HEADER ANTIMICROBIAL PROTEIN 18-MAR-09 3GO0 TITLE CRYSTAL STRUCTURE OF D-ENANTIOMER OF HUMAN ALPHA-DEFENSIN 1 (D-HNP1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUTROPHIL DEFENSIN 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HNP-1, HP-1, HP1, DEFENSIN, ALPHA 1, HP 1-56, NEUTROPHIL COMPND 5 DEFENSIN 2, HNP-2, HP-2, HP2; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: D-ENANTIOMER SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS ANTIMICROBIAL PEPTIDE, D-ENANTIOMER OF HUMAN ALPHA DEFENSIN 1, D- KEYWDS 2 ENANTIOMER OF HUMAN NEUTROPHIL PEPTIDE 1, D-HNP1, ANTIMICROBIAL KEYWDS 3 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.PAZGIER,W.-Y.LU REVDAT 7 22-NOV-23 3GO0 1 REMARK REVDAT 6 06-SEP-23 3GO0 1 LINK REVDAT 5 07-FEB-18 3GO0 1 SOURCE REVDAT 4 24-JAN-18 3GO0 1 AUTHOR REVDAT 3 13-JUL-11 3GO0 1 VERSN REVDAT 2 02-FEB-10 3GO0 1 JRNL REVDAT 1 28-JUL-09 3GO0 0 JRNL AUTH G.WEI,E.DE LEEUW,M.PAZGIER,W.YUAN,G.ZOU,J.WANG,B.ERICKSEN, JRNL AUTH 2 W.Y.LU,R.I.LEHRER,W.LU JRNL TITL THROUGH THE LOOKING GLASS, MECHANISTIC INSIGHTS FROM JRNL TITL 2 ENANTIOMERIC HUMAN DEFENSINS. JRNL REF J.BIOL.CHEM. V. 284 29180 2009 JRNL REFN ISSN 0021-9258 JRNL PMID 19640840 JRNL DOI 10.1074/JBC.M109.018085 REMARK 2 REMARK 2 RESOLUTION. 1.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0070 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 7988 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 390 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.56 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.60 REMARK 3 REFLECTION IN BIN (WORKING SET) : 559 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.50 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 36 REMARK 3 BIN FREE R VALUE : 0.2470 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 476 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 62 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.12000 REMARK 3 B22 (A**2) : 1.41000 REMARK 3 B33 (A**2) : -1.53000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.091 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.083 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.051 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.191 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.965 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 484 ; 0.008 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 644 ; 1.782 ; 2.469 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 54 ;20.279 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 64 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 354 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 292 ; 0.605 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 452 ; 1.045 