HEADER ANTIMICROBIAL PROTEIN 19-DEC-13 2MIT TITLE SOLUTION STRUCTURE OF OXIDIZED DIMERIC FORM OF HUMAN DEFENSIN 5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEFENSIN-5; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 63-94; COMPND 5 SYNONYM: DEFENSIN, ALPHA 5, HD5(63-94); 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: DEF5, DEFA5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PJ201-TEV-HD5OXIDIZED KEYWDS CYSTEINE KNOT, ANTIMICROBIAL PEPTIDE, ANTIMICROBIAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.J.WOMMACK,J.J.ZIAREK,G.WAGNER,E.M.NOLAN REVDAT 1 17-SEP-14 2MIT 0 JRNL AUTH A.J.WOMMACK,J.J.ZIAREK,G.WAGNER,E.M.NOLAN JRNL TITL SOLUTION STRUCTURE OF OXIDIZED DIMERIC FORM OF HUMAN JRNL TITL 2 DEFENSIN 5 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR_NIH, WHATIF, CYANA REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR_ REMARK 3 NIH), VRIEND (WHATIF), GUNTERT, MUMENTHALER AND REMARK 3 WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: INITIAL STRUCTURES CALCULATED BY REMARK 3 MINIMIZING TARGET FUNCTION. FINAL CYANA STRUCTURE REFINED IN REMARK 3 EXPLICIT WATER USING MOLECULAR DYNAMICS. REMARK 4 REMARK 4 2MIT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-SEP-14. REMARK 100 THE RCSB ID CODE IS RCSB103663. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-99% 13C; U-99% 15N] REMARK 210 PROTEIN, 90% H2O/10% D2O; 0.3 MM REMARK 210 [U-99% 13C; U-99% 15N] PROTEIN, REMARK 210 0.3 MM PROTEIN, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCA; 3D REMARK 210 HNCO; 3D HCACO; 3D HNCACB; 3D REMARK 210 HCCH-TOCSY; 3D C(CO)NH; 3D H(CCO) REMARK 210 NH; 3D HNHB; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, XEASY, CYANA, X-PLOR_NIH REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 THR A 12 -20.55 164.76 REMARK 500 1 ARG A 13 -96.41 60.32 REMARK 500 1 THR B 112 -28.99 166.46 REMARK 500 1 ARG B 113 -79.71 61.85 REMARK 500 1 SER B 115 66.80 -175.87 REMARK 500 2 THR A 12 -39.03 167.73 REMARK 500 2 ARG A 13 136.04 59.84 REMARK 500 2 GLU A 14 -15.04 69.78 REMARK 500 2 THR B 112 -31.00 166.44 REMARK 500 2 ARG B 113 -167.48 53.49 REMARK 500 2 GLU B 114 -69.87 70.69 REMARK 500 3 THR A 12 -50.41 173.16 REMARK 500 3 ARG A 13 -167.76 56.17 REMARK 500 3 GLU A 14 -51.57 73.18 REMARK 500 3 ALA B 111 27.64 -71.66 REMARK 500 3 THR B 112 80.48 -166.21 REMARK 500 4 THR A 12 -26.31 161.45 REMARK 500 4 ARG A 13 -84.27 59.34 REMARK 500 4 SER A 15 20.51 -153.95 REMARK 500 4 THR B 112 -21.71 158.13 REMARK 500 4 ARG B 113 -109.88 68.76 REMARK 500 5 THR A 12 -29.65 169.07 REMARK 500 5 ARG A 13 -75.42 66.51 REMARK 500 5 SER A 15 14.39 -166.65 REMARK 500 5 