HEADER ANTIMICROBIAL PROTEIN 09-OCT-15 5E5Q TITLE RACEMIC SNAKIN-1 IN P21/C COMPND MOL_ID: 1; COMPND 2 MOLECULE: SNAKIN-1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 26-88; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SOLANUM TUBEROSUM; SOURCE 4 ORGANISM_COMMON: POTATO; SOURCE 5 ORGANISM_TAXID: 4113 KEYWDS GASA/SNAKIN, CYSTEINE-RICH ANTIMICROBIAL PEPTIDE, ANTIMICROBIAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.YEUNG,C.J.SQUIRE,Y.YOSAATMADJA,S.PANJIKAR,E.N.BAKER,P.W.R.HARRIS, AUTHOR 2 M.A.BRIMBLE REVDAT 3 30-OCT-24 5E5Q 1 JRNL REMARK REVDAT 2 20-JUL-16 5E5Q 1 JRNL REVDAT 1 18-MAY-16 5E5Q 0 JRNL AUTH H.YEUNG,C.J.SQUIRE,Y.YOSAATMADJA,S.PANJIKAR,G.LOPEZ, JRNL AUTH 2 A.MOLINA,E.N.BAKER,P.W.HARRIS,M.A.BRIMBLE JRNL TITL RADIATION DAMAGE AND RACEMIC PROTEIN CRYSTALLOGRAPHY REVEAL JRNL TITL 2 THE UNIQUE STRUCTURE OF THE GASA/SNAKIN PROTEIN SUPERFAMILY. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 55 7930 2016 JRNL REFN ESSN 1521-3773 JRNL PMID 27145301 JRNL DOI 10.1002/ANIE.201602719 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 32502 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1618 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 34.1502 - 3.6618 0.98 2609 118 0.2301 0.2552 REMARK 3 2 3.6618 - 2.9070 0.99 2630 131 0.2408 0.2919 REMARK 3 3 2.9070 - 2.5396 0.99 2588 150 0.2420 0.2731 REMARK 3 4 2.5396 - 2.3075 0.99 2605 137 0.2286 0.3022 REMARK 3 5 2.3075 - 2.1421 0.98 2601 132 0.2202 0.2379 REMARK 3 6 2.1421 - 2.0159 0.98 2626 109 0.2194 0.3258 REMARK 3 7 2.0159 - 1.9149 0.97 2575 143 0.2219 0.2597 REMARK 3 8 1.9149 - 1.8316 0.97 2563 133 0.2255 0.3056 REMARK 3 9 1.8316 - 1.7611 0.96 2537 136 0.2414 0.3260 REMARK 3 10 1.7611 - 1.7003 0.96 2546 139 0.2446 0.3066 REMARK 3 11 1.7003 - 1.6471 0.95 2478 156 0.2780 0.3198 REMARK 3 12 1.6471 - 1.6000 0.95 2526 134 0.3240 0.4108 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1019 REMARK 3 ANGLE : 0.881 1384 REMARK 3 CHIRALITY : 0.048 138 REMARK 3 PLANARITY : 0.004 179 REMARK 3 DIHEDRAL : 12.764 696 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5E5Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214412. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUL-14 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 : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.4586 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS NOVEMBER 3, 2014 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.3.11 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33736 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 34.142 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.6 REMARK 200 STARTING MODEL: IN HOUSE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2 M DIBASIC SODIUM REMARK 280 PHOSPHATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21/c 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+1/2 REMARK 290 3555 -X,-Y,-Z REMARK 290 