HEADER TOXIN 17-APR-12 4EPF TITLE THE CRYSTAL STRUCTURE OF PESTICIN FROM YERSINIA PESTIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PESTICIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA PESTIS; SOURCE 3 ORGANISM_TAXID: 632; SOURCE 4 GENE: PST, YP_PPCP06, YPPCP1.05C; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BACTERIAL TOXIN, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR P.LUKACIK,T.J.BARNARD,S.K.BUCHANAN REVDAT 2 04-JUL-12 4EPF 1 JRNL REVDAT 1 20-JUN-12 4EPF 0 JRNL AUTH P.LUKACIK,T.J.BARNARD,P.W.KELLER,K.S.CHATURVEDI,N.SEDDIKI, JRNL AUTH 2 J.W.FAIRMAN,N.NOINAJ,T.L.KIRBY,J.P.HENDERSON,A.C.STEVEN, JRNL AUTH 3 B.J.HINNEBUSCH,S.K.BUCHANAN JRNL TITL STRUCTURAL ENGINEERING OF A PHAGE LYSIN THAT TARGETS JRNL TITL 2 GRAM-NEGATIVE PATHOGENS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 9857 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 22679291 JRNL DOI 10.1073/PNAS.1203472109 REMARK 2 REMARK 2 RESOLUTION. 2.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 41037 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) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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) : 2.09 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2491 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2460 REMARK 3 BIN FREE R VALUE SET COUNT : 121 REMARK 3 BIN FREE R VALUE : 0.3080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5267 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 211 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.74 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.33000 REMARK 3 B22 (A**2) : 0.47000 REMARK 3 B33 (A**2) : -2.45000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.62000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.235 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.192 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.142 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.502 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5390 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7289 ; 1.227 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 670 ; 5.354 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 269 ;34.745 ;24.647 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 935 ;15.297 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;17.504 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 809 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4117 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2359 ; 0.198 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3801 ; 0.305 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 289 ; 0.130 ; 0.200 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): 62 ; 0.204 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.196 ; 0.200 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): 3401 ; 1.853 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5374 ; 2.927 ; 5.