1EWS - Header Asymmetric Unit

HEADER ANTIMICROBIAL PROTEIN 26-APR-00 1EWS

TITLE THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE RABBIT TITLE 2 KIDNEY DEFENSIN, RK-1

COMPND MOL_ID: 1; COMPND 2 MOLECULE: RK-1 DEFENSIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALPHA-DEFISIN

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS; SOURCE 3 ORGANISM_COMMON: RABBIT; SOURCE 4 ORGANISM_TAXID: 9986; SOURCE 5 ORGAN: KIDNEY

KEYWDS ALPHA DEFENSIN, TRIPLE-STRANDED BETA-SHEET, ANTIMICROBIAL KEYWDS 2 PROTEIN

EXPDTA SOLUTION NMR

NUMMDL 20

AUTHOR A.M.MCMANUS,N.F.DAWSON,J.D.WADE,D.J.CRAIK

REVDAT 3 24-FEB-09 1EWS 1 VERSN REVDAT 2 01-APR-03 1EWS 1 JRNL REVDAT 1 02-MAY-01 1EWS 0

JRNL AUTH A.M.MCMANUS,N.F.DAWSON,J.D.WADE,L.E.CARRINGTON, JRNL AUTH 2 D.J.WINZOR,D.J.CRAIK JRNL TITL THREE-DIMENSIONAL STRUCTURE OF RK-1: A NOVEL JRNL TITL 2 ALPHA-DEFENSIN PEPTIDE. JRNL REF BIOCHEMISTRY V. 39 15757 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 11123900 JRNL DOI 10.1021/BI000457L

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.F.DAWSON,D.J.CRAIK,A.M.MCMANUS,S.G.DASHPER, REMARK 1 AUTH 2 E.G.REYNOLDS,G.W.TREGEAR,L.OTVOS,J.D.WADE REMARK 1 TITL CHEMICAL SYNTHESIS, CHARACTERIZATION AND ACTIVITY REMARK 1 TITL 2 OF RK-1, A NOVEL ALPHA-DEFENSIN-RELATED PEPTIDE REMARK 1 REF J.PEPT.SCI. V. 6 19 2000 REMARK 1 REFN ISSN 1075-2617 REMARK 1 DOI 10.1002/(SICI)1099-1387(200001)6:1<19::AID-PSC230>3 REMARK 1 DOI 2 .3.CO;2-T

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL REMARK 3 OF 509 DISTANCE RESTRAINTS CONSISTING OF 498 NOE-DERIVED REMARK 3 DISTANCE RESTRAINTS, 11 RESTRAINTS FROM HYDROGEN BONDS AND 31 REMARK 3 DIHEDRAL ANGLE RESTRAINTS

REMARK 4 REMARK 4 1EWS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAY-00. REMARK 100 THE RCSB ID CODE IS RCSB010973.

REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308; 308; 308 REMARK 210 PH : 3.5; 3.5; 3.5 REMARK 210 IONIC STRENGTH : NULL; NULL; NULL REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5 MM RK1; 1.5 MM RK1; 1.5 REMARK 210 MM RK1 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY, 2D NOESY, E-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 750 MHZ REMARK 210 SPECTROMETER MODEL : ARX, DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, X-EASY 1.3.7, X- REMARK 210 PLOR 3.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 9 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES

