HEADER ANTIMICROBIAL PROTEIN 10-MAY-05 1ZMI TITLE CRYSTAL STRUCTURE OF HUMAN ALPHA_DEFENSIN-2 (VARIANT GLY16->D-ALA), P TITLE 2 32 2 1 SPACE GROUP ) COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUTROPHIL DEFENSIN 2; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: DEFA3, DEF3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ALPHA-DEFENSIN, ANTIMICROBIAL, D-AMINO ACID SUBSTITUTION, KEYWDS 2 ANTIMICROBIAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.LUBKOWSKI,A.PRAHL,W.LU REVDAT 7 23-AUG-23 1ZMI 1 REMARK REVDAT 6 20-OCT-21 1ZMI 1 REMARK SEQADV LINK REVDAT 5 11-OCT-17 1ZMI 1 REMARK REVDAT 4 13-JUL-11 1ZMI 1 VERSN REVDAT 3 24-FEB-09 1ZMI 1 VERSN REVDAT 2 20-DEC-05 1ZMI 1 JRNL REVDAT 1 16-AUG-05 1ZMI 0 JRNL AUTH C.XIE,A.PRAHL,B.ERICKSEN,Z.WU,P.ZENG,X.LI,W.Y.LU, JRNL AUTH 2 J.LUBKOWSKI,W.LU JRNL TITL RECONSTRUCTION OF THE CONSERVED BETA-BULGE IN MAMMALIAN JRNL TITL 2 DEFENSINS USING D-AMINO ACIDS. JRNL REF J.BIOL.CHEM. V. 280 32921 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15894545 JRNL DOI 10.1074/JBC.M503084200 REMARK 2 REMARK 2 RESOLUTION. 1.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 1.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 54227 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) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2891 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7245 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.23 REMARK 3 BIN R VALUE (WORKING SET) : 0.1840 REMARK 3 BIN FREE R VALUE SET COUNT : 411 REMARK 3 BIN FREE R VALUE : 0.2070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 936 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 122 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.16000 REMARK 3 B22 (A**2) : -0.16000 REMARK 3 B33 (A**2) : 0.24000 REMARK 3 B12 (A**2) : -0.08000 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): 0.031 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.030 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.017 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.774 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1006 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 891 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1361 ; 1.890 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2032 ; 1.840 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 112 ; 8.025 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 44 ;19.987 ;18.182 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 145 ;12.241 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;15.648 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 129 ; 0.413 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1080 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 260 ; 0.000 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 137 ; 0.197 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 813 ; 0.239 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 424 ; 0.201 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): 637 ; 0.089 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 158 ; 0.223 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.060 ; 0.500 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): 9 ; 0.300 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 105 ; 0.285 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 