HEADER TOXIN 13-MAR-19 6JMP TITLE CRYSTAL STRUCTURE OF A NON-HEMOLYTIC PNEUMOLYSIN FROM STREPTOCOCCUS TITLE 2 PNEUMONIAE STRAIN ST306 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOL-ACTIVATED CYTOLYSIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 1313; SOURCE 4 GENE: PLY; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS CHOLESTEROL DEPENDENT CYTOLYSIN, TOXIN, PNEUMOLYSIN, NON-PORE KEYWDS 2 FORMING, NON-HEMOLYTIC, MEMBRANE EXPDTA X-RAY DIFFRACTION AUTHOR D.C.BADGUJAR,P.BHAUMIK REVDAT 4 22-NOV-23 6JMP 1 REMARK REVDAT 3 24-FEB-21 6JMP 1 JRNL REVDAT 2 23-SEP-20 6JMP 1 JRNL REVDAT 1 09-SEP-20 6JMP 0 JRNL AUTH D.C.BADGUJAR,A.ANIL,A.E.GREEN,M.V.SURVE,S.MADHAVAN, JRNL AUTH 2 A.BECKETT,I.A.PRIOR,B.K.GODSORA,S.B.PATIL,P.K.MORE, JRNL AUTH 3 S.G.SARKAR,A.MITCHELL,R.BANERJEE,P.S.PHALE,T.J.MITCHELL, JRNL AUTH 4 D.R.NEILL,P.BHAUMIK,A.BANERJEE JRNL TITL STRUCTURAL INSIGHTS INTO LOSS OF FUNCTION OF A PORE FORMING JRNL TITL 2 TOXIN AND ITS ROLE IN PNEUMOCOCCAL ADAPTATION TO AN JRNL TITL 3 INTRACELLULAR LIFESTYLE. JRNL REF PLOS PATHOG. V. 16 09016 2020 JRNL REFN ESSN 1553-7374 JRNL PMID 33216805 JRNL DOI 10.1371/JOURNAL.PPAT.1009016 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 22691 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) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1195 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1618 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2940 REMARK 3 BIN FREE R VALUE SET COUNT : 85 REMARK 3 BIN FREE R VALUE : 0.3380 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3712 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 317 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.98 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.17000 REMARK 3 B22 (A**2) : 0.12000 REMARK 3 B33 (A**2) : 0.05000 REMARK 3 B12 (A**2) : 0.00000 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): 0.410 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.254 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.193 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.403 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.929 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.895 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3897 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3564 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5314 ; 1.354 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8306 ; 3.752 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 493 ; 5.863 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 184 ;38.532 ;25.054 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 671 ;15.570 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;17.964 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 610 ; 0.068 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4352 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 764 ; 0.003 ; 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): 1910 ; 3.361 ; 2.938 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1909 ; 3.357 ; 2.935 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2395 ; 5.708 ; 4.382 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2396 ; 5.709 ; 4.386 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1987 ; 3.590 ; 3.327 