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2199 ; 5.481 ; 8.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1915 ; 8.058 ;12.000 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 : 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 38 A 171 REMARK 3 ORIGIN FOR THE GROUP (A): 23.2610 54.6610 -37.9000 REMARK 3 T TENSOR REMARK 3 T11: -0.0977 T22: 0.0638 REMARK 3 T33: -0.1090 T12: -0.0374 REMARK 3 T13: -0.0223 T23: -0.0562 REMARK 3 L TENSOR REMARK 3 L11: 2.4788 L22: 1.7402 REMARK 3 L33: 6.9199 L12: 0.0344 REMARK 3 L13: -0.5039 L23: -1.7683 REMARK 3 S TENSOR REMARK 3 S11: 0.0069 S12: 0.6716 S13: -0.2354 REMARK 3 S21: -0.1731 S22: 0.0522 S23: -0.0255 REMARK 3 S31: -0.0413 S32: 0.0354 S33: -0.0591 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 : A 192 A 356 REMARK 3 ORIGIN FOR THE GROUP (A): 5.5680 43.4360 -8.1710 REMARK 3 T TENSOR REMARK 3 T11: -0.1630 T22: -0.2146 REMARK 3 T33: -0.1698 T12: 0.0425 REMARK 3 T13: -0.0013 T23: 0.0018 REMARK 3 L TENSOR REMARK 3 L11: 1.6485 L22: 2.1119 REMARK 3 L33: 0.7109 L12: 0.5816 REMARK 3 L13: 0.3553 L23: 0.0740 REMARK 3 S TENSOR REMARK 3 S11: 0.1109 S12: -0.0835 S13: -0.0275 REMARK 3 S21: 0.2008 S22: -0.0624 S23: 0.0703 REMARK 3 S31: -0.0168 S32: 0.0065 S33: -0.0485 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 38 B 171 REMARK 3 ORIGIN FOR THE GROUP (A): 32.198 55.951 -74.322 REMARK 3 T TENSOR REMARK 3 T11: -0.1012 T22: 0.2044 REMARK 3 T33: -0.1680 T12: -0.0604 REMARK 3 T13: -0.0109 T23: -0.0317 REMARK 3 L TENSOR REMARK 3 L11: 2.6889 L22: 1.9862 REMARK 3 L33: 11.6814 L12: -0.0818 REMARK 3 L13: -2.2016 L23: 2.8930 REMARK 3 S TENSOR REMARK 3 S11: 0.0144 S12: -0.8284 S13: -0.0325 REMARK 3 S21: 0.2070 S22: -0.2384 S23: 0.1647 REMARK 3 S31: 0.0682 S32: -0.2059 S33: 0.2241 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 : B 192 B 356 REMARK 3 ORIGIN FOR THE GROUP (A): 49.940 45.610 -101.536 REMARK 3 T TENSOR REMARK 3 T11: -0.1733 T22: -0.2279 REMARK 3 T33: -0.1598 T12: -0.0399 REMARK 3 T13: 0.0095 T23: 0.0039 REMARK 3 L TENSOR REMARK 3 L11: 2.0085 L22: 2.7162 REMARK 3 L33: 1.7714 L12: -0.9776 REMARK 3 L13: -0.1528 L23: 1.1334 REMARK 3 S TENSOR REMARK 3 S11: 0.0187 S12: -0.0328 S13: -0.1127 REMARK 3 S21: -0.0662 S22: 0.0757 S23: -0.1107 REMARK 3 S31: 0.1165 S32: -0.0137 S33: -0.0945 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 : 1.40 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 4EPF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-APR-12. REMARK 100 THE RCSB ID CODE IS RCSB071907. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-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) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97925, 0.97939, 0.97172 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41037 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.090 REMARK 200 RESOLUTION RANGE LOW (A) : 37.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05200 REMARK 200 FOR THE DATA SET : 20.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.36400 REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% W/V PEG3350, 0.25 M CALCIUM REMARK 280 CHLORIDE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 43.45000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 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 HIS A -3 REMARK 465 MSE A -2 REMARK 465 LEU A -1 REMARK 465 GLU A 0 REMARK 465 MSE A 1 REMARK 465 SER A 2 REMARK 465 ASP A 3 REMARK 465 THR A 4 REMARK 465 MSE A 5 REMARK 465 VAL A 6 REMARK 465 VAL A 7 REMARK 465 ASN A 8 REMARK 465 GLY A 9 REMARK 465 SER A 10 REMARK 465 GLY A 11 REMARK 465 GLY A 12 REMARK 465 VAL A 13 REMARK 465 SER A 25 REMARK 465 TYR A 26 REMARK 465 ARG A 27 REMARK 465 PRO A 28 REMARK 465 ASN A 29 REMARK 465 PHE A 30 REMARK 465 GLU A 31 REMARK 465 ALA A 32 REMARK 465 ASN A 33 REMARK 465 SER A 34 REMARK 465 LYS A 357 REMARK 465 HIS B -3 REMARK 465 MSE B -2 REMARK 465 LEU B -1 REMARK 465 GLU B 0 REMARK 465 MSE B 1 REMARK 465 SER B 2 REMARK 465 ASP B 3 REMARK 465 THR B 4 REMARK 465 MSE B 5 REMARK 465 VAL B 6 REMARK 465 VAL B 7 REMARK 465 ASN B 8 REMARK 465 GLY B 9 REMARK 465 SER B 10 REMARK 465 GLY B 11 REMARK 465 GLY B 12 REMARK 465 VAL B 13 REMARK 465 SER B 25 REMARK 465 TYR B 26 REMARK 465 ARG B 27 REMARK 465 PRO B 28 REMARK 465 ASN B 29 REMARK 465 PHE B 30 REMARK 465 GLU B 31 REMARK 465 ALA B 32 REMARK 465 LYS B 357 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 ASP A 103 CG OD1 OD2 REMARK 470 LYS A 127 CG CD CE NZ REMARK 470 ARG A 245 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 341 CG CD CE NZ REMARK 470 LYS B 74 CG CD CE NZ REMARK 470 GLN B 77 CG CD OE1 NE2 REMARK 470 LYS B 102 CG CD CE NZ REMARK 470 LYS B 127 CG CD CE NZ REMARK 470 LYS B 238 CG CD CE NZ 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 LYS A 102 114.48 -161.07 REMARK 500 PHE A 177 -115.15 -119.27 REMARK 500 SER A 204 66.57 -104.96 REMARK 500 MSE A 336 38.69 -147.79 REMARK 500 SER B 19 69.33 -102.22 REMARK 500 SER B 34 -20.06 -150.61 REMARK 500 LYS B 102 121.84 177.83 REMARK 500 PHE B 177 -116.77 -125.12 REMARK 500 PHE B 180 118.01 -161.04 REMARK 500 SER B 204 72.27 -101.27 REMARK 500 MSE B 234 -15.40 75.72 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 LYS B 127 -10.