31 ; 0.194 ; 0.500 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): 594 ; 2.198 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 244 ; 1.116 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 914 ; 2.887 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 498 ; 3.020 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 447 ; 3.785 ; 3.000 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): 2243 ; 1.659 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 122 ; 9.570 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 1865 ; 3.721 ; 3.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 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 29 REMARK 3 ORIGIN FOR THE GROUP (A): -12.7495 29.8509 26.3762 REMARK 3 T TENSOR REMARK 3 T11: -0.0284 T22: -0.0272 REMARK 3 T33: -0.0179 T12: -0.0144 REMARK 3 T13: 0.0060 T23: 0.0028 REMARK 3 L TENSOR REMARK 3 L11: 1.7646 L22: 3.1093 REMARK 3 L33: 3.0384 L12: 0.2769 REMARK 3 L13: 0.7832 L23: -1.3167 REMARK 3 S TENSOR REMARK 3 S11: 0.0765 S12: -0.0672 S13: -0.0720 REMARK 3 S21: 0.0438 S22: -0.0374 S23: 0.0925 REMARK 3 S31: 0.1025 S32: -0.0869 S33: -0.0391 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 : C 1 C 29 REMARK 3 ORIGIN FOR THE GROUP (A): 19.9121 10.0010 41.8245 REMARK 3 T TENSOR REMARK 3 T11: -0.0360 T22: -0.0036 REMARK 3 T33: 0.0093 T12: -0.0145 REMARK 3 T13: 0.0308 T23: -0.0422 REMARK 3 L TENSOR REMARK 3 L11: 3.6585 L22: 2.7275 REMARK 3 L33: 3.5518 L12: -1.5905 REMARK 3 L13: -1.0417 L23: 0.8289 REMARK 3 S TENSOR REMARK 3 S11: -0.1007 S12: 0.2469 S13: -0.3560 REMARK 3 S21: 0.0385 S22: -0.1701 S23: 0.2862 REMARK 3 S31: 0.2184 S32: -0.3021 S33: 0.2708 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 29 REMARK 3 ORIGIN FOR THE GROUP (A): -0.8245 35.5529 25.7336 REMARK 3 T TENSOR REMARK 3 T11: -0.0216 T22: -0.0151 REMARK 3 T33: -0.0128 T12: -0.0055 REMARK 3 T13: -0.0049 T23: -0.0002 REMARK 3 L TENSOR REMARK 3 L11: 1.0248 L22: 1.6687 REMARK 3 L33: 2.9649 L12: -0.7160 REMARK 3 L13: -1.0676 L23: 1.4211 REMARK 3 S TENSOR REMARK 3 S11: -0.0080 S12: -0.0465 S13: 0.0556 REMARK 3 S21: 0.0494 S22: 0.0507 S23: -0.1038 REMARK 3 S31: 0.0466 S32: 0.1501 S33: -0.0427 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 19 D 29 REMARK 3 ORIGIN FOR THE GROUP (A): 15.8658 15.9737 51.1493 REMARK 3 T TENSOR REMARK 3 T11: -0.0422 T22: -0.0291 REMARK 3 T33: -0.0229 T12: 0.0246 REMARK 3 T13: 0.0364 T23: -0.0038 REMARK 3 L TENSOR REMARK 3 L11: 3.6638 L22: 6.0841 REMARK 3 L33: 4.1569 L12: -1.7500 REMARK 3 L13: -0.7703 L23: -1.7508 REMARK 3 S TENSOR REMARK 3 S11: -0.1986 S12: 0.0437 S13: -0.0553 REMARK 3 S21: 0.2157 S22: 0.0995 S23: 0.2664 REMARK 3 S31: -0.0622 S32: -0.1182 S33: 0.0991 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1ZMI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAY-05. REMARK 100 THE DEPOSITION ID IS D_1000032893. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57187 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 8.