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 192 ; 1.444 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 192 ; 2.334 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 30 6 REMARK 3 1 B 1 B 30 6 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 LOOSE POSITIONAL 1 A (A): 238 ; 0.540 ; 5.000 REMARK 3 LOOSE THERMAL 1 A (A**2): 238 ; 2.060 ;10.000 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 30 REMARK 3 ORIGIN FOR THE GROUP (A): -14.5940 8.3882 -14.0998 REMARK 3 T TENSOR REMARK 3 T11: 0.0974 T22: 0.1052 REMARK 3 T33: 0.1227 T12: -0.0036 REMARK 3 T13: -0.0062 T23: -0.0025 REMARK 3 L TENSOR REMARK 3 L11: 0.7603 L22: 2.8341 REMARK 3 L33: 1.4101 L12: 0.3749 REMARK 3 L13: -0.2439 L23: -0.0729 REMARK 3 S TENSOR REMARK 3 S11: 0.0404 S12: -0.0275 S13: 0.0755 REMARK 3 S21: -0.0151 S22: -0.0173 S23: -0.0094 REMARK 3 S31: -0.1261 S32: 0.0623 S33: -0.0231 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 30 REMARK 3 ORIGIN FOR THE GROUP (A): -11.0741 -1.2174 -5.8351 REMARK 3 T TENSOR REMARK 3 T11: 0.1015 T22: 0.1189 REMARK 3 T33: 0.1096 T12: 0.0006 REMARK 3 T13: -0.0117 T23: 0.0039 REMARK 3 L TENSOR REMARK 3 L11: 2.6096 L22: 2.4455 REMARK 3 L33: 2.9536 L12: -0.7679 REMARK 3 L13: -0.0069 L23: 0.5863 REMARK 3 S TENSOR REMARK 3 S11: -0.0310 S12: -0.0973 S13: 0.0749 REMARK 3 S21: 0.1873 S22: 0.0309 S23: -0.1141 REMARK 3 S31: 0.0404 S32: 0.2425 S33: 0.0001 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: U VALUES, RESIDUAL ONLY REMARK 4 REMARK 4 3GO0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000052099. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : CONFOCAL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8404 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.560 REMARK 200 RESOLUTION RANGE LOW (A) : 40.281 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : 0.11200 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.21700 REMARK 200 R SYM FOR SHELL (I) : 0.20400 REMARK 200 FOR SHELL : 9.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3GNY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 SODIUM CITRATE TRIBASIC DEHYDRATE, REMARK 280 0.1 M HEPES, PH 7.5, 20% ISOPROPANOL, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 22.63850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.54900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.63850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 15.54900 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -81.