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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 20 MET A 1 N MET A 1 CA -0.969 REMARK 500 20 MET A 1 CA MET A 1 CB -1.353 REMARK 500 20 MET A 1 CB MET A 1 CG -1.309 REMARK 500 20 MET A 1 CG MET A 1 SD -1.717 REMARK 500 20 MET A 1 SD MET A 1 CE -1.607 REMARK 500 20 MET A 1 CA MET A 1 C -0.852 REMARK 500 20 MET A 1 C MET A 1 O -0.605 REMARK 500 20 PRO A 2 N PRO A 2 CA -0.843 REMARK 500 20 PRO A 2 CA PRO A 2 CB -0.942 REMARK 500 20 PRO A 2 CB PRO A 2 CG -0.727 REMARK 500 20 PRO A 2 CG PRO A 2 CD -1.306 REMARK 500 20 PRO A 2 CD PRO A 2 N -0.704 REMARK 500 20 PRO A 2 C PRO A 2 O -0.128 REMARK 500 20 MET A 1 C PRO A 2 N -1.127 REMARK 500 20 CYS A 3 CA CYS A 3 CB -0.092 REMARK 500 20 CYS A 3 CB CYS A 3 SG -0.314 REMARK 500 20 CYS A 3 C CYS A 3 O -0.126 REMARK 500 20 PRO A 2 C CYS A 3 N -0.159 REMARK 500 20 SER A 4 CB SER A 4 OG -0.959 REMARK 500 20 LYS A 6 CG LYS A 6 CD -0.684 REMARK 500 20 LYS A 6 CD LYS A 6 CE -0.753 REMARK 500 20 LYS A 6 CE LYS A 6 NZ -1.033 REMARK 500 20 LYS A 7 CB LYS A 7 CG -0.639 REMARK 500 20 LYS A 7 CG LYS A 7 CD -0.864 REMARK 500 20 LYS A 7 CD LYS A 7 CE -0.649 REMARK 500 20 LYS A 7 CE LYS A 7 NZ -0.971 REMARK 500 20 TYR A 8 CB TYR A 8 CG -0.843 REMARK 500 20 TYR A 8 CG TYR A 8 CD2 -0.809 REMARK 500 20 TYR A 8 CG TYR A 8 CD1 -1.294 REMARK 500 20 TYR A 8 CD1 TYR A 8 CE1 -0.788 REMARK 500 20 TYR A 8 CE1 TYR A 8 CZ -0.805 REMARK 500 20 TYR A 8 CZ TYR A 8 OH -0.774 REMARK 500 20 TYR A 8 CZ TYR A 8 CE2 -1.289 REMARK 500 20 TYR A 8 CE2 TYR A 8 CD2 -0.788 REMARK 500 20 TYR A 8 C TYR A 8 O -0.118 REMARK 500 20 ASP A 10 CG ASP A 10 OD1 -0.680 REMARK 500 20 ASP A 10 CG ASP A 10 OD2 -0.673 REMARK 500 20 TRP A 12 CG TRP A 12 CD2 -0.136 REMARK 500 20 TRP A 12 CD1 TRP A 12 NE1 -0.129 REMARK 500 20 TRP A 12 NE1 TRP A 12 CE2 -0.123 REMARK 500 20 TRP A 12 CE2 TRP A 12 CD2 -0.082 REMARK 500 20 GLU A 13 CG GLU A 13 CD -0.338 REMARK 500 20 GLU A 13 CD GLU A 13 OE1 -0.874 REMARK 500 20 GLU A 13 CD GLU A 13 OE2 -0.595 REMARK 500 20 VAL A 14 CB VAL A 14 CG1 -0.619 REMARK 500 20 VAL A 14 CB VAL A 14 CG2 -0.865 REMARK 500 20 ASP A 16 CB ASP A 16 CG -0.440 REMARK 500 20 ASP A 16 CG ASP A 16 OD1 -0.784 REMARK 500 20 ASP A 16 CG ASP A 16 OD2 -0.940 REMARK 500 20 SER A 18 CB SER A 18 OG -0.636 REMARK 500 REMARK 500 THIS ENTRY HAS 96 BOND DEVIATIONS. 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 TRP A 12 CD1 - NE1 - CE2 ANGL. DEV. = 7.2 DEGREES REMARK 500 2 TRP A 12 CD1 - NE1 - CE2 ANGL. DEV. = 7.2 DEGREES REMARK 500 3 TRP A 12 CD1 - NE1 - CE2 ANGL. DEV. = 7.2 DEGREES REMARK 500 4 TRP A 12 CD1 - NE1 - CE2 ANGL. DEV. = 7.2 DEGREES REMARK 500 5 TRP A 12 CD1 - NE1 - CE2 ANGL. DEV. = 7.2 DEGREES REMARK 500 6 CYS A 9 CA - CB - SG ANGL. DEV. = 6.9 DEGREES REMARK 500 6 TRP A 12 CD1 - NE1 - CE2 ANGL. DEV. = 7.2 DEGREES REMARK 500 7 TRP A 12 CD1 - NE1 - CE2 ANGL. DEV. = 7.2 DEGREES