNL REVDAT 1 05-JUL-17 2NDK 0 JRNL AUTH V.S.NGUYEN,K.W.TAN,K.RAMESH,F.T.CHEW,Y.K.MOK JRNL TITL STRUCTURAL BASIS FOR THE BACTERIAL MEMBRANE INSERTION OF JRNL TITL 2 DERMCIDIN PEPTIDE, DCD-1L. JRNL REF SCI REP V. 7 13923 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 29066724 JRNL DOI 10.1038/S41598-017-13600-Z REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS, CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNS), BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG, REMARK 3 KUSZEWSKI,NILGES, PANNU,READ,RICE,SIMONSON,WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2NDK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1000104730. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 13C; U-100% 15N] REMARK 210 TRIS-1 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D C(CO)NH; 3D H(CCO) REMARK 210 NH; 3D 1H-15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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: 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 VAL A 32 -123.62 -65.47 REMARK 500 2 VAL A 32 -123.68 -65.96 REMARK 500 3 VAL A 32 -123.48 -65.17 REMARK 500 4 VAL A 32 -123.77 -66.00 REMARK 500 5 SER A 2 97.41 60.72 REMARK 500 5 VAL A 32 -123.94 -65.90 REMARK 500 6 VAL A 32 -123.94 -65.81 REMARK 500 7 VAL A 32 -123.84 -65.71 REMARK 500 8 VAL A 32 -123.93 -66.39 REMARK 500 9 SER A 2 94.38 -170.16 REMARK 500 9 VAL A 32 -123.86 -65.88 REMARK 500 10 VAL A 32 -123.76 -65.91 REMARK 500 11 VAL A 32 -123.88 -65.58 REMARK 500 12 VAL A 32 -123.98 -66.18 REMARK 500 13 VAL A 32 -123.77 -65.81 REMARK 500 14 VAL A 32 -123.90 -65.97 REMARK 500 15 VAL A 32 -123.67 -65.43 REMARK 500 16 VAL A 32 -123.80 -65.89 REMARK 500 17 SER A 2 86.84 -69.37 REMARK 500 17 VAL A 32 -123.89 -66.01 REMARK 500 18 VAL A 32 -123.80 -65.93 REMARK 500 19 VAL A 32 -123.88 -65.69 REMARK 500 20 SER A 2 128.90 63.61 REMARK 500 20 VAL A 32 -123.66 -66.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 26063 RELATED DB: BMRB DBREF 2NDK A 1 48 UNP P81605 DCD_HUMAN 63 110 SEQRES 1 A 48 SER SER LEU LEU GLU LYS GLY LEU ASP GLY ALA LYS LYS SEQRES 2 A 48 ALA VAL GLY GLY LEU GLY LYS LEU GLY LYS ASP ALA VAL SEQRES 3 A 48 GLU ASP LEU GLU SER VAL GLY LYS GLY ALA VAL HIS ASP SEQRES 4 A 48 VAL LYS ASP VAL LEU ASP SER VAL LEU HELIX 1 1 SER A 2 GLY A 22 1 21 HELIX 2 2 GLY A 22 SER A 31 1 10 HELIX 3 3 VAL A 32 LEU A 48 1 17 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