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -45.27700 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL 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: 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 DPR A 7 C - N - CD ANGL. DEV. = -22.1 DEGREES REMARK 500 DPR A 7 CA - N - CD ANGL. DEV. = -10.2 DEGREES REMARK 500 DPR A 7 N - CA - CB ANGL. DEV. = 10.5 DEGREES REMARK 500 DPR B 7 C - N - CD ANGL. DEV. = -22.9 DEGREES REMARK 500 DPR B 7 N - CA - CB ANGL. DEV. = 8.3 DEGREES REMARK 500 DAR B 24 NE - CZ - NH1 ANGL. DEV. = 4.1 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 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 DPR B 7 38.19 134.75 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 DIL A 6 DPR A 7 -67.85 REMARK 500 DIL B 6 DPR B 7 -97.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 DIL A 6 -12.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DFN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN ALPHA-DEFENSIN 3 (HNP3) REMARK 900 RELATED ID: 2PM1 RELATED DB: PDB REMARK 900 DERIVATIVE OF HUMAN ALPHA-DEFENSIN 1 REMARK 900 RELATED ID: 2PM4 RELATED DB: PDB REMARK 900 HUMAN ALPHA-DEFENSIN 1 (MULTIPLE ARG TO LYS MUTANT) REMARK 900 RELATED ID: 2PM5 RELATED DB: PDB REMARK 900 HUMAN ALPHA-DEFENSIN 1 DERIVATIVE REMARK 900 RELATED ID: 3GNY RELATED DB: PDB REMARK 900 CRYSTAL STRCTURE OF HUMAN ALPHA-DEFENSIN 1 (HNP1) REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE DATABASE REFERENCE FOR THE L-FORM SEQUENCE IS UNP REMARK 999 ENTRY P59665 AND INCLUDES RESIDUES 65-94. THE SEQUENCE TRANSLATES REMARK 999 TO L-PROTEIN AS FOLLOWS ACYCRIPACIAGERRYGTCIYQGRLWAFCC. DBREF 3GO0 A 1 30 PDB 3GO0 3GO0 1 30 DBREF 3GO0 B 1 30 PDB 3GO0 3GO0 1 30 SEQRES 1 A 30 DAL DCY DTY DCY DAR DIL DPR DAL DCY DIL DAL GLY DGL SEQRES 2 A 30 DAR DAR DTY GLY DTH DCY DIL DTY DGN GLY DAR DLE DTR SEQRES 3 A 30 DAL DPN DCY DCY SEQRES 1 B 30 DAL DCY DTY DCY DAR DIL DPR DAL DCY DIL DAL GLY DGL SEQRES 2 B 30 DAR DAR DTY GLY DTH DCY DIL DTY DGN GLY DAR DLE DTR SEQRES 3 B 30 DAL DPN DCY DCY HET DAL A 1 5 HET DCY A 2 6 HET DTY A 3 12 HET DCY A 4 6 HET DAR A 5 11 HET DIL A 6 8 HET DPR A 7 7 HET DAL A 8 5 HET DCY A 9 6 HET DIL A 10 8 HET DAL A 11 5 HET DGL A 13 9 HET DAR A 14 11 HET DAR A 15 11 HET DTY A 16 12 HET DTH A 18 7 HET DCY A 19 6 HET DIL A 20 8 HET DTY A 21 12 HET DGN A 22 9 HET DAR A 24 11 HET DLE A 25 8 HET DTR A 26 14 HET DAL A 27 5 HET DPN A 28 11 HET DCY A 29 6 HET DCY A 30 7 HET DAL B 1 5 HET DCY B 2 6 HET DTY B 3 12 HET DCY B 4 6 HET DAR B 5 11 HET DIL B 6 8 HET DPR B 7 7 HET DAL B 8 5 HET DCY B 9 6 HET DIL B 10 8 HET DAL B 11 5 HET DGL B 13 9 HET DAR B 14 11 HET DAR B 15 11 HET DTY B 16 12 HET DTH B 18 7 HET DCY B 19 6 HET DIL B 20 8 HET DTY B 21 12 HET DGN B 22 9 HET DAR B 24 11 HET DLE B 25 8 HET DTR B 26 14 HET DAL B 27 5 HET DPN B 28 11 HET DCY B 29 6 HET DCY B 30 7 HET CL A 31 1 HET CL A 32 1 HET CL B 31 1 HETNAM DAL D-ALANINE HETNAM DCY D-CYSTEINE HETNAM DTY D-TYROSINE HETNAM DAR D-ARGININE HETNAM DIL D-ISOLEUCINE