HEADER ANTIMICROBIAL PROTEIN 06-JUL-12 4FZM TITLE CRYSTAL STRUCTURE OF THE BACTERIOCIN SYRINGACIN M FROM PSEUDOMONAS TITLE 2 SYRINGAE PV. TOMATO DC3000 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACTERIOCIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS SYRINGAE PV. TOMATO; SOURCE 3 ORGANISM_TAXID: 223283; SOURCE 4 STRAIN: DC3000; SOURCE 5 GENE: PSPTO_0572; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PET21A; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETMDC KEYWDS PHOSPHATASE, DIVALENT CATION BINDING, LIPID II BINDING, ANTIMICROBIAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.W.ROSZAK,R.GRINTER,J.R.COGDELL,D.WALKER REVDAT 3 28-FEB-24 4FZM 1 REMARK SEQADV LINK REVDAT 2 28-NOV-12 4FZM 1 JRNL REVDAT 1 03-OCT-12 4FZM 0 JRNL AUTH R.GRINTER,A.W.ROSZAK,R.J.COGDELL,J.J.MILNER,D.WALKER JRNL TITL THE CRYSTAL STRUCTURE OF THE LIPID II-DEGRADING BACTERIOCIN JRNL TITL 2 SYRINGACIN M SUGGESTS UNEXPECTED EVOLUTIONARY RELATIONSHIPS JRNL TITL 3 BETWEEN COLICIN M-LIKE BACTERIOCINS. JRNL REF J.BIOL.CHEM. V. 287 38876 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22995910 JRNL DOI 10.1074/JBC.M112.400150 REMARK 2 REMARK 2 RESOLUTION. 2.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 2.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 17330 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 929 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) : 2.84 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.91 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1125 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.75 REMARK 3 BIN R VALUE (WORKING SET) : 0.3530 REMARK 3 BIN FREE R VALUE SET COUNT : 63 REMARK 3 BIN FREE R VALUE : 0.3610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2083 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 35 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 102.3 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 84.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.03000 REMARK 3 B22 (A**2) : 1.03000 REMARK 3 B33 (A**2) : -1.55000 REMARK 3 B12 (A**2) : 0.52000 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): 0.286 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.243 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.174 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.822 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2152 ; 0.020 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1423 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2937 ; 2.028 ; 1.956 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3473 ; 1.096 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 279 ; 8.673 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 97 ;40.497 ;24.536 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 320 ;19.887 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;15.320 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 327 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2467 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 430 ; 0.001 ; 0.020 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 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 2 A 277 REMARK 3 ORIGIN FOR THE GROUP (A): -70.0341 16.3540 -10.0954 REMARK 3 T TENSOR REMARK 3 T11: 0.6911 T22: 0.3659 REMARK 3 T33: 0.4552 T12: 0.0556 REMARK 3 T13: -0.0155 T23: 0.1345 REMARK 3 L TENSOR REMARK 3 L11: 7.8304 L22: 4.1527 REMARK 3 L33: 4.2854 L12: 2.9152 REMARK 3 L13: -2.3017 L23: -2.1350 REMARK 3 S TENSOR REMARK 3 S11: 0.1313 S12: -1.4122 S13: -0.7912 REMARK 3 S21: 0.5507 S22: -0.0534 S23: -0.3122 REMARK 3 S31: -0.3917 S32: 0.3978 S33: -0.0778 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 4FZM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000073551. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795, 0.9796, 0.9253 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17330 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.830 REMARK 200 RESOLUTION RANGE LOW (A) : 46.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.60 REMARK 200 R MERGE FOR SHELL (I) : 0.69300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 7% W/V PEG 8000, 30% V/V ETHYLENE REMARK 280 GLYCOL 0.03 M CACL2, 0.03 M MGCL2, 5% DIMETHYL SULFOXIDE, 0.1 M REMARK 280 BICINE/TRIS BASE, PH 8.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 -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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 50.08650 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 50.08650 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 50.08650 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 50.08650 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 50.08650 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 50.08650 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: MONOMERIC 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: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL 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 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 -50.08650 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 GLU A 278 REMARK 465 HIS A 279 REMARK 465 HIS A 280 REMARK 465 HIS A 281 REMARK 465 HIS A 282 REMARK 465 HIS A 283 REMARK 465 HIS A 284 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 LEU A 29 CG CD1 CD2 REMARK 470 SER A 30 OG 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 HIS A 125 CG HIS A 125 CD2 0.056 REMARK 500 HIS A 241 CG HIS A 241 CD2 0.078 REMARK 500 TRP A 244 CE2 TRP A 244 CZ2 -0.108 REMARK 500 TRP A 244 CE2 TRP A 244 CD2 0.080 REMARK 500 TRP A 244 CD2 TRP A 244 CE3 -0.122 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 LYS A 193 CD - CE - NZ ANGL. DEV. = 16.5 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 ILE A 3 112.67 40.15 REMARK 500 LEU A 5 127.84 94.34 REMARK 500 ILE A 10 93.02 79.14 REMARK 500 ILE A 16 -76.61 61.18 REMARK 500 ALA A 18 119.54 -25.87 REMARK 500 ARG A 25 151.56 80.96 REMARK 500 LEU A 29 -131.39 -130.45 REMARK 500 GLN A 33 -137.64 -125.85 REMARK 500 SER A 34 -13.85 82.10 REMARK 500 PHE A 35 160.68 179.98 REMARK 500 LEU A 145 26.29 48.50 REMARK 500 ASN A 159 78.24 -166.91 REMARK 500 SER A 174 120.15 -173.53 REMARK 500 ALA A 175 143.73 -35.30 REMARK 500 SER A 181 138.70 -180.00 REMARK 500 PHE A 187 146.89 -173.16 REMARK 500 VAL A 191 -19.93 -49.21 REMARK 500 ALA A 217 -66.48 72.45 REMARK 500 SER A 218 -69.50 -109.37 REMARK 500 ALA A 220 -155.38 -97.59 REMARK 500 ASN A 231 133.15 -34.51 REMARK 500 ASN A 276 -109.16 -154.12 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 GLY A 123 ASN A 124 -149.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 202 O REMARK 620 2 ASN A 204 O 83.3 REMARK 620 3 ASP A 232 OD2 71.8 100.6 REMARK 620 4 ASP A 232 OD1 108.3 69.3 52.3 REMARK 620 5 EDO A 302 O1 122.0 147.0 71.8 81.8 REMARK 620 6 EDO A 302 O2 167.7 84.7 113.1 69.5 70.1 REMARK 620 7 HOH A 423 O 116.3 93.7 164.5 129.8 92.9 61.9 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2XMX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE BACTERIOCIN COLICIN M REMARK 900 RELATED ID: 4FZL RELATED DB: PDB REMARK 900 RELATED ID: 4FZN RELATED DB: PDB DBREF 4FZM A 1 276 UNP Q88A25 Q88A25_PSESM 1 276 SEQADV 4FZM