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1987 ; 3.585 ; 3.327 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2910 ; 6.046 ; 4.794 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4209 ;10.012 ;34.573 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4209 ;10.011 ;34.571 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 1 A 156 REMARK 3 ORIGIN FOR THE GROUP (A): 50.6420 181.0590 239.0680 REMARK 3 T TENSOR REMARK 3 T11: 0.2057 T22: 0.1821 REMARK 3 T33: 0.0079 T12: -0.0211 REMARK 3 T13: 0.0253 T23: -0.0047 REMARK 3 L TENSOR REMARK 3 L11: 0.0322 L22: 0.6177 REMARK 3 L33: 1.1469 L12: 0.0626 REMARK 3 L13: 0.1207 L23: 0.6600 REMARK 3 S TENSOR REMARK 3 S11: 0.0425 S12: 0.0246 S13: 0.0050 REMARK 3 S21: 0.0790 S22: -0.0152 S23: -0.0358 REMARK 3 S31: -0.0153 S32: -0.0629 S33: -0.0273 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 157 A 290 REMARK 3 ORIGIN FOR THE GROUP (A): 54.0620 183.5930 247.6920 REMARK 3 T TENSOR REMARK 3 T11: 0.2144 T22: 0.1626 REMARK 3 T33: 0.0203 T12: -0.0493 REMARK 3 T13: 0.0091 T23: -0.0125 REMARK 3 L TENSOR REMARK 3 L11: 0.1193 L22: 1.2622 REMARK 3 L33: 2.0889 L12: 0.3414 REMARK 3 L13: 0.3723 L23: 0.8292 REMARK 3 S TENSOR REMARK 3 S11: 0.0617 S12: 0.0423 S13: -0.0138 REMARK 3 S21: 0.2876 S22: -0.0395 S23: -0.0413 REMARK 3 S31: -0.0716 S32: 0.1012 S33: -0.0222 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 : A 291 A 350 REMARK 3 ORIGIN FOR THE GROUP (A): 53.4300 188.1330 244.1350 REMARK 3 T TENSOR REMARK 3 T11: 0.2938 T22: 0.1987 REMARK 3 T33: 0.0591 T12: -0.0759 REMARK 3 T13: 0.0636 T23: -0.0328 REMARK 3 L TENSOR REMARK 3 L11: 0.3186 L22: 1.0806 REMARK 3 L33: 3.2653 L12: 0.5724 REMARK 3 L13: 0.2997 L23: 0.7571 REMARK 3 S TENSOR REMARK 3 S11: 0.1564 S12: -0.0036 S13: 0.1075 REMARK 3 S21: 0.2278 S22: -0.0633 S23: 0.1929 REMARK 3 S31: -0.4333 S32: 0.2435 S33: -0.0932 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 : A 351 A 469 REMARK 3 ORIGIN FOR THE GROUP (A): 56.7710 182.9390 301.0040 REMARK 3 T TENSOR REMARK 3 T11: 0.2246 T22: 0.1706 REMARK 3 T33: 0.0073 T12: 0.0134 REMARK 3 T13: -0.0139 T23: 0.0041 REMARK 3 L TENSOR REMARK 3 L11: 0.0741 L22: 0.8705 REMARK 3 L33: 3.2192 L12: -0.2313 REMARK 3 L13: -0.2672 L23: 0.4441 REMARK 3 S TENSOR REMARK 3 S11: 0.0382 S12: -0.0156 S13: -0.0206 REMARK 3 S21: -0.2106 S22: -0.0601 S23: 0.0745 REMARK 3 S31: 0.2955 S32: 0.0119 S33: 0.0219 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 6JMP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1300011394. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-APR-16 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 : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95372 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23881 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 38.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.70 REMARK 200 R MERGE (I) : 0.24000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.10 REMARK 200 R MERGE FOR SHELL (I) : 1.31800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5CR6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6 MM PHOSPHOCHOLINE, 0.2 M MGCL2, 20% REMARK 280 PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 12.24000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 