HETNAM DPR D-PROLINE HETNAM DGL D-GLUTAMIC ACID HETNAM DTH D-THREONINE HETNAM DGN D-GLUTAMINE HETNAM DLE D-LEUCINE HETNAM DTR D-TRYPTOPHAN HETNAM DPN D-PHENYLALANINE HETNAM CL CHLORIDE ION FORMUL 1 DAL 8(C3 H7 N O2) FORMUL 1 DCY 12(C3 H7 N O2 S) FORMUL 1 DTY 6(C9 H11 N O3) FORMUL 1 DAR 8(C6 H15 N4 O2 1+) FORMUL 1 DIL 6(C6 H13 N O2) FORMUL 1 DPR 2(C5 H9 N O2) FORMUL 1 DGL 2(C5 H9 N O4) FORMUL 1 DTH 2(C4 H9 N O3) FORMUL 1 DGN 2(C5 H10 N2 O3) FORMUL 1 DLE 2(C6 H13 N O2) FORMUL 1 DTR 2(C11 H12 N2 O2) FORMUL 1 DPN 2(C9 H11 N O2) FORMUL 3 CL 3(CL 1-) FORMUL 6 HOH *62(H2 O) SHEET 1 A 6 DTY A 3 DAR A 5 0 SHEET 2 A 6 DAR A 24 DCY A 30 -1 O DCY A 29 N DTY A 3 SHEET 3 A 6 DAR A 14 DTY A 21 -1 N DTY A 16 O DPN A 28 SHEET 4 A 6 DAR B 14 DTY B 21 -1 O DIL B 20 N DTH A 18 SHEET 5 A 6 DAR B 24 DCY B 30 -1 O DPN B 28 N DTY B 16 SHEET 6 A 6 DTY B 3 DAR B 5 -1 N DAR B 5 O DAL B 27 SSBOND 1 DCY A 2 DCY A 30 1555 1555 2.10 SSBOND 2 DCY A 4 DCY A 19 1555 1555 2.04 SSBOND 3 DCY A 9 DCY A 29 1555 1555 2.08 SSBOND 4 DCY B 2 DCY B 30 1555 1555 2.18 SSBOND 5 DCY B 4 DCY B 19 1555 1555 2.06 SSBOND 6 DCY B 9 DCY B 29 1555 1555 2.05 LINK C DAL A 1 N DCY A 2 1555 1555 1.33 LINK C DCY A 2 N DTY A 3 1555 1555 1.33 LINK C DTY A 3 N DCY A 4 1555 1555 1.33 LINK C DCY A 4 N DAR A 5 1555 1555 1.34 LINK C DAR A 5 N DIL A 6 1555 1555 1.33 LINK C DIL A 6 N DPR A 7 1555 1555 1.33 LINK C DPR A 7 N DAL A 8 1555 1555 1.34 LINK C DAL A 8 N DCY A 9 1555 1555 1.33 LINK C DCY A 9 N DIL A 10 1555 1555 1.33 LINK C DIL A 10 N DAL A 11 1555 1555 1.33 LINK C DAL A 11 N GLY A 12 1555 1555 1.33 LINK C GLY A 12 N DGL A 13 1555 1555 1.34 LINK C DGL A 13 N DAR A 14 1555 1555 1.33 LINK C DAR A 14 N DAR A 15 1555 1555 1.33 LINK C DAR A 15 N DTY A 16 1555 1555 1.33 LINK C DTY A 16 N GLY A 17 1555 1555 1.33 LINK C GLY A 17 N DTH A 18 1555 1555 1.33 LINK C DTH A 18 N DCY A 19 1555 1555 1.34 LINK C DCY A 19 N DIL A 20 1555 1555 1.33 LINK C DIL A 20 N DTY A 21 1555 1555 1.33 LINK C DTY A 21 N DGN A 22 1555 1555 1.33 LINK C DGN A 22 N GLY A 23 1555 1555 1.34 LINK C GLY A 23 N DAR A 24 1555 1555 1.33 LINK C DAR A 24 N DLE A 25 1555 1555 1.38 LINK C DLE A 25 N DTR A 26 1555 1555 1.26 LINK C DTR A 26 N DAL A 27 1555 1555 1.24 LINK C DAL A 27 N DPN A 28 1555 1555 1.33 LINK C DPN A 28 N DCY A 29 1555 1555 1.34 LINK C DCY A 29 N DCY A 30 1555 1555 1.33 LINK C DAL B 1 N DCY B 2 1555 1555 1.33 LINK C DCY B 2 N DTY B 3 1555 1555 1.33 LINK C DTY B 3 N DCY B 4 1555 1555 1.33 LINK C DCY B 4 N DAR B 5 1555 1555 1.34 LINK C DAR B 5 N DIL B 6 1555 1555 1.34 LINK C DIL B 6 N DPR B 7 1555 1555 1.32 LINK C DPR B 7 N DAL B 8 1555 1555 1.34 LINK C DAL B 8 N DCY B 9 1555 1555 1.34 LINK C DCY B 9 N DIL B 10 1555 1555 1.33 LINK C DIL B 10 N DAL B 11 1555 1555 1.33 