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4EPA RELATED DB: PDB REMARK 900 RELATED ID: 4EPI RELATED DB: PDB DBREF 4EPF A 1 357 UNP Q57159 Q57159_YERPE 1 357 DBREF 4EPF B 1 357 UNP Q57159 Q57159_YERPE 1 357 SEQADV 4EPF HIS A -3 UNP Q57159 EXPRESSION TAG SEQADV 4EPF MSE A -2 UNP Q57159 EXPRESSION TAG SEQADV 4EPF LEU A -1 UNP Q57159 EXPRESSION TAG SEQADV 4EPF GLU A 0 UNP Q57159 EXPRESSION TAG SEQADV 4EPF HIS B -3 UNP Q57159 EXPRESSION TAG SEQADV 4EPF MSE B -2 UNP Q57159 EXPRESSION TAG SEQADV 4EPF LEU B -1 UNP Q57159 EXPRESSION TAG SEQADV 4EPF GLU B 0 UNP Q57159 EXPRESSION TAG SEQRES 1 A 361 HIS MSE LEU GLU MSE SER ASP THR MSE VAL VAL ASN GLY SEQRES 2 A 361 SER GLY GLY VAL PRO ALA PHE LEU PHE SER GLY SER THR SEQRES 3 A 361 LEU SER SER TYR ARG PRO ASN PHE GLU ALA ASN SER ILE SEQRES 4 A 361 THR ILE ALA LEU PRO HIS TYR VAL ASP LEU PRO GLY ARG SEQRES 5 A 361 SER ASN PHE LYS LEU MSE TYR ILE MSE GLY PHE PRO ILE SEQRES 6 A 361 ASP THR GLU MSE GLU LYS ASP SER GLU TYR SER ASN LYS SEQRES 7 A 361 ILE ARG GLN GLU SER LYS ILE SER LYS THR GLU GLY THR SEQRES 8 A 361 VAL SER TYR GLU GLN LYS ILE THR VAL GLU THR GLY GLN SEQRES 9 A 361 GLU LYS ASP GLY VAL LYS VAL TYR ARG VAL MSE VAL LEU SEQRES 10 A 361 GLU GLY THR ILE ALA GLU SER ILE GLU HIS LEU ASP LYS SEQRES 11 A 361 LYS GLU ASN GLU ASP ILE LEU ASN ASN ASN ARG ASN ARG SEQRES 12 A 361 ILE VAL LEU ALA ASP ASN THR VAL ILE ASN PHE ASP ASN SEQRES 13 A 361 ILE SER GLN LEU LYS GLU PHE LEU ARG ARG SER VAL ASN SEQRES 14 A 361 ILE VAL ASP HIS ASP ILE PHE SER SER ASN GLY PHE GLU SEQRES 15 A 361 GLY PHE ASN PRO THR SER HIS PHE PRO SER ASN PRO SER SEQRES 16 A 361 SER ASP TYR PHE ASN SER THR GLY VAL THR PHE GLY SER SEQRES 17 A 361 GLY VAL ASP LEU GLY GLN ARG SER LYS GLN ASP LEU LEU SEQRES 18 A 361 ASN ASP GLY VAL PRO GLN TYR ILE ALA ASP ARG LEU ASP SEQRES 19 A 361 GLY TYR TYR MSE LEU ARG GLY LYS GLU ALA TYR ASP LYS SEQRES 20 A 361 VAL ARG THR ALA PRO LEU THR LEU SER ASP ASN GLU ALA SEQRES 21 A 361 HIS LEU LEU SER ASN ILE TYR ILE ASP LYS PHE SER HIS SEQRES 22 A 361 LYS ILE GLU GLY LEU PHE ASN ASP ALA ASN ILE GLY LEU SEQRES 23 A 361 ARG PHE SER ASP LEU PRO LEU ARG THR ARG THR ALA LEU SEQRES 24 A 361 VAL SER ILE GLY TYR GLN LYS GLY PHE LYS LEU SER ARG SEQRES 25 A 361 THR ALA PRO THR VAL TRP ASN LYS VAL ILE ALA LYS ASP SEQRES 26 A 361 TRP ASN GLY LEU VAL ASN ALA PHE ASN ASN ILE VAL ASP SEQRES 27 A 361 GLY MSE SER ASP ARG ARG LYS ARG GLU GLY ALA LEU VAL SEQRES 28 A 361 GLN LYS ASP ILE ASP SER GLY LEU LEU LYS SEQRES 1 B 361 HIS MSE LEU GLU MSE SER ASP THR MSE VAL VAL ASN GLY SEQRES 2 B 361 SER GLY GLY VAL PRO ALA PHE LEU PHE SER GLY SER THR SEQRES 3 B 361 LEU SER SER TYR ARG PRO ASN PHE GLU ALA ASN SER ILE SEQRES 4 B 361 THR ILE ALA LEU PRO HIS TYR VAL ASP LEU PRO GLY ARG SEQRES 5 B 361 SER ASN PHE LYS LEU MSE TYR ILE MSE GLY PHE PRO ILE SEQRES 6 B 361 ASP THR GLU MSE GLU LYS ASP SER GLU TYR SER ASN LYS SEQRES 7 B 361 ILE ARG GLN GLU SER LYS ILE SER LYS THR GLU GLY THR SEQRES 8 B 361 VAL SER TYR GLU GLN LYS ILE THR VAL