HEADER TOXIN 13-DEC-06 2E4M TITLE CRYSTAL STRUCTURE OF HEMAGGLUTININ SUBCOMPONENT COMPLEX (HA-33/HA-17) TITLE 2 FROM CLOSTRIDIUM BOTULINUM SEROTYPE D STRAIN 4947 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAIN HEMAGGLUTININ COMPONENT; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HA 33 KDA SUBUNIT, HA1, HA-33; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HA-17; COMPND 7 CHAIN: C SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM BOTULINUM; SOURCE 3 ORGANISM_TAXID: 1491; SOURCE 4 STRAIN: SEROTYPE D STRAIN 4947; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: CLOSTRIDIUM BOTULINUM; SOURCE 7 ORGANISM_TAXID: 1491; SOURCE 8 STRAIN: SEROTYPE D STRAIN 4947 KEYWDS CLOSTRIDIUM BOTULINUM, BOTULINUM TOXIN, HEMAGGLUTININ SUBCOMPONENT KEYWDS 2 COMPLEX, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR K.HASEGAWA,T.WATANABE,T.SUZUKI,A.YAMANO,K.NIWA,T.OHYAMA REVDAT 4 25-OCT-23 2E4M 1 SEQADV REVDAT 3 24-FEB-09 2E4M 1 VERSN REVDAT 2 11-SEP-07 2E4M 1 JRNL REVDAT 1 19-JUN-07 2E4M 0 JRNL AUTH K.HASEGAWA,T.WATANABE,T.SUZUKI,A.YAMANO,T.OIKAWA,Y.SATO, JRNL AUTH 2 H.KOUGUCHI,T.YONEYAMA,K.NIWA,T.IKEDA,T.OHYAMA JRNL TITL A NOVEL SUBUNIT STRUCTURE OF CLOSTRIDIUM BOTULINUM SEROTYPE JRNL TITL 2 D TOXIN COMPLEX WITH THREE EXTENDED ARMS JRNL REF J.BIOL.CHEM. V. 282 24777 2007 JRNL REFN ISSN 0021-9258 JRNL PMID 17581814 JRNL DOI 10.1074/JBC.M703446200 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 87820 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4626 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6468 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE SET COUNT : 335 REMARK 3 BIN FREE R VALUE : 0.3110 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5913 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 718 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.21000 REMARK 3 B22 (A**2) : 0.21000 REMARK 3 B33 (A**2) : -0.31000 REMARK 3 B12 (A**2) : 0.10000 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): 0.120 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.118 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.081 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6041 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8238 ; 1.480 ; 1.914 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 710 ; 8.069 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 335 ;39.363 ;25.910 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1026 ;14.202 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;17.461 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 918 ; 0.120 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4649 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2811 ; 0.208 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4137 ; 0.302 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 612 ; 0.137 ; 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): 49 ; 0.151 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.135 ; 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): 3676 ; 0.962 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5820 ; 1.578 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2811 ; 2.285 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2418 ; 3.353 ; 4.500 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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; CNS 1.1 WAS ALSO USED FOR THE REFINEMENT. REMARK 4 REMARK 4 2E4M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-DEC-06. REMARK 100 THE DEPOSITION ID IS D_1000026218. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-06; 19-JUL-06 REMARK 200 TEMPERATURE (KELVIN) : 100.0; 100.0 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N; Y REMARK 200 RADIATION SOURCE : ROTATING ANODE; SPRING-8 REMARK 200 BEAMLINE : NULL; BL26B2 REMARK 200 X-RAY GENERATOR MODEL : RIGAKU; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418; 1.000 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : RIGAKU MAXSCREEN; NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS VII; RIGAKU JUPITER REMARK 200 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 92648 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 119.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: XTALVIEW REMARK 200 STARTING MODEL: PDB ENTRY 1QXM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 7% PEG 8000, 0.1M MES, 0.1M MAGNESIUM REMARK 280 CHLORIDE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 119.56600 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 69.03146 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 33.34133 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 119.56600 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 69.03146 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 33.34133 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 119.56600 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 69.03146 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 33.34133 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 119.56600 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 69.03146 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 33.34133 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 119.56600 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 69.03146 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 33.34133 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 119.56600 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 69.03146 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 33.34133 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 138.06292 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 66.68267 