LINK C DAL B 11 N GLY B 12 1555 1555 1.33 LINK C GLY B 12 N DGL B 13 1555 1555 1.33 LINK C DGL B 13 N DAR B 14 1555 1555 1.33 LINK C DAR B 14 N DAR B 15 1555 1555 1.33 LINK C DAR B 15 N DTY B 16 1555 1555 1.33 LINK C DTY B 16 N GLY B 17 1555 1555 1.33 LINK C GLY B 17 N DTH B 18 1555 1555 1.33 LINK C DTH B 18 N DCY B 19 1555 1555 1.33 LINK C DCY B 19 N DIL B 20 1555 1555 1.33 LINK C DIL B 20 N DTY B 21 1555 1555 1.33 LINK C DTY B 21 N DGN B 22 1555 1555 1.33 LINK C DGN B 22 N GLY B 23 1555 1555 1.33 LINK C GLY B 23 N DAR B 24 1555 1555 1.24 LINK C DAR B 24 N DLE B 25 1555 1555 1.38 LINK C DLE B 25 N DTR B 26 1555 1555 1.40 LINK C DTR B 26 N DAL B 27 1555 1555 1.33 LINK C DAL B 27 N DPN B 28 1555 1555 1.33 LINK C DPN B 28 N DCY B 29 1555 1555 1.33 LINK C DCY B 29 N DCY B 30 1555 1555 1.33 CRYST1 45.277 31.098 40.281 90.00 90.00 90.00 P 21 21 2 8 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 0.022086 0.000000 0.000000 0.00000 SCALE2 0.000000 0.032156 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024826 0.00000 HETATM 1 N DAL A 1 -4.903 12.545 -7.962 1.00 21.01 N HETATM 2 CA DAL A 1 -5.457 11.171 -7.983 1.00 19.94 C HETATM 3 CB DAL A 1 -4.572 10.257 -8.842 1.00 20.23 C HETATM 4 C DAL A 1 -6.892 11.177 -8.503 1.00 19.19 C HETATM 5 O DAL A 1 -7.373 12.190 -9.004 1.00 20.08 O HETATM 6 N DCY A 2 -7.571 10.047 -8.355 1.00 17.42 N HETATM 7 CA DCY A 2 -8.882 9.865 -8.949 1.00 16.48 C HETATM 8 C DCY A 2 -8.760 8.962 -10.154 1.00 15.97 C HETATM 9 O DCY A 2 -7.843 8.151 -10.246 1.00 16.15 O HETATM 10 CB DCY A 2 -9.852 9.241 -7.954 1.00 16.26 C HETATM 11 SG DCY A 2 -10.181 10.318 -6.536 1.00 16.83 S HETATM 12 N DTY A 3 -9.707 9.115 -11.080 1.00 14.94 N HETATM 13 CA DTY A 3 -9.712 8.395 -12.335 1.00 14.64 C HETATM 14 C DTY A 3 -11.112 7.951 -12.695 1.00 14.24 C HETATM 15 O DTY A 3 -12.063 8.696 -12.501 1.00 14.38 O HETATM 16 CB DTY A 3 -9.220 9.306 -13.469 1.00 14.72 C HETATM 17 CG DTY A 3 -7.800 9.759 -13.227 1.00 16.50 C HETATM 18 CD1 DTY A 3 -6.735 8.954 -13.619 1.00 18.37 C HETATM 19 CD2 DTY A 3 -7.578 10.973 -12.594 1.00 17.22 C HETATM 20 CE1 DTY A 3 -5.427 9.383 -13.376 1.00 20.07 C HETATM 21 CE2 DTY A 3 -6.280 11.401 -12.350 1.00 17.77 C HETATM 22 CZ DTY A 3 -5.211 10.604 -12.742 1.00 18.91 C HETATM 23 OH DTY A 3 -3.937 11.028 -12.501 1.00 21.78 O HETATM 24 N DCY A 4 -11.236 6.735 -13.221 1.00 13.38 N HETATM 25 CA DCY A 4 -12.474 6.320 -13.891 1.00 13.36 C HETATM 26 C DCY A 4 -12.335 6.740 -15.340 1.00 12.84 C HETATM 27 O DCY A 4 -11.336 6.401 -15.982 1.00 13.89 O HETATM 28 CB DCY A 4 -12.650 4.801 -13.827 1.00 13.55 C HETATM 29 SG DCY A 4 -12.883 4.157 -12.148 1.00 14.49 S HETATM 30 N DAR A 5 -13.318 7.486 -15.857 1.00 12.22 N HETATM 31 CA DAR A 5 -13.211 8.070 -17.188 