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09000 REMARK 200 FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.51300 REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: BASED ON MONOMER OF HNP-3 (PDB CODE 1DFN) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LITHIUM SULFATE, PEG8000, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.58800 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 18.29400 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 18.29400 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 36.58800 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5, 6 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 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: 1050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -135.0 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 36.58800 REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -18.29400 REMARK 350 BIOMT1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 4 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 54.88200 REMARK 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 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 APPLY THE FOLLOWING TO CHAINS: C, D REMARK 350 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 54.88200 REMARK 350 REMARK 350 BIOMOLECULE: 5 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 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 APPLY THE FOLLOWING TO CHAINS: C, D REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 -35.84250 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 62.08103 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 73.17600 REMARK 350 REMARK 350 BIOMOLECULE: 6 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 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 APPLY THE FOLLOWING TO CHAINS: C, D REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -18.29400 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ARG C 13 O HOH C 184 1.88 REMARK 500 O HOH B 130 O HOH B 152 2.11 REMARK 500 O CYS C 29 O HOH C 184 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 186 O HOH C 150 4556 2.12 REMARK 500 REMARK 500 REMARK: NULL 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 THR A 17 CB THR A 17 CG2 -0.220 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 ARG A 23 NH1 - CZ - NH2 ANGL. DEV. = -8.7 DEGREES REMARK 500 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 9.0 DEGREES REMARK 500 ARG D 23 NE - CZ - NH1 ANGL. DEV. = -4.0 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 ALA D 10 122.20 -36.57 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 SO4 B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 507 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DFN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RELATED ALPHA-DEFENSIN REMARK 900 RELATED ID: 1ZMH RELATED DB: PDB REMARK 900 RELATED ID: 1ZMK RELATED DB: PDB REMARK 900 RELATED ID: 1ZMM RELATED DB: PDB REMARK 900 RELATED ID: 1ZMP RELATED DB: PDB REMARK 900 RELATED ID: 1ZMQ RELATED DB: PDB DBREF 1ZMI A 1 29 UNP P59666 DEF3_HUMAN 66 94 DBREF 1ZMI B 1 29 UNP P59666 DEF3_HUMAN 66 94 DBREF 1ZMI C 1 29 UNP P59666 DEF3_HUMAN 66 94 DBREF 1ZMI D 1 29 UNP P59666 DEF3_HUMAN 66 94 SEQADV 1ZMI DAL A 16 UNP P59666 GLY 81 ENGINEERED MUTATION SEQADV 1ZMI DAL B 16 UNP P59666 GLY 81 ENGINEERED MUTATION SEQADV 1ZMI DAL C 16 UNP P59666 GLY 81 ENGINEERED MUTATION SEQADV 1ZMI DAL D 16 UNP P59666 GLY 81 ENGINEERED MUTATION SEQRES 1 A 29 CYS TYR CYS ARG ILE PRO ALA CYS ILE ALA GLY GLU ARG SEQRES 2 A 29 ARG TYR DAL THR CYS ILE TYR GLN GLY ARG LEU TRP ALA SEQRES 3 A 29 PHE CYS CYS SEQRES 1 B 29 CYS TYR CYS ARG ILE PRO ALA CYS