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 138.06292 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 66.68267 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 138.06292 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 66.68267 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 138.06292 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 66.68267 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 138.06292 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 66.68267 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 138.06292 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 66.68267 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A TRIMER 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 586 LIES ON A SPECIAL POSITION. 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 MET B 1 REMARK 465 MET C 1 REMARK 465 SER C 2 REMARK 465 SER C 3 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 HOH A 374 O HOH A 596 2.17 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 ARG B 102 NE - CZ - NH1 ANGL. DEV. = -7.3 DEGREES REMARK 500 ARG B 102 NE - CZ - NH2 ANGL. DEV. = 5.8 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 GLN A 3 -85.07 48.88 REMARK 500 ASP A 237 -67.35 -19.49 REMARK 500 GLN B 3 -88.04 55.27 REMARK 500 ASP B 237 -69.95 -17.35 REMARK 500 SER B 260 24.66 49.29 REMARK 500 THR C 6 -84.09 -118.92 REMARK 500 SER C 28 -100.09 -119.84 REMARK 500 SER C 53 17.51 -152.75 REMARK 500 ASN C 54 175.43 62.57 REMARK 500 GLU C 63 75.33 -150.29 REMARK 500 ASN C 65 -15.64 89.44 REMARK 500 SER C 81 -158.01 -93.87 REMARK 500 SER C 82 -18.94 -149.61 REMARK 500 SER C 103 -82.23 -151.70 REMARK 500 ASN C 106 -17.30 69.74 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 SER C 80 SER C 81 -136.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE DIFFERENCE BETWEEN THE SEQUENCE AND THE SEQRES REMARK 999 OCCURS NATURALLY IN SEROTYPE D OF THIS ORGANISM. REMARK 999 THESE RESIDUES REFER FROM EMBL/GB AB037920; REMARK 999 BAA90659.1. DBREF 2E4M A 2 286 UNP P46084 HA33_CLOBO 1 285 DBREF 2E4M B 2 286 UNP P46084 HA33_CLOBO 1 285 DBREF 2E4M C 2 146 UNP Q9LBR4 Q9LBR4_CLOBO 2 146 SEQADV 2E4M MET A 1 UNP P46084 INITIATING METHIONINE SEQADV 2E4M THR A 60 UNP P46084 LYS 59 SEE REMARK 999 SEQADV 2E4M ASP A 74 UNP P46084 ASN 73 SEE REMARK 999 SEQADV 2E4M THR A 88 UNP P46084 GLY 87 SEE REMARK 999 SEQADV 2E4M ASN A 89 UNP P46084 ASP 88 SEE REMARK 999 SEQADV 2E4M ASP A 98 UNP P46084 ASN 97 SEE REMARK 999 SEQADV 2E4M LEU A 106 UNP P46084 ILE 105 SEE REMARK 999 SEQADV 2E4M THR A 120 UNP P46084 ILE 119 SEE REMARK 999 SEQADV 2E4M ILE A 125 UNP P46084 MET 124 SEE REMARK 999 SEQADV 2E4M ASN A 131 UNP P46084 SER 130 SEE REMARK 999 SEQADV 2E4M ASN A 133 UNP P46084 SER 132 SEE REMARK 999 SEQADV 2E4M THR A 187 UNP P46084 ILE 186 SEE REMARK 999 SEQADV 2E4M THR A 262 UNP