GLU THR GLY GLN SEQRES 9 B 361 GLU LYS ASP GLY VAL LYS VAL TYR ARG VAL MSE VAL LEU SEQRES 10 B 361 GLU GLY THR ILE ALA GLU SER ILE GLU HIS LEU ASP LYS SEQRES 11 B 361 LYS GLU ASN GLU ASP ILE LEU ASN ASN ASN ARG ASN ARG SEQRES 12 B 361 ILE VAL LEU ALA ASP ASN THR VAL ILE ASN PHE ASP ASN SEQRES 13 B 361 ILE SER GLN LEU LYS GLU PHE LEU ARG ARG SER VAL ASN SEQRES 14 B 361 ILE VAL ASP HIS ASP ILE PHE SER SER ASN GLY PHE GLU SEQRES 15 B 361 GLY PHE ASN PRO THR SER HIS PHE PRO SER ASN PRO SER SEQRES 16 B 361 SER ASP TYR PHE ASN SER THR GLY VAL THR PHE GLY SER SEQRES 17 B 361 GLY VAL ASP LEU GLY GLN ARG SER LYS GLN ASP LEU LEU SEQRES 18 B 361 ASN ASP GLY VAL PRO GLN TYR ILE ALA ASP ARG LEU ASP SEQRES 19 B 361 GLY TYR TYR MSE LEU ARG GLY LYS GLU ALA TYR ASP LYS SEQRES 20 B 361 VAL ARG THR ALA PRO LEU THR LEU SER ASP ASN GLU ALA SEQRES 21 B 361 HIS LEU LEU SER ASN ILE TYR ILE ASP LYS PHE SER HIS SEQRES 22 B 361 LYS ILE GLU GLY LEU PHE ASN ASP ALA ASN ILE GLY LEU SEQRES 23 B 361 ARG PHE SER ASP LEU PRO LEU ARG THR ARG THR ALA LEU SEQRES 24 B 361 VAL SER ILE GLY TYR GLN LYS GLY PHE LYS LEU SER ARG SEQRES 25 B 361 THR ALA PRO THR VAL TRP ASN LYS VAL ILE ALA LYS ASP SEQRES 26 B 361 TRP ASN GLY LEU VAL ASN ALA PHE ASN ASN ILE VAL ASP SEQRES 27 B 361 GLY MSE SER ASP ARG ARG LYS ARG GLU GLY ALA LEU VAL SEQRES 28 B 361 GLN LYS ASP ILE ASP SER GLY LEU LEU LYS MODRES 4EPF MSE A 54 MET SELENOMETHIONINE MODRES 4EPF MSE A 57 MET SELENOMETHIONINE MODRES 4EPF MSE A 65 MET SELENOMETHIONINE MODRES 4EPF MSE A 111 MET SELENOMETHIONINE MODRES 4EPF MSE A 234 MET SELENOMETHIONINE MODRES 4EPF MSE A 336 MET SELENOMETHIONINE MODRES 4EPF MSE B 54 MET SELENOMETHIONINE MODRES 4EPF MSE B 57 MET SELENOMETHIONINE MODRES 4EPF MSE B 65 MET SELENOMETHIONINE MODRES 4EPF MSE B 111 MET SELENOMETHIONINE MODRES 4EPF MSE B 234 MET SELENOMETHIONINE MODRES 4EPF MSE B 336 MET SELENOMETHIONINE HET MSE A 54 8 HET MSE A 57 8 HET MSE A 65 8 HET MSE A 111 8 HET MSE A 234 8 HET MSE A 336 8 HET MSE B 54 8 HET MSE B 57 8 HET MSE B 65 8 HET MSE B 111 8 HET MSE B 234 8 HET MSE B 336 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 12(C5 H11 N O2 SE) FORMUL 3 HOH *211(H2 O) HELIX 1 1 ILE A 35 LEU A 39 5 5 HELIX 2 2 THR A 116 LYS A 126 1 11 HELIX 3 3 ASN A 129 ASN A 135 1 7 HELIX 4 4 ASN A 152 ASN A 165 1 14 HELIX 5 5 ASP A 168 SER A 174 1 7 HELIX 6 6 TYR A 194 THR A 198 5 5 HELIX 7 7 SER A 212 ASP A 219 1 8 HELIX 8 8 PRO A 222 LEU A 229 1 8 HELIX 9 9 GLY A 237 ALA A 247 1 11 HELIX 10 10 SER A 252 ALA A 278 1 27 HELIX 11 11 ARG A 283 LEU A 287 5 5 HELIX 12 12 PRO A 288 GLY A 303 1 16 HELIX 13 13 LYS A 305 ALA A 310 1 6 HELIX 14 14 ALA A 310 ALA A 319 1 10 HELIX 15 15 ASP A 321 ILE A 332 1 12 HELIX 16 16 MSE A 336 SER A 353 1 18 HELIX 17 17 SER B 34 LEU B 39 5 6 HELIX 18 18 THR B 116 LYS B 126 