THR B 112 -29.53 165.71 REMARK 500 5 ARG B 113 -79.25 62.59 REMARK 500 5 SER B 115 21.67 -157.46 REMARK 500 6 GLU B 114 -45.93 73.46 REMARK 500 7 ARG B 113 177.29 58.19 REMARK 500 7 GLU B 114 -61.27 69.83 REMARK 500 8 THR A 12 -39.34 173.72 REMARK 500 8 ARG A 13 -177.39 58.00 REMARK 500 8 GLU A 14 -26.20 69.82 REMARK 500 8 THR B 112 -34.21 166.32 REMARK 500 8 ARG B 113 -98.95 52.31 REMARK 500 8 GLU B 114 -64.89 61.44 REMARK 500 9 ALA A 11 31.91 -73.37 REMARK 500 9 THR A 12 36.64 -169.65 REMARK 500 9 GLU A 14 18.07 -156.02 REMARK 500 9 GLU B 114 88.09 63.01 REMARK 500 9 SER B 115 76.37 -112.85 REMARK 500 10 THR A 12 -40.60 173.15 REMARK 500 10 ARG A 13 132.01 57.15 REMARK 500 10 THR B 112 79.19 -107.61 REMARK 500 10 SER B 115 32.99 -92.66 REMARK 500 11 THR B 112 -43.39 171.70 REMARK 500 11 ARG B 113 -172.99 56.22 REMARK 500 11 GLU B 114 -55.70 70.16 REMARK 500 12 THR A 12 -44.99 174.11 REMARK 500 12 ARG A 13 -179.68 60.42 REMARK 500 REMARK 500 THIS ENTRY HAS 92 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 5 ARG B 106 0.08 SIDE CHAIN REMARK 500 7 ARG A 6 0.08 SIDE CHAIN REMARK 500 13 ARG A 6 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 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE 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 4 GLU B 114 24.7 L L OUTSIDE RANGE REMARK 500 9 ARG B 113 18.9 L L OUTSIDE RANGE REMARK 500 9 GLU B 114 24.1 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2LXZ RELATED DB: PDB REMARK 900 RELATED ID: 18705 RELATED DB: BMRB REMARK 900 RELATED ID: 1ZMP RELATED DB: PDB REMARK 900 RELATED ID: 19693 RELATED DB: BMRB DBREF 2MIT A 1 32 UNP Q01523 DEF5_HUMAN 63 94 DBREF 2MIT B 101 132 UNP Q01523 DEF5_HUMAN 63 94 SEQRES 1 A 32 ALA THR CYS TYR CYS ARG THR GLY ARG CYS ALA THR ARG SEQRES 2 A 32 GLU SER LEU SER GLY VAL CYS GLU ILE SER GLY ARG LEU SEQRES 3 A 32 TYR ARG LEU CYS CYS ARG SEQRES 1 B 32 ALA THR CYS TYR CYS ARG THR GLY ARG CYS ALA THR ARG SEQRES 2 B 32 GLU SER LEU SER GLY VAL CYS GLU ILE SER GLY ARG LEU SEQRES 3 B 32 TYR ARG LEU CYS CYS ARG SHEET 1 A 3 THR A 2 ARG A 6 0 SHEET 2 A 3 ARG A 25 ARG A 32 -1 O ARG A 28 N ARG A 6 SHEET 3 A 3 LEU A 16 ILE A 22 -1 N GLY A 18 O LEU A 29 SHEET 1 B 3 THR B 102 ARG B 106 0 SHEET 2 B 3 ARG B 125 ARG B 132 -1 O ARG B 128 N ARG B 106 SHEET 3 B 3 GLY B 118 ILE B 122 -1 N GLY B 118 O LEU B 129 SSBOND 1 CYS A 3 CYS A 31 1555 1555 2.03 SSBOND 2 CYS A 5 CYS B 120 1555 1555 2.04 SSBOND 3 CYS A 10 CYS A 30 1555 1555 2.04 SSBOND 4 CYS A 20 CYS B 105 1555 1555 2.03 SSBOND 5 CYS B 103 CYS B 131 1555 1555 2.03 SSBOND 6 CYS B 110 CYS B 130 1555 1555 2.05 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