P46084 ILE 261 SEE REMARK 999 SEQADV 2E4M MET B 1 UNP P46084 INITIATING METHIONINE SEQADV 2E4M THR B 60 UNP P46084 LYS 59 SEE REMARK 999 SEQADV 2E4M ASP B 74 UNP P46084 ASN 73 SEE REMARK 999 SEQADV 2E4M THR B 88 UNP P46084 GLY 87 SEE REMARK 999 SEQADV 2E4M ASN B 89 UNP P46084 ASP 88 SEE REMARK 999 SEQADV 2E4M ASP B 98 UNP P46084 ASN 97 SEE REMARK 999 SEQADV 2E4M LEU B 106 UNP P46084 ILE 105 SEE REMARK 999 SEQADV 2E4M THR B 120 UNP P46084 ILE 119 SEE REMARK 999 SEQADV 2E4M ILE B 125 UNP P46084 MET 124 SEE REMARK 999 SEQADV 2E4M ASN B 131 UNP P46084 SER 130 SEE REMARK 999 SEQADV 2E4M ASN B 133 UNP P46084 SER 132 SEE REMARK 999 SEQADV 2E4M THR B 187 UNP P46084 ILE 186 SEE REMARK 999 SEQADV 2E4M THR B 262 UNP P46084 ILE 261 SEE REMARK 999 SEQADV 2E4M MET C 1 UNP Q9LBR4 INITIATING METHIONINE SEQRES 1 A 286 MET SER GLN THR ASN ALA ASN ASP LEU ARG ASN ASN GLU SEQRES 2 A 286 VAL PHE PHE ILE SER PRO SER ASN ASN THR ASN LYS VAL SEQRES 3 A 286 LEU ASP LYS ILE SER GLN SER GLU VAL LYS LEU TRP ASN SEQRES 4 A 286 LYS LEU SER GLY ALA ASN GLN LYS TRP ARG LEU ILE TYR SEQRES 5 A 286 ASP THR ASN LYS GLN ALA TYR THR ILE LYS VAL MET ASP SEQRES 6 A 286 ASN THR SER LEU ILE LEU THR TRP ASP ALA PRO LEU SER SEQRES 7 A 286 SER VAL SER VAL LYS THR ASP THR ASN THR ASN ASN GLN SEQRES 8 A 286 TYR TRP TYR LEU LEU GLN ASP TYR ILE SER ARG ASN VAL SEQRES 9 A 286 ILE LEU ARG ASN TYR MET ASN PRO ASN LEU VAL LEU GLN SEQRES 10 A 286 TYR ASN THR ASP ASP THR LEU ILE VAL SER THR GLN THR SEQRES 11 A 286 ASN SER ASN ASN GLN PHE PHE LYS PHE SER ASN CYS ILE SEQRES 12 A 286 TYR GLU ALA LEU ASN ASN ARG ASN CYS LYS LEU GLN THR SEQRES 13 A 286 GLN LEU ASN SER ASP ARG PHE LEU SER LYS ASN LEU ASN SEQRES 14 A 286 SER GLN ILE ILE VAL LEU TRP GLN TRP PHE ASP SER SER SEQRES 15 A 286 ARG GLN LYS TRP THR ILE GLU TYR ASN GLU THR LYS SER SEQRES 16 A 286 ALA TYR THR LEU LYS CYS GLN GLU ASN ASN ARG TYR LEU SEQRES 17 A 286 THR TRP ILE GLN ASN SER ASN ASN TYR VAL GLU THR TYR SEQRES 18 A 286 GLN SER THR ASP SER LEU ILE GLN TYR TRP ASN ILE ASN SEQRES 19 A 286 TYR LEU ASP ASN ASP ALA SER LYS TYR ILE LEU TYR ASN SEQRES 20 A 286 LEU GLN ASP THR ASN ARG VAL LEU ASP VAL TYR ASN SER SEQRES 21 A 286 GLN THR ALA ASN GLY THR HIS VAL ILE VAL ASP SER TYR SEQRES 22 A 286 HIS GLY ASN THR ASN GLN GLN TRP ILE ILE ASN LEU ILE SEQRES 1 B 286 MET SER GLN THR ASN ALA ASN ASP LEU ARG ASN ASN GLU SEQRES 2 B 286 VAL PHE PHE ILE SER PRO SER ASN ASN THR ASN LYS VAL SEQRES 3 B 286 LEU ASP LYS ILE SER GLN SER GLU VAL LYS LEU TRP ASN SEQRES 4 B 286 LYS LEU SER GLY ALA ASN GLN LYS TRP ARG LEU ILE TYR SEQRES 5 B 286 ASP THR ASN LYS GLN ALA TYR THR ILE LYS VAL MET ASP SEQRES 6 B 286 ASN THR SER LEU ILE LEU THR TRP ASP ALA PRO LEU SER SEQRES 7 B 286 SER VAL SER VAL LYS THR ASP THR ASN THR ASN ASN GLN SEQRES 8 B 286 TYR TRP TYR LEU LEU GLN ASP TYR ILE SER ARG ASN VAL SEQRES 9 