PDB Short entry for 1M7D HEADER IMMUNE SYSTEM 19-JUL-02 1M7D TITLE CRYSTAL STRUCTURE OF A MONOCLONAL FAB SPECIFIC FOR SHIGELLA FLEXNERI Y TITLE 2 LIPOPOLYSACCHARIDE COMPLEXED WITH A TRISACCHARIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIGHT CHAIN OF THE MONOCLONAL ANTIBODY FAB SYA/J6; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HEAVY CHAIN OF THE MONOCLONAL ANTIBODY FAB SYA/J6; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 STRAIN: BALB/C; SOURCE 6 CELL_LINE: SYA/J6 HYBRIDOMA; SOURCE 7 ORGAN: SPLEEN; SOURCE 8 CELL: PLASMACYTOMA CELL; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 13 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 14 ORGANISM_TAXID: 10090; SOURCE 15 STRAIN: BALB/C; SOURCE 16 CELL_LINE: SYA/J6 HYBRIDOMA; SOURCE 17 ORGAN: SPLEEN; SOURCE 18 CELL: PLASMACYTOMA CELL; SOURCE 19 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FAB-CARBOHYDRATE INTERACTIONS, SHIGELLA O-ANTIGEN, ANTI-CARBOHYDRATE KEYWDS 2 ANTIBODY, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR N.K.VYAS,M.N.VYAS,M.C.CHERVENAK,M.A.JOHNSON,B.M.PINTO,D.R.BUNDLE, AUTHOR 2 F.A.QUIOCHO REVDAT 6 29-JUL-20 1M7D 1 COMPND REMARK HETNAM LINK REVDAT 6 2 1 SITE ATOM REVDAT 5 11-OCT-17 1M7D 1 REMARK REVDAT 4 16-NOV-11 1M7D 1 VERSN HETATM REVDAT 3 08-DEC-09 1M7D 1 HET HETATM HETNAM REMARK REVDAT 2 24-FEB-09 1M7D 1 VERSN REVDAT 1 22-JUL-03 1M7D 0 JRNL AUTH N.K.VYAS,M.N.VYAS,M.C.CHERVENAK,M.A.JOHNSON,B.M.PINTO, JRNL AUTH 2 D.R.BUNDLE,F.A.QUIOCHO JRNL TITL MOLECULAR RECOGNITION OF OLIGOSACCHARIDE EPITOPES BY A JRNL TITL 2 MONOCLONAL FAB SPECIFIC FOR SHIGELLA FLEXNERI Y JRNL TITL 3 LIPOPOLYSACCHARIDE: X-RAY STRUCTURES AND THERMODYNAMICS JRNL REF BIOCHEMISTRY V. 41 13575 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 12427018 JRNL DOI 10.1021/BI0261387 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.K.VYAS,M.N.VYAS,P.J.MEIKELE,B.SINNOTT,B.M.PINTO, REMARK 1 AUTH 2 D.R.BUNDLE,F.A.QUIOCHO REMARK 1 TITL PRELIMINARY CRYSTALLOGRAPHIC ANALYSIS OF A FAB SPECIFIC FOR REMARK 1 TITL 2 THE O-ANTIGEN OF SHIGELLA FLEXNERI CELL SURFACE REMARK 1 TITL 3 LIPOPLYSACHARIDE WITH AND AND WITHOUT BOUND SACCHARIDES REMARK 1 REF J.MOL.BIOL. V. 231 133 1993 REMARK 1 REFN ISSN 0022-2836 REMARK 1 DOI 10.1006/JMBI.1993.1262 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 76031.280 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 76.6 REMARK 3 NUMBER OF REFLECTIONS : 17923 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 SET) : 0.216 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 869 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 51.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1844 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE : 0.3270 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 114 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.031 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3322 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 121 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.59000 REMARK 3 B22 (A**2) : 4.59000 REMARK 3 B33 (A**2) : -9.18000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.29 REMARK 3 ESD FROM SIGMAA (A) : 0.32 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.37 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.37 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.920 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 39.67 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : PARAM1NKV.CHO REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 3 : TOPH1NKV.CHO REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: AUTHOR STATES RESIDUES 127-135 OF CHAIN REMARK 3 B IS PART OF A DISORDERED SEGMENT. REMARK 4 REMARK 4 1M7D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-DEC-02. REMARK 100 THE DEPOSITION ID IS D_1000016687. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUN-90 REMARK 200 TEMPERATURE (KELVIN) : 281 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : WEISSENBERG REMARK 200 INTENSITY-INTEGRATION SOFTWARE : WEIS, PROTEIN, WEISSENBERG REMARK 200 DATA SCALING SOFTWARE : WEIS, PROTEIN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17923 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 76.7 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : 0.06000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 51.3 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MERLOT REMARK 200 STARTING MODEL: PDB ENTRY 1MCP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, POTASSIUM PHOSHATE, , PH 6.5, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 99.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.50000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.50000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 148.50000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.50000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.50000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 49.50000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.50000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.50000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 148.50000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.50000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.50000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 49.50000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 99.00000 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: 4650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 B 229 LIES ON A SPECIAL POSITION. 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 PRO B 14 N GLY B 15 1.32 REMARK 500 CA PRO B 14 N GLY B 15 1.35 REMARK 500 C PRO B 14 CA GLY B 15 1.35 REMARK 500 O PRO B 126 CA GLY B 127 1.35 REMARK 500 CA PRO B 126 N GLY B 127 1.45 REMARK 500 C PRO B 126 N CYS B 128 1.65 REMARK 500 O PRO B 126 C GLY B 127 1.72 REMARK 500 O PRO B 126 N CYS B 128 1.73 REMARK 500 O VAL B 125 N GLY B 127 2.12 REMARK 500 O SER B 134 CG2 THR B 182 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 GLN B 13 C PRO B 14 N -0.131 REMARK 500 PRO B 14 C GLY B 15 N -1.150 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 CYS A 134 CA - CB - SG ANGL. DEV. = 6.9 DEGREES REMARK 500 GLN B 13 CA - C - N ANGL. DEV. = 17.3 DEGREES REMARK 500 GLN B 13 O - C - N ANGL. DEV. = -16.8 DEGREES REMARK 500 PRO B 14 C - N - CA ANGL. DEV. = 10.0 DEGREES REMARK 500 PRO B 14 CA - C - N ANGL. DEV. = 103.2 DEGREES REMARK 500 GLY B 15 C - N - CA ANGL. DEV. = -68.3 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 VAL A 51 -48.94 71.72 REMARK 500 SER A 67 91.99 -167.69 REMARK 500 ALA A 80 -57.26 -29.11 REMARK 500 HIS A 93 -160.26 -115.18 REMARK 500 TYR A 140 137.62 -173.47 REMARK 500 PRO A 141 -179.33 -58.69 REMARK 500 LYS A 169 -75.15 -79.36 REMARK 500 THR A 200 17.91 -66.73 REMARK 500 PRO B 14 21.88 -74.64 REMARK 500 MET B 18 144.05 -170.14 REMARK 500 THR B 28 90.02 -66.56 REMARK 500 ARG B 52 -149.65 -84.37 REMARK 500 CYS B 128 95.77 0.97 REMARK 500 THR B 131 94.45 -60.34 REMARK 500 SER B 132 56.07 -148.59 REMARK 500 SER B 185 2.92 -55.72 REMARK 500 THR B 187 21.53 -69.34 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 PRO B 14 GLY B 15 71.11 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 PRO B 14 116.