4555 X,-Y+1/2,Z+1/2 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 -6.48802 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 13.87200 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 36.09503 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 -6.48802 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 13.87200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 36.09503 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 10 NZ REMARK 470 LYS A 15 NZ REMARK 470 ARG A 21 CZ NH1 NH2 REMARK 470 LYS A 34 CE NZ REMARK 470 LYS A 57 CD CE NZ REMARK 470 LYS B 10 CE NZ REMARK 470 LYS B 15 NZ REMARK 470 ARG B 21 NH1 NH2 REMARK 470 LYS B 44 CE NZ REMARK 470 LYS B 53 CE NZ REMARK 470 LYS B 57 CG CD CE NZ REMARK 470 LYS B 59 CE NZ REMARK 470 LYS B 61 NZ 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 CYS A 47 CA - CB - SG ANGL. DEV. = 7.0 DEGREES REMARK 500 CYS B 47 CA - CB - SG ANGL. DEV. = 7.0 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 LEU A 18 79.39 -105.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5E5T RELATED DB: PDB REMARK 900 RELATED ID: 5E5Y RELATED DB: PDB DBREF 5E5Q A 1 63 UNP B6E1W5 B6E1W5_SOLTU 26 88 DBREF 5E5Q B 1 63 UNP B6E1W5 B6E1W5_SOLTU 26 88 SEQRES 1 A 63 GLY SER ASN PHE CYS ASP SER LYS CYS LYS LEU ARG CYS SEQRES 2 A 63 SER LYS ALA GLY LEU ALA ASP ARG CYS LEU LYS TYR CYS SEQRES 3 A 63 GLY ILE CYS CYS GLU GLU CYS LYS CYS VAL PRO SER GLY SEQRES 4 A 63 THR TYR GLY ASN LYS HIS GLU CYS PRO CYS TYR ARG ASP SEQRES 5 A 63 LYS LYS ASN SER LYS GLY LYS SER LYS CYS PRO SEQRES 1 B 63 GLY SER ASN PHE CYS ASP SER LYS CYS LYS LEU ARG CYS SEQRES 2 B 63 SER LYS ALA GLY LEU ALA ASP ARG CYS LEU LYS TYR CYS SEQRES 3 B 63 GLY ILE CYS CYS GLU GLU CYS LYS CYS VAL PRO SER GLY SEQRES 4 B 63 THR TYR GLY ASN LYS HIS GLU CYS PRO CYS TYR ARG ASP SEQRES 5 B 63 LYS LYS ASN SER LYS GLY LYS SER LYS CYS PRO FORMUL 3 HOH *154(H2 O) HELIX 1 AA1 SER A 2 CYS A 13 1 12 HELIX 2 AA2 LEU A 18 LYS A 34 1 17 HELIX 3 AA3 ASN A 43 GLU A 46 5 4 HELIX 4 AA4 CYS A 47 LYS A 53 1 7 HELIX 5 AA5 SER B 2 CYS B 13 1 12 HELIX 6 AA6 LEU B 18 LYS B 34 1 17 HELIX 7 AA7 ASN B 43 GLU B 46 5 4 HELIX 8 AA8 CYS B 47 LYS B 53 1 7 SSBOND 1 CYS A 5 CYS A 30 1555 1555 2.04 SSBOND 2 CYS A 9 CYS A 26 1555 1555 2.04 SSBOND 3 CYS A 13 CYS A 22 1555 1555 2.06 SSBOND 4 CYS A 29 CYS A 62 1555 1555 2.02 SSBOND 5 CYS A 33 CYS A 49 1555 1555 2.08 SSBOND 6 CYS A 35 CYS A 47 1555 1555 2.01 SSBOND 7 CYS B 5 CYS B 30 1555 1555 2.04 SSBOND 8 CYS B 9 CYS B 26 1555 1555 2.05 SSBOND 9 CYS B 13 CYS B 22 1555 1555 2.05 SSBOND 10 CYS B 29 CYS B 62 1555 1555 2.02 SSBOND 11 CYS B 33 CYS B 49 1555 1555 2.06 SSBOND 12 CYS B 35 CYS B 47 1555 1555 2.02 CRYST1 65.149 27.744 73.347 90.00 100.19 90.00 P 1 21/c 1 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 0.015349 0.000000 0.002760 0.00000 SCALE2 0.000000 0.036044 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013852 0.00000