REMARK 500 8 CYS A 9 CA - CB - SG ANGL. DEV. = 7.2 DEGREES REMARK 500 8 TRP A 12 CD1 - NE1 - CE2 ANGL. DEV. = 7.2 DEGREES REMARK 500 8 ARG A 30 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 9 CYS A 9 CA - CB - SG ANGL. DEV. = 7.4 DEGREES REMARK 500 9 TRP A 12 CD1 - NE1 - CE2 ANGL. DEV. = 7.3 DEGREES REMARK 500 10 CYS A 9 CA - CB - SG ANGL. DEV. = 7.0 DEGREES REMARK 500 10 TRP A 12 CD1 - NE1 - CE2 ANGL. DEV. = 7.2 DEGREES REMARK 500 11 TRP A 12 CD1 - NE1 - CE2 ANGL. DEV. = 7.2 DEGREES REMARK 500 12 CYS A 9 CA - CB - SG ANGL. DEV. = 7.0 DEGREES REMARK 500 12 TRP A 12 CD1 - NE1 - CE2 ANGL. DEV. = 7.2 DEGREES REMARK 500 13 TRP A 12 CD1 - NE1 - CE2 ANGL. DEV. = 7.3 DEGREES REMARK 500 14 CYS A 9 CA - CB - SG ANGL. DEV. = 7.0 DEGREES REMARK 500 14 TRP A 12 CD1 - NE1 - CE2 ANGL. DEV. = 7.2 DEGREES REMARK 500 15 CYS A 9 CA - CB - SG ANGL. DEV. = 7.2 DEGREES REMARK 500 15 TRP A 12 CD1 - NE1 - CE2 ANGL. DEV. = 7.2 DEGREES REMARK 500 16 CYS A 9 CA - CB - SG ANGL. DEV. = 6.8 DEGREES REMARK 500 16 TRP A 12 CD1 - NE1 - CE2 ANGL. DEV. = 7.2 DEGREES REMARK 500 16 CYS A 29 CA - CB - SG ANGL. DEV. = 7.8 DEGREES REMARK 500 17 TRP A 12 CD1 - NE1 - CE2 ANGL. DEV. = 7.1 DEGREES REMARK 500 18 TRP A 12 CD1 - NE1 - CE2 ANGL. DEV. = 7.2 DEGREES REMARK 500 19 TRP A 12 CD1 - NE1 - CE2 ANGL. DEV. = 7.1 DEGREES REMARK 500 19 ARG A 30 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 20 MET A 1 CB - CA - C ANGL. DEV. = -79.7 DEGREES REMARK 500 20 MET A 1 N - CA - CB ANGL. DEV. = 39.0 DEGREES REMARK 500 20 MET A 1 CA - CB - CG ANGL. DEV. = -58.2 DEGREES REMARK 500 20 MET A 1 CB - CG - SD ANGL. DEV. = -54.9 DEGREES REMARK 500 20 MET A 1 CG - SD - CE ANGL. DEV. = -23.0 DEGREES REMARK 500 20 MET A 1 N - CA - C ANGL. DEV. = 68.0 DEGREES REMARK 500 20 MET A 1 CA - C - O ANGL. DEV. = 44.8 DEGREES REMARK 500 20 PRO A 2 CA - N - CD ANGL. DEV. = 51.3 DEGREES REMARK 500 20 PRO A 2 CB - CA - C ANGL. DEV. = 48.6 DEGREES REMARK 500 20 PRO A 2 N - CA - CB ANGL. DEV. = -75.1 DEGREES REMARK 500 20 PRO A 2 CA - CB - CG ANGL. DEV. = 56.6 DEGREES REMARK 500 20 PRO A 2 N - CD - CG ANGL. DEV. = -21.6 DEGREES REMARK 500 20 PRO A 2 N - CA - C ANGL. DEV. = 51.7 DEGREES REMARK 500 20 MET A 1 CA - C - N ANGL. DEV. = -58.2 DEGREES REMARK 500 20 MET A 1 O - C - N ANGL. DEV. = 15.1 DEGREES REMARK 500 20 PRO A 2 C - N - CA ANGL. DEV. = -59.3 DEGREES REMARK 500 20 CYS A 3 CA - CB - SG ANGL. DEV. = 11.9 DEGREES REMARK 500 20 SER A 4 CA - CB - OG ANGL. DEV. = 29.5 DEGREES REMARK 500 20 LYS A 6 CB - CG - CD ANGL. DEV. = 18.9 DEGREES REMARK 500 20 LYS A 6 CG - CD - CE ANGL. DEV. = 58.