ILE ALA GLY GLU ARG SEQRES 2 B 29 ARG TYR DAL THR CYS ILE TYR GLN GLY ARG LEU TRP ALA SEQRES 3 B 29 PHE CYS CYS SEQRES 1 C 29 CYS TYR CYS ARG ILE PRO ALA CYS ILE ALA GLY GLU ARG SEQRES 2 C 29 ARG TYR DAL THR CYS ILE TYR GLN GLY ARG LEU TRP ALA SEQRES 3 C 29 PHE CYS CYS SEQRES 1 D 29 CYS TYR CYS ARG ILE PRO ALA CYS ILE ALA GLY GLU ARG SEQRES 2 D 29 ARG TYR DAL THR CYS ILE TYR GLN GLY ARG LEU TRP ALA SEQRES 3 D 29 PHE CYS CYS MODRES 1ZMI DAL A 16 ALA D-ALANINE MODRES 1ZMI DAL B 16 ALA D-ALANINE MODRES 1ZMI DAL C 16 ALA D-ALANINE MODRES 1ZMI DAL D 16 ALA D-ALANINE HET DAL A 16 5 HET DAL B 16 5 HET DAL C 16 5 HET DAL D 16 5 HET GOL A 501 6 HET GOL A 507 6 HET SO4 B 401 5 HET SO4 B 402 5 HET SO4 B 403 5 HET GOL B 502 6 HET GOL B 503 6 HETNAM DAL D-ALANINE HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 DAL 4(C3 H7 N O2) FORMUL 5 GOL 4(C3 H8 O3) FORMUL 7 SO4 3(O4 S 2-) FORMUL 12 HOH *122(H2 O) SHEET 1 A 6 TYR A 2 ARG A 4 0 SHEET 2 A 6 ARG A 23 CYS A 29 -1 O CYS A 28 N TYR A 2 SHEET 3 A 6 ARG A 13 TYR A 20 -1 N TYR A 15 O PHE A 27 SHEET 4 A 6 ARG B 13 TYR B 20 -1 O ILE B 19 N THR A 17 SHEET 5 A 6 ARG B 23 CYS B 29 -1 O CYS B 29 N ARG B 13 SHEET 6 A 6 TYR B 2 ARG B 4 -1 N TYR B 2 O CYS B 28 SHEET 1 B 6 TYR C 2 ARG C 4 0 SHEET 2 B 6 ARG C 23 CYS C 29 -1 O CYS C 28 N TYR C 2 SHEET 3 B 6 ARG C 13 TYR C 20 -1 N TYR C 15 O PHE C 27 SHEET 4 B 6 ARG D 13 TYR D 20 -1 O ILE D 19 N THR C 17 SHEET 5 B 6 ARG D 23 CYS D 29 -1 O CYS D 29 N ARG D 13 SHEET 6 B 6 TYR D 2 ARG D 4 -1 N TYR D 2 O CYS D 28 SSBOND 1 CYS A 1 CYS A 29 1555 1555 2.12 SSBOND 2 CYS A 3 CYS A 18 1555 1555 2.05 SSBOND 3 CYS A 8 CYS A 28 1555 1555 2.05 SSBOND 4 CYS B 1 CYS B 29 1555 1555 2.12 SSBOND 5 CYS B 3 CYS B 18 1555 1555 2.06 SSBOND 6 CYS B 8 CYS B 28 1555 1555 2.06 SSBOND 7 CYS C 1 CYS C 29 1555 1555 2.08 SSBOND 8 CYS C 3 CYS C 18 1555 1555 2.03 SSBOND 9 CYS C 8 CYS C 28 1555 1555 2.02 SSBOND 10 CYS D 1 CYS D 29 1555 1555 2.07 SSBOND 11 CYS D 3 CYS D 18 1555 1555 2.06 SSBOND 12 CYS D 8 CYS D 28 1555 1555 2.06 LINK C TYR A 15 N DAL A 16 1555 1555 1.34 LINK C DAL A 16 N THR A 17 1555 1555 1.32 LINK C TYR B 15 N DAL B 16 1555 1555 1.31 LINK C DAL B 16 N THR B 17 1555 1555 1.32 LINK C TYR C 15 N DAL C 16 1555 1555 1.33 LINK C DAL C 16 N THR C 17 1555 1555 1.33 LINK C TYR D 15 N DAL D 16 1555 1555 1.32 LINK C DAL D 16 N THR D 17 1555 1555 1.32 CISPEP 1 ILE A 5 PRO A 6 0 6.06 CISPEP 2 ILE B 5 PRO B 6 0 2.75 CISPEP 3 ILE C 5 PRO C 6 0 7.02 CISPEP 4 ILE D 5 PRO D 6 0 5.18 SITE 1 AC1 5 ARG B 13 CYS B 29 HOH B 137 HOH B 167 SITE 2 AC1 5 ARG C 14 SITE 1 AC2 5 GLY B 11 HOH B 138 HOH B 219 ARG C 14 SITE 2 AC2 5 THR C 17 SITE 1 AC3 8 ILE B 5 ARG B 23 HOH B 112 HOH B 114 SITE 2 AC3 8 HOH B 128 HOH B 140 HOH B 227 HOH B 228 SITE 1 AC4 10 CYS A 3 TRP A 25 HOH A 102 HOH A 106 SITE 2 AC4 10 HOH A 186 HOH A 203 GOL A 507 PHE B 27 SITE 3 AC4 10 ILE C 5 HOH C 150 SITE 1 AC5 5 CYS A 1 TYR B 2 CYS B 3 HOH B 153 SITE 2 AC5 5 HOH B 178 SITE 1 AC6 6 PRO B 6 ARG B 14 LEU B 24 ALA B 26 SITE 2 AC6 6 HOH B 206 HOH C 113 SITE 1 AC7 6 PRO A 6 ALA A 7 GOL A 501 ILE C 5 SITE 2 AC7 6 ARG C 23 TRP C 25 CRYST1 71.685 71.685 54.882 90.00 90.00 120.00 P 32 2 1 24 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 0.013950 0.008054 0.000000 0.00000 SCALE2 0.000000 0.016108 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018221 0.00000