PDB Short entry for 3PSM HEADER ANTIMICROBIAL PROTEIN 01-DEC-10 3PSM TITLE .98A CRYSTAL STRUCTURE OF A DIMERIC PLANT DEFENSIN SPE10 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEFENSIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SPE10 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PACHYRHIZUS EROSUS; SOURCE 3 ORGANISM_COMMON: JICAMA,POTATO-BEAN,YAM-BEAN; SOURCE 4 ORGANISM_TAXID: 109171 KEYWDS DIMER, DEFENSIN, ANTIMICROBIAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.ZHOU,X.SONG,W.GONG REVDAT 1 29-DEC-10 3PSM 0 JRNL AUTH H.ZHOU,X.SONG,W.GONG JRNL TITL 0.98A CRYSTAL STRUCTURE OF A DIMERIC PLANT DEFENSIN SPE10 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 0.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.125 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.125 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.164 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2635 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 52719 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.120 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.120 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.157 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 0.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 47165 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 758 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 183 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 997.37 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 657.62 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 5 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 9169 REMARK 3 NUMBER OF RESTRAINTS : 10500 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 ANGLE DISTANCES (A) : 0.030 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.032 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.098 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.102 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.115 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.041 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.101 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) REMARK 4 REMARK 4 3PSM COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-DEC-10. REMARK 100 THE RCSB ID CODE IS RCSB062766. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-NOV-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BSRF REMARK 200 BEAMLINE : 3W1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 130 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL2000 REMARK 200 DATA SCALING SOFTWARE : HKL2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55557 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.980 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 18.200 REMARK 200 R MERGE (I) : 0.02800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 31.8300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.48600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.480 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: SHAKE & BAKE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35% PEG 8000, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 14.05550 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: 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 34 NE - CZ - NH2 ANGL. DEV. = -5.1 DEGREES REMARK 500 ARG A 45 NH1 - CZ - NH2 ANGL. DEV. = 12.7 DEGREES REMARK 500 ARG A 45 NE - CZ - NH1 ANGL. DEV. = -10.0 DEGREES REMARK 500 PHE B 15 CB - CG - CD2 ANGL. DEV. = 5.1 DEGREES REMARK 500 ARG B 40 NH1 - CZ - NH2 ANGL. DEV. = -8.8 DEGREES REMARK 500 ARG B 40 NE - CZ - NH2 ANGL. DEV. = 7.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 3PSM A 1 47 UNP Q6B519 Q6B519_9FABA 1 47 DBREF 3PSM B 1 47 UNP Q6B519 Q6B519_9FABA 1 47 SEQRES 1 A 47 LYS THR CYS GLU ASN LEU ALA ASP THR PHE ARG GLY PRO SEQRES 2 A 47 CYS PHE THR ASP GLY SER CYS ASP ASP HIS CYS LYS ASN SEQRES 3 A 47 LYS GLU HIS LEU ILE LYS GLY ARG CYS ARG ASP ASP PHE SEQRES 4 A 47 ARG CYS TRP CYS THR ARG ASN CYS SEQRES 1 B 47 LYS THR CYS GLU ASN LEU ALA ASP THR PHE ARG GLY PRO SEQRES 2 B 47 CYS PHE THR ASP GLY SER CYS ASP ASP HIS CYS LYS ASN SEQRES 3 B 47 LYS GLU HIS LEU ILE LYS GLY ARG CYS ARG ASP ASP PHE SEQRES 4 B 47 ARG CYS TRP CYS THR ARG ASN CYS FORMUL 3 HOH *183(H2 O) HELIX 1 1 THR A 16 LYS A 27 1 12 HELIX 2 2 THR B 16 LYS B 27 1 12 SHEET 1 A 3 THR A 2 LEU A 6 0 SHEET 2 A 3 CYS A 41 ASN A 46 -1 O CYS A 43 N ASN A 5 SHEET 3 A 3 LYS A 32 CYS A 35 -1 N LYS A 32 O THR A 44 SHEET 1 B 3 THR B 2 LEU B 6 0 SHEET 2 B 3 CYS B 41 ASN B 46 -1 O CYS B 43 N ASN B 5 SHEET 3 B 3 LYS B 32 CYS B 35 -1 N LYS B 32 O THR B 44 SSBOND 1 CYS A 3 CYS A 47 1555 1555 2.04 SSBOND 2 CYS A 14 CYS A 35 1555 1555 2.03 SSBOND 3 CYS A 20 CYS A 41 1555 1555 2.04 SSBOND 4 CYS A 24 CYS A 43 1555 1555 2.04 SSBOND 5 CYS B 3 CYS B 47 1555 1555 2.00 SSBOND 6 CYS B 14 CYS B 35 1555 1555 2.05 SSBOND 7 CYS B 20 CYS B 41 1555 1555 2.03 SSBOND 8 CYS B 24 CYS B 43 1555 1555 2.04 CRYST1 32.714 28.111 54.853 90.00 103.78 90.00 P 1 21 1 4 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 0.030568 0.000000 0.007497 0.00000 SCALE2 0.000000 0.035573 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018771 0.00000