107.31000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.36500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 107.31000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.24000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.36500 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 ARG A 147 CG CD NE CZ NH1 NH2 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 ALA A 146 CE MET A 148 2.13 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 MET A 148 CA - C - O ANGL. DEV. = 18.4 DEGREES REMARK 500 MET A 148 CA - C - N ANGL. DEV. = -16.5 DEGREES REMARK 500 TRP A 431 CA - C - O ANGL. DEV. = 15.6 DEGREES REMARK 500 TRP A 431 CA - C - O ANGL. DEV. = 16.8 DEGREES REMARK 500 TRP A 431 CA - C - N ANGL. DEV. = -13.4 DEGREES REMARK 500 TRP A 431 CA - C - N ANGL. DEV. = -14.5 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 ASN A 86 59.29 -141.48 REMARK 500 ASN A 86 59.29 -141.00 REMARK 500 ALA A 91 64.74 -101.29 REMARK 500 LEU A 106 108.95 -163.87 REMARK 500 ASP A 137 15.57 -143.18 REMARK 500 TYR A 138 -40.88 -168.26 REMARK 500 SER A 295 -165.12 -103.03 REMARK 500 VAL A 305 -37.89 -34.16 REMARK 500 ASP A 336 11.82 -142.85 REMARK 500 ALA A 368 55.68 -91.49 REMARK 500 ASN A 468 59.23 -149.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 915 DISTANCE = 6.11 ANGSTROMS REMARK 525 HOH A 916 DISTANCE = 6.11 ANGSTROMS REMARK 525 HOH A 917 DISTANCE = 8.72 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 504 DBREF 6JMP A 1 469 UNP Q2XU25 Q2XU25_STREE 1 469 SEQRES 1 A 469 MET ALA ASN LYS ALA VAL ASN ASP PHE ILE LEU ALA MET SEQRES 2 A 469 ASN TYR ASP LYS LYS LYS LEU LEU THR HIS GLN GLY GLU SEQRES 3 A 469 SER ILE GLU ASN ARG PHE ILE LYS GLU GLY ASN GLN LEU SEQRES 4 A 469 PRO ASP GLU PHE VAL VAL ILE GLU ARG LYS LYS ARG SER SEQRES 5 A 469 LEU SER THR ASN THR SER ASP ILE SER VAL THR ALA THR SEQRES 6 A 469 ASN ASP SER ARG LEU TYR PRO GLY ALA LEU LEU VAL VAL SEQRES 7 A 469 ASP GLU THR LEU LEU GLU ASN ASN PRO THR LEU LEU ALA SEQRES 8 A 469 VAL ASP ARG ALA PRO MET THR TYR SER ILE ASP LEU PRO SEQRES 9 A 469 GLY LEU ALA SER SER ASP SER PHE LEU GLN VAL GLU ASP SEQRES 10 A 469 PRO SER ASN SER SER VAL ARG GLY ALA VAL ASN ASP LEU SEQRES 11 A 469 LEU ALA LYS TRP HIS GLN ASP TYR GLY GLN VAL ASN ASN SEQRES 12 A 469 VAL PRO ALA ARG MET GLN HIS GLU LYS ILE THR ALA HIS SEQRES 13 A 469 SER MET GLU GLN LEU LYS VAL LYS PHE GLY SER ASP PHE SEQRES 14 A 469 GLU LYS ILE GLY ASN SER LEU ASP ILE ASP PHE ASN SER SEQRES 15 A 469 VAL HIS SER GLY GLU LYS GLN ILE GLN ILE VAL ASN PHE SEQRES 16 A 469 LYS GLN ILE TYR TYR THR VAL SER VAL ASP ALA VAL LYS SEQRES 17 A 469 ASN PRO GLY ASP VAL PHE GLN ASP THR VAL THR VAL GLU SEQRES 18 A 469 ASP LEU ARG GLN ARG GLY ILE SER ALA GLU ARG PRO LEU SEQRES 19 A 469 VAL TYR ILE SER SER VAL ALA TYR GLY ARG GLN VAL TYR SEQRES 20 A 469 LEU LYS LEU GLU THR THR SER LYS SER ASP GLU VAL GLU SEQRES 21 A 469 ALA ALA PHE GLU SER LEU ILE LYS GLY VAL ALA PRO GLN SEQRES 22 A 469 THR GLU TRP LYS GLN ILE LEU ASP ASN THR GLU VAL LYS SEQRES 23 A 469 ALA VAL ILE LEU GLY GLY ASP PRO SER SER GLY ALA ARG SEQRES 24 A 469 VAL VAL THR GLY LYS VAL ASP MET VAL GLU ASP LEU ILE SEQRES 25 A 469 GLN GLU GLY SER ARG PHE THR ALA ASP HIS PRO GLY LEU SEQRES 26 A 469 PRO ILE SER TYR THR THR SER PHE LEU ARG ASP ASN VAL SEQRES 27 A 469 VAL ALA THR PHE GLN ASN SER THR ASP TYR VAL GLU THR SEQRES 