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 128 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 ASP A 16 -18.02 -150.21 REMARK 500 1 PHE A 22 36.42 -90.49 REMARK 500 2 PRO A 2 96.68 -66.00 REMARK 500 2 CYS A 3 -144.49 -143.11 REMARK 500 2 TYR A 8 -148.12 -134.06 REMARK 500 2 ASP A 16 -14.30 -147.07 REMARK 500 2 LEU A 21 -99.99 -89.75 REMARK 500 2 ASN A 23 19.45 57.96 REMARK 500 2 GLU A 31 -53.85 -144.69 REMARK 500 3 TYR A 8 -132.66 -147.42 REMARK 500 3 ASP A 16 -20.97 -148.99 REMARK 500 3 LEU A 21 -113.56 -89.80 REMARK 500 3 ASN A 23 20.97 43.03 REMARK 500 4 ASP A 16 -13.81 -147.24 REMARK 500 4 LEU A 21 -113.01 -89.69 REMARK 500 4 ASN A 23 29.02 41.96 REMARK 500 5 TYR A 8 -122.58 -122.13 REMARK 500 5 ASP A 16 -85.75 -143.03 REMARK 500 5 LEU A 21 -75.98 -90.04 REMARK 500 5 PHE A 22 58.29 -90.30 REMARK 500 5 ASN A 23 26.44 45.44 REMARK 500 6 LEU A 21 -118.84 -89.72 REMARK 500 6 ASN A 23 26.04 42.01 REMARK 500 7 CYS A 3 -160.65 -111.35 REMARK 500 7 ASP A 16 -14.48 -149.36 REMARK 500 7 LEU A 21 -102.96 -89.69 REMARK 500 7 ASN A 23 12.75 57.65 REMARK 500 8 ASP A 16 -55.21 -143.20 REMARK 500 8 LEU A 21 -94.92 -89.72 REMARK 500 9 LEU A 21 -98.36 -89.80 REMARK 500 10 TYR A 8 -155.72 -150.32 REMARK 500 10 ILE A 15 153.55 -47.16 REMARK 500 10 ASP A 16 -22.68 -148.97 REMARK 500 10 LEU A 21 -97.27 -89.77 REMARK 500 10 ASN A 23 24.83 43.09 REMARK 500 11 ASP A 16 -21.32 -149.78 REMARK 500 11 CYS A 19 -168.90 -108.99 REMARK 500 11 LEU A 21 -102.12 -89.61 REMARK 500 11 ASN A 23 18.90 57.01 REMARK 500 12 ASP A 16 -20.08 -149.21 REMARK 500 12 LEU A 21 -98.05 -89.86 REMARK 500 12 ASN A 23 28.63 41.77 REMARK 500 13 ASP A 16 -14.48 -145.08 REMARK 500 13 LEU A 21 -98.18 -89.74 REMARK 500 13 ASN A 23 28.88 42.20 REMARK 500 14 ASP A 16 -24.79 -150.12 REMARK 500 14 LEU A 21 -120.03 -94.01 REMARK 500 14 ASN A 23 28.01 40.21 REMARK 500 14 ARG A 30 56.53 -99.09 REMARK 500 15 PRO A 2 89.32 -64.98 REMARK 500 15 ASP A 16 -30.09 -150.17 REMARK 500 15 LEU A 21 -75.07 -90.01 REMARK 500 15 PHE A 22 44.41 -90.09 REMARK 500 16 ASP A 16 -23.40 -149.98 REMARK 500 16 LEU A 21 -113.18 -89.90 REMARK 500 16 ASN A 23 27.39 42.01 REMARK 500 16 ARG A 30 45.96 -93.61 REMARK 500 17 LEU A 21 -108.08 -89.71 REMARK 500 17 ASN A 23 18.27 56.97 REMARK 500 17 GLU A 31 50.29 -108.58 REMARK 500 18 ASP A 16 -37.94 -146.95 REMARK 500 18 LEU A 21 -95.74 -89.81 REMARK 500 18 ASN A 23 19.79 55.43 REMARK 500 19 ASP A 16 -20.56 -147.43 REMARK 500 19 LEU A 21 -95.10 -89.84 REMARK 500 20 PRO A 2 51.20 -57.02 REMARK 500 20 ASP A 16 -25.06 -143.86 REMARK 500 20 LEU A 21 -100.73 -89.79 REMARK 500 20 ASN A 23 23.53 49.54 REMARK 500 REMARK 500 REMARK: NULL

DBREF 1EWS A 1 32 UNP P81655 RK1_RABIT 1 32

SEQRES 1 A 32 MET PRO CYS SER CYS LYS LYS TYR CYS ASP PRO TRP GLU SEQRES 2 A 32 VAL ILE ASP GLY SER CYS GLY LEU PHE ASN SER LYS TYR SEQRES 3 A 32 ILE CYS CYS ARG GLU LYS

SHEET 1 A 3 SER A 4 LYS A 6 0 SHEET 2 A 3 TYR A 26 ARG A 30 -1 O TYR A 26 N LYS A 6 SHEET 3 A 3 GLU A 13 GLY A 17 -1 N VAL A 14 O CYS A 29

SSBOND 1 CYS A 3 CYS A 29 1555 1555 2.02 SSBOND 2 CYS A 5 CYS A 19 1555 1555 2.02 SSBOND 3 CYS A 9 CYS A 28 1555 1555 2.01

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