B 286 ILE LEU ARG ASN TYR MET ASN PRO ASN LEU VAL LEU GLN SEQRES 10 B 286 TYR ASN THR ASP ASP THR LEU ILE VAL SER THR GLN THR SEQRES 11 B 286 ASN SER ASN ASN GLN PHE PHE LYS PHE SER ASN CYS ILE SEQRES 12 B 286 TYR GLU ALA LEU ASN ASN ARG ASN CYS LYS LEU GLN THR SEQRES 13 B 286 GLN LEU ASN SER ASP ARG PHE LEU SER LYS ASN LEU ASN SEQRES 14 B 286 SER GLN ILE ILE VAL LEU TRP GLN TRP PHE ASP SER SER SEQRES 15 B 286 ARG GLN LYS TRP THR ILE GLU TYR ASN GLU THR LYS SER SEQRES 16 B 286 ALA TYR THR LEU LYS CYS GLN GLU ASN ASN ARG TYR LEU SEQRES 17 B 286 THR TRP ILE GLN ASN SER ASN ASN TYR VAL GLU THR TYR SEQRES 18 B 286 GLN SER THR ASP SER LEU ILE GLN TYR TRP ASN ILE ASN SEQRES 19 B 286 TYR LEU ASP ASN ASP ALA SER LYS TYR ILE LEU TYR ASN SEQRES 20 B 286 LEU GLN ASP THR ASN ARG VAL LEU ASP VAL TYR ASN SER SEQRES 21 B 286 GLN THR ALA ASN GLY THR HIS VAL ILE VAL ASP SER TYR SEQRES 22 B 286 HIS GLY ASN THR ASN GLN GLN TRP ILE ILE ASN LEU ILE SEQRES 1 C 146 MET SER SER GLU ARG THR PHE LEU PRO ASN GLY ASN TYR SEQRES 2 C 146 LYS ILE LYS SER LEU PHE SER ASP SER LEU TYR LEU THR SEQRES 3 C 146 TYR SER SER GLY SER LEU SER PHE LEU ASN THR SER SER SEQRES 4 C 146 LEU ASP ASN GLN LYS TRP LYS LEU GLU TYR ILE SER SER SEQRES 5 C 146 SER ASN GLY PHE ARG PHE SER ASN VAL ALA GLU PRO ASN SEQRES 6 C 146 LYS TYR LEU ALA TYR ASN ASP TYR GLY PHE ILE TYR LEU SEQRES 7 C 146 SER SER SER SER ASN ASN SER LEU TRP ASN PRO ILE LYS SEQRES 8 C 146 ILE ALA ILE ASN SER TYR ILE ILE CYS THR LEU SER ILE SEQRES 9 C 146 VAL ASN VAL THR ASP TYR ALA TRP THR ILE TYR ASP ASN SEQRES 10 C 146 ASN ASN ASN ILE THR ASP GLN PRO ILE LEU ASN LEU PRO SEQRES 11 C 146 ASN PHE ASP ILE ASN ASN SER ASN GLN ILE LEU LYS LEU SEQRES 12 C 146 GLU LYS LEU FORMUL 4 HOH *718(H2 O) HELIX 1 1 GLY A 43 GLN A 46 5 4 HELIX 2 2 THR A 88 GLN A 91 5 4 HELIX 3 3 SER A 132 GLN A 135 5 4 HELIX 4 4 CYS A 142 ASN A 148 1 7 HELIX 5 5 SER A 181 GLN A 184 5 4 HELIX 6 6 SER A 226 GLN A 229 5 4 HELIX 7 7 ASN A 259 GLN A 261 5 3 HELIX 8 8 ASN A 276 GLN A 279 5 4 HELIX 9 9 GLY B 43 GLN B 46 5 4 HELIX 10 10 THR B 88 GLN B 91 5 4 HELIX 11 11 SER B 132 GLN B 135 5 4 HELIX 12 12 CYS B 142 ASN B 148 1 7 HELIX 13 13 SER B 181 GLN B 184 5 4 HELIX 14 14 SER B 226 GLN B 229 5 4 HELIX 15 15 ASN B 259 GLN B 261 5 3 HELIX 16 16 ASN B 276 GLN B 279 5 4 HELIX 17 17 LEU C 40 GLN C 43 5 4 HELIX 18 18 ASN C 136 GLN C 139 5 4 SHEET 1 A 4 ALA A 58 VAL A 63 0 SHEET 2 A 4 TRP A 48 ASP A 53 -1 N ASP A 53 O ALA A 58 SHEET 3 A 4 VAL A 14 PRO A 19 -1 N PHE A 15 O TRP A 48 SHEET 4 A 4 PHE A 137 ASN A 141 -1 O LYS A 138 N SER A 18 SHEET 1 B 2 LYS A 25 LYS A 29 0 SHEET 2 B 2 VAL A 35 ASN A 39 -1 O LYS A 36 N ASP A 28 SHEET 1 C 2 ILE A 70 TRP A 73 0 SHEET 2 C 2 VAL A 80 LYS A 83 -1 O SER A 81 N THR A 72 SHEET 1 D 4 VAL A 104 ASN A 108 0 SHEET 2 D 4 TRP A 93 ASP A 98 -1 N TYR A 94 O ARG A 107 SHEET 3 D 