28 A 469 LYS VAL THR ALA TYR ARG ASN GLY ASP LEU LEU LEU ASP SEQRES 29 A 469 HIS SER GLY ALA TYR VAL ALA GLN TYR TYR ILE THR TRP SEQRES 30 A 469 ASP GLU LEU SER TYR ASP HIS GLN GLY LYS GLU VAL LEU SEQRES 31 A 469 THR PRO LYS ALA TRP ASP ARG ASN GLY GLN ASP LEU THR SEQRES 32 A 469 ALA HIS PHE THR THR SER ILE PRO LEU LYS GLY ASN VAL SEQRES 33 A 469 ARG ASN LEU SER VAL LYS ILE ARG GLU CYS THR GLY LEU SEQRES 34 A 469 ALA TRP GLU TRP TRP ARG THR VAL TYR GLU LYS THR ASP SEQRES 35 A 469 LEU PRO LEU VAL ARG LYS ARG THR ILE SER ILE TRP GLY SEQRES 36 A 469 THR THR LEU TYR PRO GLN VAL GLU ASP LYS VAL GLU ASN SEQRES 37 A 469 ASP HET GOL A 501 6 HET GOL A 502 6 HET GOL A 503 6 HET GOL A 504 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 4(C3 H8 O3) FORMUL 6 HOH *317(H2 O) HELIX 1 AA1 MET A 1 MET A 13 1 13 HELIX 2 AA2 ASP A 16 LEU A 21 1 6 HELIX 3 AA3 ASP A 79 GLU A 84 1 6 HELIX 4 AA4 SER A 119 GLN A 136 1 18 HELIX 5 AA5 SER A 157 GLY A 166 1 10 HELIX 6 AA6 PHE A 169 ASN A 174 1 6 HELIX 7 AA7 ASP A 179 SER A 185 1 7 HELIX 8 AA8 ASN A 209 PHE A 214 5 6 HELIX 9 AA9 THR A 219 ARG A 226 1 8 HELIX 10 AB1 GLU A 258 LYS A 268 1 11 HELIX 11 AB2 GLN A 273 ASN A 282 1 10 HELIX 12 AB3 MET A 307 GLU A 314 1 8 SHEET 1 AA1 4 THR A 22 GLN A 24 0 SHEET 2 AA1 4 PHE A 342 ARG A 357 1 O GLN A 343 N HIS A 23 SHEET 3 AA1 4 GLU A 42 THR A 57 -1 N THR A 57 O PHE A 342 SHEET 4 AA1 4 PHE A 32 GLN A 38 -1 N GLU A 35 O ILE A 46 SHEET 1 AA2 4 ILE A 60 SER A 61 0 SHEET 2 AA2 4 LEU A 325 PHE A 333 -1 O TYR A 329 N ILE A 60 SHEET 3 AA2 4 LEU A 234 THR A 252 -1 N ALA A 241 O ILE A 327 SHEET 4 AA2 4 LEU A 75 VAL A 77 -1 N LEU A 76 O VAL A 235 SHEET 1 AA3 6 ALA A 298 LYS A 304 0 SHEET 2 AA3 6 THR A 283 LEU A 290 -1 N ALA A 287 O VAL A 301 SHEET 3 AA3 6 LEU A 234 THR A 252 -1 N GLU A 251 O GLU A 284 SHEET 4 AA3 6 GLN A 189 VAL A 204 -1 N VAL A 193 O LEU A 248 SHEET 5 AA3 6 MET A 97 ASP A 102 -1 N SER A 100 O SER A 203 SHEET 6 AA3 6 PHE A 112 VAL A 115 -1 O LEU A 113 N TYR A 99 SHEET 1 AA4 4 LEU A 75 VAL A 77 0 SHEET 2 AA4 4 LEU A 234 THR A 252 -1 O VAL A 235 N LEU A 76 SHEET 3 AA4 4 GLN A 189 VAL A 204 -1 N VAL A 193 O LEU A 248 SHEET 4 AA4 4 ARG A 147 THR A 154 -1 N GLN A 149 O LYS A 196 SHEET 1 AA5 4 PHE A 406 LEU A 412 0 SHEET 2 AA5 4 GLY A 359 GLY A 367 -1 N GLY A 359 O LEU A 412 SHEET 3 AA5 4 LYS A 448 GLY A 455 1 O ARG A 449 N LEU A 362 SHEET 4 AA5 4 PRO A 460 GLU A 467 -1 O LYS A 465 N THR A 450 SHEET 1 AA6 4 GLU A 388 ALA A 394 0 SHEET 2 AA6 4 ALA A 371 TYR A 382 -1 N TRP A 377 O LYS A 393 SHEET 3 AA6 4 VAL A 416 LEU A 429 -1 O ARG A 417 N ASP A 378 SHEET 4 AA6 4 GLU A 432 LEU A 443 -1 O TYR A 438 N ILE A 423 CISPEP 1 PRO A 294 SER A 295 0 5.20 CISPEP 2 ALA A 404 HIS A 405 0 -7.37 SITE 1 AC1 5 ASN A 14 HOH A 645 HOH A 651 HOH A 668 SITE 2 AC1 5 HOH A 678 SITE 1 AC2 8 THR A 57 ASP A 59 GLU A 151 LYS A 164 SITE 2 AC2 8 PHE A 165 HOH A 626 HOH A 673 HOH A 750 SITE 1 AC3 6 ASP A 401 CYS A 426 TRP A 434 HOH A 620 SITE 2 AC3 6 HOH A 625 HOH A 847 SITE 1 AC4 5 TYR A 374 LYS A 422 HOH A 602 HOH A 608 SITE 2 AC4 5 HOH A 788 CRYST1 24.480 84.730 214.620 90.00 90.00 90.00 P 21 21 21 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 0.040850 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011802 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004659 0.00000