1.00 11.98 C HETATM 32 CB DAR A 5 -13.037 9.582 -17.092 1.00 11.43 C HETATM 33 CG DAR A 5 -11.714 10.010 -16.476 1.00 10.36 C HETATM 34 CD DAR A 5 -11.481 11.467 -16.860 1.00 9.73 C HETATM 35 NE DAR A 5 -10.323 11.943 -16.120 1.00 9.62 N HETATM 36 CZ DAR A 5 -9.044 11.740 -16.449 1.00 11.69 C HETATM 37 NH1 DAR A 5 -8.729 10.940 -17.481 1.00 11.99 N HETATM 38 NH2 DAR A 5 -8.085 12.307 -15.718 1.00 11.71 N HETATM 39 C DAR A 5 -14.432 7.840 -18.045 1.00 12.26 C HETATM 40 O DAR A 5 -15.568 7.843 -17.564 1.00 12.64 O HETATM 41 N DIL A 6 -14.173 7.645 -19.336 1.00 12.22 N HETATM 42 CA DIL A 6 -15.201 7.673 -20.346 1.00 13.14 C HETATM 43 C DIL A 6 -14.872 8.638 -21.464 1.00 13.33 C HETATM 44 O DIL A 6 -13.767 8.507 -21.961 1.00 13.56 O HETATM 45 CB DIL A 6 -15.517 6.292 -20.955 1.00 12.75 C HETATM 46 CG1 DIL A 6 -16.221 5.376 -19.964 1.00 13.42 C HETATM 47 CG2 DIL A 6 -16.369 6.397 -22.218 1.00 13.36 C HETATM 48 CD1 DIL A 6 -16.224 3.946 -20.477 1.00 12.69 C HETATM 49 N DPR A 7 -15.570 9.773 -21.453 1.00 14.25 N HETATM 50 CA DPR A 7 -17.009 9.858 -21.715 1.00 14.19 C HETATM 51 CB DPR A 7 -17.338 10.598 -22.999 1.00 14.02 C HETATM 52 CG DPR A 7 -16.054 11.331 -23.301 1.00 15.66 C HETATM 53 CD DPR A 7 -15.007 10.393 -22.703 1.00 14.63 C HETATM 54 C DPR A 7 -17.405 10.708 -20.458 1.00 13.77 C HETATM 55 O DPR A 7 -18.582 10.731 -20.062 1.00 14.66 O HETATM 56 N DAL A 8 -16.427 11.373 -19.830 1.00 13.78 N HETATM 57 CA DAL A 8 -16.709 12.347 -18.762 1.00 13.14 C HETATM 58 CB DAL A 8 -17.389 13.601 -19.347 1.00 13.70 C HETATM 59 C DAL A 8 -15.446 12.767 -18.038 1.00 12.91 C HETATM 60 O DAL A 8 -14.343 12.580 -18.547 1.00 12.94 O HETATM 61 N DCY A 9 -15.606 13.373 -16.861 1.00 12.69 N HETATM 62 CA DCY A 9 -14.480 13.983 -16.149 1.00 12.94 C HETATM 63 C DCY A 9 -13.925 15.145 -16.943 1.00 12.77 C HETATM 64 O DCY A 9 -14.618 15.698 -17.787 1.00 14.04 O HETATM 65 CB DCY A 9 -14.942 14.488 -14.783 1.00 12.67 C HETATM 66 SG DCY A 9 -15.656 13.208 -13.719 1.00 13.17 S HETATM 67 N DIL A 10 -12.670 15.507 -16.686 1.00 11.92 N HETATM 68 CA DIL A 10 -12.004 16.560 -17.452 1.00 11.39 C HETATM 69 C DIL A 10 -11.913 17.819 -16.624 1.00 10.91 C HETATM 70 O DIL A 10 -12.229 17.814 -15.439 1.00 11.42 O HETATM 71 CB DIL A 10 -10.635 16.105 -17.992 1.00 11.70 C HETATM 72 CG1 DIL A 10 -9.597 15.798 -16.899 1.00 12.03 C HETATM 73 CG2 DIL A 10 -10.824 14.933 -18.967 1.00 11.68 C HETATM 74 CD1 DIL A 10 -8.177 15.713 -17.441 1.00 11.46 C HETATM 75 N DAL A 11 -11.476 18.909 -17.250 1.00 10.69 N HETATM 76 CA DAL A 11 -11.292 20.178 -16.557 1.00 10.20 C HETATM 77 CB DAL A 11 -10.648 21.208 -17.487 1.00 10.27 C HETATM 78 C DAL A 11 -10.439 19.974 -15.318 1.00 10.43 C HETATM 79 O DAL A 11 -9.457 19.222 -15.330 1.00 11.38 O