4 TRP B 93 ASP B 98 -1 O GLN B 97 N GLN A 97 SHEET 4 D 4 VAL B 104 ASN B 108 -1 O ARG B 107 N TYR B 94 SHEET 1 E 2 VAL A 115 TYR A 118 0 SHEET 2 E 2 LEU A 124 SER A 127 -1 O ILE A 125 N GLN A 117 SHEET 1 F 4 ALA A 196 CYS A 201 0 SHEET 2 F 4 TRP A 186 ASN A 191 -1 N ASN A 191 O ALA A 196 SHEET 3 F 4 ARG A 150 THR A 156 -1 N CYS A 152 O TRP A 186 SHEET 4 F 4 TRP A 281 LEU A 285 -1 O ASN A 284 N LYS A 153 SHEET 1 G 2 PHE A 163 LYS A 166 0 SHEET 2 G 2 ILE A 173 TRP A 176 -1 O VAL A 174 N SER A 165 SHEET 1 H 2 TYR A 207 TRP A 210 0 SHEET 2 H 2 VAL A 218 TYR A 221 -1 O TYR A 221 N TYR A 207 SHEET 1 I 2 TRP A 231 LEU A 236 0 SHEET 2 I 2 ASP A 239 ASN A 247 -1 O TYR A 246 N ASN A 232 SHEET 1 J 2 ARG A 253 VAL A 257 0 SHEET 2 J 2 VAL A 268 SER A 272 -1 O ILE A 269 N ASP A 256 SHEET 1 K 4 ALA B 58 VAL B 63 0 SHEET 2 K 4 TRP B 48 ASP B 53 -1 N ASP B 53 O ALA B 58 SHEET 3 K 4 VAL B 14 PRO B 19 -1 N PHE B 15 O TRP B 48 SHEET 4 K 4 PHE B 137 ASN B 141 -1 O LYS B 138 N SER B 18 SHEET 1 L 2 LYS B 25 LYS B 29 0 SHEET 2 L 2 VAL B 35 ASN B 39 -1 O LYS B 36 N ASP B 28 SHEET 1 M 2 ILE B 70 TRP B 73 0 SHEET 2 M 2 VAL B 80 LYS B 83 -1 O SER B 81 N THR B 72 SHEET 1 N 2 VAL B 115 TYR B 118 0 SHEET 2 N 2 LEU B 124 SER B 127 -1 O ILE B 125 N GLN B 117 SHEET 1 O 4 ALA B 196 CYS B 201 0 SHEET 2 O 4 TRP B 186 ASN B 191 -1 N ASN B 191 O ALA B 196 SHEET 3 O 4 ARG B 150 THR B 156 -1 N CYS B 152 O TRP B 186 SHEET 4 O 4 TRP B 281 LEU B 285 -1 O ILE B 282 N GLN B 155 SHEET 1 P 2 PHE B 163 LYS B 166 0 SHEET 2 P 2 ILE B 173 TRP B 176 -1 O VAL B 174 N SER B 165 SHEET 1 Q 2 TYR B 207 TRP B 210 0 SHEET 2 Q 2 VAL B 218 TYR B 221 -1 O TYR B 221 N TYR B 207 SHEET 1 R 2 TRP B 231 LEU B 236 0 SHEET 2 R 2 ASP B 239 ASN B 247 -1 O TYR B 246 N ASN B 232 SHEET 1 S 2 ARG B 253 VAL B 257 0 SHEET 2 S 2 VAL B 268 SER B 272 -1 O ILE B 269 N ASP B 256 SHEET 1 T 9 ILE C 76 SER C 79 0 SHEET 2 T 9 GLU C 63 TYR C 70 -1 N TYR C 67 O SER C 79 SHEET 3 T 9 PHE C 56 ASN C 60 -1 N PHE C 58 O LEU C 68 SHEET 4 T 9 TRP C 87 ALA C 93 -1 O TRP C 87 N PHE C 56 SHEET 5 T 9 SER C 96 THR C 101 -1 O ILE C 98 N ILE C 90 SHEET 6 T 9 LEU C 141 LYS C 145 -1 O LEU C 141 N TYR C 97 SHEET 7 T 9 GLY C 11 SER C 17 -1 N LYS C 16 O LYS C 142 SHEET 8 T 9 TRP C 45 TYR C 49 -1 O TRP C 45 N TYR C 13 SHEET 9 T 9 PHE C 56 ASN C 60 -1 O SER C 59 N LYS C 46 SHEET 1 U 2 LEU C 23 TYR C 27 0 SHEET 2 U 2 LEU C 32 ASN C 36 -1 O SER C 33 N THR C 26 SHEET 1 V 2 ASP C 109 ILE C 114 0 SHEET 2 V 2 ILE C 126 ASN C 131 -1 O ASN C 131 N ASP C 109 CISPEP 1 ALA A 75 PRO A 76 0 8.78 CISPEP 2 ALA B 75 PRO B 76 0 2.52 CISPEP 3 SER C 82 ASN C 83 0 9.92 CRYST1 239.132 239.132 100.024 90.00 90.00 120.00 H 3 2 36 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 0.004182 0.002414 0.000000 0.00000 SCALE2 0.000000 0.004829 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009998 0.00000