1 11 HELIX 19 19 ASN B 129 ASN B 135 1 7 HELIX 20 20 ASN B 152 ASN B 165 1 14 HELIX 21 21 ASP B 168 SER B 173 1 6 HELIX 22 22 SER B 212 ASP B 219 1 8 HELIX 23 23 PRO B 222 LEU B 229 1 8 HELIX 24 24 ARG B 236 ALA B 247 1 12 HELIX 25 25 SER B 252 ALA B 278 1 27 HELIX 26 26 ARG B 283 LEU B 287 5 5 HELIX 27 27 PRO B 288 GLY B 303 1 16 HELIX 28 28 LYS B 305 ALA B 310 1 6 HELIX 29 29 ALA B 310 ILE B 318 1 9 HELIX 30 30 ASP B 321 ILE B 332 1 12 HELIX 31 31 MSE B 336 SER B 353 1 18 SHEET 1 A 7 HIS A 41 ASP A 44 0 SHEET 2 A 7 LYS A 52 ILE A 56 -1 O LEU A 53 N VAL A 43 SHEET 3 A 7 PHE A 59 MSE A 65 -1 O ILE A 61 N MSE A 54 SHEET 4 A 7 VAL A 105 GLY A 115 -1 O TYR A 108 N ASP A 62 SHEET 5 A 7 ILE A 94 GLU A 101 -1 N ILE A 94 O GLY A 115 SHEET 6 A 7 ARG A 137 VAL A 141 -1 O VAL A 141 N THR A 95 SHEET 7 A 7 VAL A 147 PHE A 150 -1 O PHE A 150 N ASN A 138 SHEET 1 B 3 ASN A 181 HIS A 185 0 SHEET 2 B 3 THR A 201 GLY A 203 -1 O THR A 201 N HIS A 185 SHEET 3 B 3 VAL A 206 ASP A 207 -1 O VAL A 206 N PHE A 202 SHEET 1 C 7 HIS B 41 ASP B 44 0 SHEET 2 C 7 LYS B 52 ILE B 56 -1 O TYR B 55 N HIS B 41 SHEET 3 C 7 PHE B 59 MSE B 65 -1 O PHE B 59 N ILE B 56 SHEET 4 C 7 VAL B 105 GLY B 115 -1 O TYR B 108 N ASP B 62 SHEET 5 C 7 ILE B 94 GLU B 101 -1 N VAL B 96 O MSE B 111 SHEET 6 C 7 ARG B 137 VAL B 141 -1 O ARG B 139 N GLU B 97 SHEET 7 C 7 VAL B 147 PHE B 150 -1 O PHE B 150 N ASN B 138 SHEET 1 D 3 ASN B 181 HIS B 185 0 SHEET 2 D 3 THR B 201 GLY B 203 -1 O THR B 201 N HIS B 185 SHEET 3 D 3 VAL B 206 ASP B 207 -1 O VAL B 206 N PHE B 202 LINK C LEU A 53 N MSE A 54 1555 1555 1.33 LINK C MSE A 54 N TYR A 55 1555 1555 1.33 LINK C ILE A 56 N MSE A 57 1555 1555 1.33 LINK C MSE A 57 N GLY A 58 1555 1555 1.33 LINK C GLU A 64 N MSE A 65 1555 1555 1.32 LINK C MSE A 65 N GLU A 66 1555 1555 1.33 LINK C VAL A 110 N MSE A 111 1555 1555 1.33 LINK C MSE A 111 N VAL A 112 1555 1555 1.33 LINK C TYR A 233 N MSE A 234 1555 1555 1.33 LINK C MSE A 234 N LEU A 235 1555 1555 1.33 LINK C GLY A 335 N MSE A 336 1555 1555 1.32 LINK C MSE A 336 N SER A 337 1555 1555 1.33 LINK C LEU B 53 N MSE B 54 1555 1555 1.33 LINK C MSE B 54 N TYR B 55 1555 1555 1.33 LINK C ILE B 56 N MSE B 57 1555 1555 1.34 LINK C MSE B 57 N GLY B 58 1555 1555 1.33 LINK C GLU B 64 N MSE B 65 1555 1555 1.33 LINK C MSE B 65 N GLU B 66 1555 1555 1.33 LINK C VAL B 110 N MSE B 111 1555 1555 1.33 LINK C MSE B 111 N VAL B 112 1555 1555 1.33 LINK C TYR B 233 N MSE B 234 1555 1555 1.32 LINK C MSE B 234 N LEU B 235 1555 1555 1.34 LINK C GLY B 335 N MSE B 336 1555 1555 1.33 LINK C MSE B 336 N SER B 337 1555 1555 1.33 CRYST1 36.498 86.900 122.226 90.00 96.20 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 0.027399 0.000000 0.002975 0.00000 SCALE2 0.000000 0.011507 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008230 0.00000