LEU A 277 UNP Q88A25 EXPRESSION TAG SEQADV 4FZM GLU A 278 UNP Q88A25 EXPRESSION TAG SEQADV 4FZM HIS A 279 UNP Q88A25 EXPRESSION TAG SEQADV 4FZM HIS A 280 UNP Q88A25 EXPRESSION TAG SEQADV 4FZM HIS A 281 UNP Q88A25 EXPRESSION TAG SEQADV 4FZM HIS A 282 UNP Q88A25 EXPRESSION TAG SEQADV 4FZM HIS A 283 UNP Q88A25 EXPRESSION TAG SEQADV 4FZM HIS A 284 UNP Q88A25 EXPRESSION TAG SEQRES 1 A 284 MET PRO ILE GLU LEU PRO PRO THR TYR ILE THR PRO TYR SEQRES 2 A 284 PRO GLU ILE SER ALA GLY GLY ASN GLY THR TYR ARG GLY SEQRES 3 A 284 GLN ASP LEU SER SER GLY GLN SER PHE PRO ARG GLY MET SEQRES 4 A 284 GLN ASN PRO VAL ALA THR VAL LEU LEU LEU GLN GLY ASP SEQRES 5 A 284 LEU TYR CYS SER PRO ASN CYS LEU ALA THR PHE GLN ASP SEQRES 6 A 284 GLN ALA ARG ARG ASP SER PHE GLY ILE GLN SER LYS VAL SEQRES 7 A 284 ALA LEU LYS THR PHE ALA ALA ALA ASP GLN ARG GLU ALA SEQRES 8 A 284 GLU GLY ARG ASP LEU ARG THR ALA TYR ASN GLU ILE ALA SEQRES 9 A 284 THR ASP ILE GLY ARG SER GLN GLN ILE ASN GLU ASN ILE SEQRES 10 A 284 ILE LYS TYR PRO PRO GLY ASN HIS VAL LEU SER GLY GLY SEQRES 11 A 284 LEU MET THR PRO PHE HIS ALA LEU ALA HIS GLY MET PHE SEQRES 12 A 284 GLY LEU GLY ALA PRO LEU THR PHE PRO ILE GLN ASN VAL SEQRES 13 A 284 GLY LEU ASN VAL ASP ILE ARG GLY ILE PRO ASP VAL MET SEQRES 14 A 284 ASN VAL ILE GLN SER ALA ARG PRO VAL GLY THR SER SER SEQRES 15 A 284 LEU ASP VAL ASN PHE ALA TYR ASP VAL GLY LYS ASP SER SEQRES 16 A 284 ASN ALA SER TRP LEU THR LEU GLY ASN ILE THR LEU ARG SEQRES 17 A 284 LEU VAL GLY THR ILE ASP LYS ASN ALA SER GLY ALA TRP SEQRES 18 A 284 THR PHE SER GLY GLU ILE ARG ALA PHE ASN ASP VAL TYR SEQRES 19 A 284 ASP ALA ASN PRO SER ASN HIS ARG GLY TRP LEU GLY GLU SEQRES 20 A 284 ASN LEU THR SER LEU LEU SER ALA VAL PRO PHE THR SER SEQRES 21 A 284 TYR SER ILE GLU ILE PRO GLY SER LEU PRO VAL THR VAL SEQRES 22 A 284 SER GLY ASN LEU GLU HIS HIS HIS HIS HIS HIS HET CA A 301 1 HET EDO A 302 4 HETNAM CA CALCIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 CA CA 2+ FORMUL 3 EDO C2 H6 O2 FORMUL 4 HOH *35(H2 O) HELIX 1 1 ASN A 41 CYS A 55 1 15 HELIX 2 2 ASN A 58 SER A 71 1 14 HELIX 3 3 GLY A 73 GLU A 92 1 20 HELIX 4 4 ASP A 95 ARG A 109 1 15 HELIX 5 5 MET A 132 GLY A 144 1 13 HELIX 6 6 PRO A 152 VAL A 156 5 5 HELIX 7 7 ASP A 161 GLY A 164 5 4 HELIX 8 8 ILE A 165 GLN A 173 1 9 HELIX 9 9 GLY A 192 ASP A 194 5 3 HELIX 10 10 SER A 195 GLY A 203 1 9 HELIX 11 11 ASN A 237 ASN A 240 5 4 HELIX 12 12 HIS A 241 GLY A 246 1 6 HELIX 13 13 GLY A 246 ALA A 255 1 10 SHEET 1 A 3 LEU A 149 THR A 150 0 SHEET 2 A 3 TYR A 261 GLU A 264 1 O GLU A 264 N LEU A 149 SHEET 3 A 3 ASP A 232 TYR A 234 -1 N ASP A 232 O ILE A 263 SHEET 1 B 4 SER A 182 ASP A 190 0 SHEET 2 B 4 ASN A 204 LYS A 215 -1 O LEU A 209 N VAL A 185 SHEET 3 B 4 TRP A 221 ALA A 229 -1 O ARG A 228 N ARG A 208 SHEET 4 B 4 LEU A 269 GLY A 275 -1 O VAL A 271 N GLY A 225 LINK O LEU A 202 CA CA A 301 1555 1555 2.29 LINK O ASN A 204 CA CA A 301 1555 1555 2.47 LINK OD2 ASP A 232 CA CA A 301 1555 1555 2.43 LINK OD1 ASP A 232 CA CA A 301 1555 1555 2.57 LINK CA CA A 301 O1 EDO A 302 1555 1555 2.36 LINK CA CA A 301 O2 EDO A 302 1555 1555 2.47 LINK CA CA A 301 O HOH A 423 1555 1555 2.76 CISPEP 1 SER A 30 SER A 31 0 -8.88 CISPEP 2 SER A 218 GLY A 219 0 2.63 SITE 1 AC1 5 LEU A 202 ASN A 204 ASP A 232 EDO A 302 SITE 2 AC1 5 HOH A 423 SITE 1 AC2 5 ASN A 204 ASP A 232 VAL A 233 CA A 301 SITE 2 AC2 5 HOH A 423 CRYST1 159.687 159.687 100.173 90.00 90.00 120.00 P 63 2 2 12 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 0.006262 0.003616 0.000000 0.00000 SCALE2 0.000000 0.007231 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009983 0.00000