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MCP RELATED DB: PDB REMARK 900 PHOSPHOCHOLINE BINDING IMMUNOGLOBULIN FAB MCPC603. AN X-RAY REMARK 900 DIFFRACTION STUDY AT 2.7 A REMARK 900 RELATED ID: 1M71 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A MONOCLONAL FAB SPECIFIC FOR SHIGELLA REMARK 900 FLEXNERI Y LIPOPOLYSACCHARIDE REMARK 900 RELATED ID: 1M7I RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A MONOCLONAL FAB SPECIFIC FOR SHIGELLA REMARK 900 FLEXNERI Y LIPOPOLYSACCHARIDE COMPLEXED WITH A PENTASACCHARIDE REMARK 999 REMARK 999 SEQUENCE AT THE TIME OF PROCESSING, THIS SEQUENCE OF CHAIN A AND REMARK 999 CHAIN B HAVE NOT YET BEEN DEPOSITED IN A SEQUENCE DATABASE. DBREF 1M7D A 1 211 PDB 1M7D 1M7D 1 211 DBREF 1M7D B 1 213 PDB 1M7D 1M7D 1 213 SEQRES 1 A 215 ASP VAL VAL LEU THR GLN THR PRO LEU SER LEU PRO VAL SEQRES 2 A 215 ARG LEU GLY ASP GLN ALA SER ILE SER CYS ARG SER SER SEQRES 3 A 215 GLN SER LEU LEU HIS SER ASP GLY ASN THR TYR LEU HIS SEQRES 4 A 215 TRP TYR LEU GLN LYS PRO GLY GLN SER PRO LYS LEU LEU SEQRES 5 A 215 ILE TYR LYS VAL SER ASN ARG PHE SER GLY VAL PRO ASP SEQRES 6 A 215 ARG PHE SER GLY SER GLY SER GLY THR ASP PHE THR LEU SEQRES 7 A 215 LYS ILE SER ARG VAL GLU ALA GLU ASP LEU GLY VAL TYR SEQRES 8 A 215 PHE CYS SER GLN THR THR HIS VAL PRO THR PHE GLY GLY SEQRES 9 A 215 GLY THR LYS LEU GLU ILE LYS ARG ALA ASP ALA ALA PRO SEQRES 10 A 215 THR VAL SER ILE PHE PRO PRO SER SER GLU GLN LEU THR SEQRES 11 A 215 SER GLY GLY ALA SER VAL VAL CYS PHE LEU ASN ASN PHE SEQRES 12 A 215 TYR PRO LYS ASP ILE ASN VAL LYS TRP LYS ILE ASP GLY SEQRES 13 A 215 SER GLU ARG GLN ASN GLY VAL LEU ASN SER TRP THR ASP SEQRES 14 A 215 GLN ASP SER LYS ASP SER THR TYR SER MET SER SER THR SEQRES 15 A 215 LEU THR LEU THR LYS ASP GLU TYR GLU ARG HIS ASN SER SEQRES 16 A 215 TYR THR CYS GLU ALA THR HIS LYS THR SER THR SER PRO SEQRES 17 A 215 ILE VAL LYS SER PHE ASN ARG SEQRES 1 B 220 GLU VAL LYS VAL GLU GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 220 PRO GLY GLY SER MET LYS LEU SER CYS VAL ALA SER GLY SEQRES 3 B 220 PHE THR PHE SER ASN TYR TRP MET GLU TRP VAL ARG GLN SEQRES 4 B 220 SER PRO GLU LYS GLY LEU GLU TRP VAL ALA GLU ILE ARG SEQRES 5 B 220 LEU LYS SER ASN ASN TYR ALA THR HIS TYR ALA GLU SER SEQRES 6 B 220 VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASP SER LYS SEQRES 7 B 220 SER SER VAL TYR LEU GLN MET ASN ASN LEU ARG ALA GLU SEQRES 8 B 220 ASP THR GLY ILE TYR TYR CYS THR ARG GLY GLY ALA VAL SEQRES 9 B 220 GLY ALA MET ASP TYR TRP GLY GLN GLY THR SER VAL THR SEQRES 10 B 220 VAL SER SER ALA THR THR THR ALA PRO SER VAL TYR PRO SEQRES 11 B 220 LEU VAL PRO GLY CYS SER ASP THR SER GLY SER SER VAL SEQRES 12 B 220 THR LEU GLY CYS LEU VAL LYS GLY TYR PHE PRO GLU PRO SEQRES 13 B 220 VAL THR VAL LYS TRP ASN TYR GLY ALA LEU SER SER GLY SEQRES 14 B 220 VAL ARG THR VAL SER SER VAL LEU GLN SER GLY PHE TYR SEQRES 15 B 220 SER LEU SER SER LEU VAL THR VAL PRO SER SER THR TRP SEQRES 16 B 220 PRO SER GLN THR VAL ILE CYS ASN VAL ALA HIS PRO ALA SEQRES 17 B 220 SER LYS VAL ASP LEU ILE LYS GLU PRO SER GLY PRO HET MAG C 1 16 HET RAE C 2 9 HET RAM C 3 10 HETNAM MAG METHYL 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSIDE HETNAM RAE ALPHA-L-OLIVOPYRANOSE HETNAM RAM ALPHA-L-RHAMNOPYRANOSE FORMUL 3 MAG C9 H17 N O6 FORMUL 3 RAE C6 H12 O4 FORMUL 3 RAM C6 H12 O5 FORMUL 4 HOH *121(H2 O) HELIX 1 1 GLU A 79 LEU A 83 5 5 HELIX 2 2 SER A 121 SER A 127 5 7 HELIX 3 3 LYS A 183 ARG A 188 1 6 HELIX 4 4 THR B 28 TYR B 32 5 5 HELIX 5 5 LEU B 52A ASN B 54 5 5 HELIX 6 6 ARG B 83 THR B 87 5 5 HELIX 7 7 TYR B 156 ALA B 158 5 3 HELIX 8 8 PRO B 200 LYS B 203 5 4 SHEET 1 A 4 LEU A 4 THR A 7 0 SHEET 2 A 4 ALA A 19 SER A 25 -1 N SER A 22 O THR A 7 SHEET 3 A 4 ASP A 70 ILE A 75 -1 O PHE A 71 N CYS A 23 SHEET 4 A 4 PHE A 62 SER A 67 -1 O SER A 63 N LYS A 74 SHEET 1 B 8 SER A 10 ARG A 14 0 SHEET 2 B 8 THR A 102 LYS A 107 1 O LYS A 103 N LEU A 11 SHEET 3 B 8 GLY A 84 GLN A 90 -1 O GLY A 84 N LEU A 104 SHEET 4 B 8 THR A 97 PHE A 98 -1 O THR A 97 N GLN A 90 SHEET 5 B 8 GLY A 84 GLN A 90 -1 N GLN A 90 O THR A 97 SHEET 6 B 8 LEU A 33 GLN A 38 -1 N HIS A 34 O SER A 89 SHEET 7 B 8 LYS A 45 TYR A 49 -1 O LYS A 45 N LEU A 37 SHEET 8 B 8 ASN A 53 ARG A 54 -1 O ASN A 53 N TYR A 49 SHEET 1 C 4 THR A 114 PHE A 118 0 SHEET 2 C 4 GLY A 129 PHE A 139 -1 O VAL A 133 N PHE A 118 SHEET 3 C 4 TYR A 173 THR A 182 -1 N TYR A 173 O PHE A 139 SHEET 4 C 4 VAL A 159 TRP A 163 -1 O LEU A 160 N THR A 178 SHEET 1 D 4 SER A 153 ARG A 155 0 SHEET 2 D 4 ASN A 145 ILE A 150 -1 O TRP A 148 N ARG A 155 SHEET 3 D 4 SER A 191 THR A 197 -1 O THR A 193 N LYS A 149 SHEET 4 D 4 ILE A 205 ASN A 210 -1 N ILE A 205 O ALA A 196 SHEET 1 E 4 LYS B 3 SER B 7 0 SHEET 2 E 4 MET B 18 SER B 25 -1 N SER B 21 O SER B 7 SHEET 3 E 4 SER B 77 MET B 82 -1 N VAL B 78 O CYS B 22 SHEET 4 E 4 PHE B 67 ASP B 72 -1 O THR B 68 N GLN B 81 SHEET 1 F 8 GLY B 10 VAL B 12 0 SHEET 2 F 8 THR B 107 VAL B 111 1 O SER B 108 N GLY B 10 SHEET 3 F 8 GLY B 88 GLY B 95 -1 N GLY B 88 O VAL B 109 SHEET 4 F 8 MET B 100A TRP B 103 -1 N ASP B 101 O ARG B 94 SHEET 5 F 8 GLY B 88 GLY B 95 -1 N ARG B 94 O TYR B 102 SHEET 6 F 8 TRP B 33 SER B 40 -1 O TRP B 33 N GLY B 95 SHEET 7 F 8 GLY B 44 ILE B 51 -1 N GLY B 44 O SER B 40 SHEET 8 F 8 THR B 57 TYR B 59 -1 N HIS B 58 O GLU B 50 SHEET 1 G 6 VAL B 163 THR B 165 0 SHEET 2 G 6 PHE B 174 VAL B 183 -1 O LEU B 180 N ARG B 164 SHEET 3 G 6 VAL B 169 GLN B 171 -1 N VAL B 169 O SER B 176 SHEET 4 G 6 PHE B 174 VAL B 183 -1 O PHE B 174 N GLN B 171 SHEET 5 G 6 VAL B 136 TYR B 145 -1 N VAL B 136 O VAL B 183 SHEET 6 G 6 SER B 120 LEU B 124 -1 N SER B 120 O LYS B 143 SHEET 1 H 3 THR B 151 TRP B 154 0 SHEET 2 H 3 CYS B 195 HIS B 199 -1 N ASN B 196 O LYS B 153 SHEET 3 H 3 VAL B 204 LYS B 208 -1 O VAL B 204 N HIS B 199 SSBOND 1 CYS A 23 CYS A 88 1555 1555 2.02 SSBOND 2 CYS A 134 CYS A 194 1555 1555 2.04 SSBOND 3 CYS B 22 CYS B 92 1555 1555 2.44 SSBOND 4 CYS B 140 CYS B 195 1555 1555 2.02 LINK O3 MAG C 1 C1 RAE C 2 1555 1555 1.43 LINK O3 RAE C 2 C1 RAM C 3 1555 1555 1.45 CISPEP 1 THR A 7 PRO A 8 0 0.04 CISPEP 2 TYR A 140 PRO A 141 0 0.16 CISPEP 3 PHE B 146 PRO B 147 0 -0.12 CISPEP 4 GLU B 148 PRO B 149 0 -0.07 CISPEP 5 TRP B 188 PRO B 189 0 -0.12 CRYST1 71.000 71.000 198.000 90.00 90.00 90.00 P 43 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.014085 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014085 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005051 0.00000