HEADER ANTIBODY/ANTIGEN 03-FEB-95 1BQL TITLE STRUCTURE OF AN ANTI-HEL FAB FRAGMENT COMPLEXED WITH BOBWHITE QUAIL TITLE 2 LYSOZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYHEL-5 FAB (LIGHT CHAIN); COMPND 3 CHAIN: L; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HYHEL-5 FAB (HEAVY CHAIN); COMPND 7 CHAIN: H; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: BOBWHITE QUAIL LYSOZYME; COMPND 11 CHAIN: Y; COMPND 12 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 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 7 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 8 ORGANISM_TAXID: 10090; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: COLINUS VIRGINIANUS; SOURCE 11 ORGANISM_COMMON: NORTHERN BOBWHITE; SOURCE 12 ORGANISM_TAXID: 9014 KEYWDS ANTIBODY-ANTIGEN COMPLEX, HYHEL-5, ANTI-LYSOZYME, BOBWHITE QUAIL EXPDTA X-RAY DIFFRACTION AUTHOR S.CHACKO,D.R.DAVIES REVDAT 3 20-DEC-17 1BQL 1 JRNL REVDAT 2 24-FEB-09 1BQL 1 VERSN REVDAT 1 20-APR-95 1BQL 0 JRNL AUTH S.CHACKO,E.W.SILVERTON,S.J.SMITH-GILL,D.R.DAVIES,K.A.SHICK, JRNL AUTH 2 K.A.XAVIER,R.C.WILLSON,P.D.JEFFREY,C.Y.CHANG,L.C.SIEKER, JRNL AUTH 3 S.SHERIFF JRNL TITL REFINED STRUCTURES OF BOBWHITE QUAIL LYSOZYME UNCOMPLEXED JRNL TITL 2 AND COMPLEXED WITH THE HYHEL-5 FAB FRAGMENT. JRNL REF PROTEINS V. 26 55 1996 JRNL REFN ISSN 0887-3585 JRNL PMID 8880929 JRNL DOI 10.1002/(SICI)1097-0134(199609)26:1<55::AID-PROT5>3.0.CO;2-F REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.CHACKO,E.SILVERTON,L.KAM-MORGAN,S.SMITH-GILL,G.COHEN, REMARK 1 AUTH 2 D.DAVIES REMARK 1 TITL STRUCTURE OF AN ANTIBODY-LYSOZYME COMPLEX UNEXPECTED EFFECT REMARK 1 TITL 2 OF CONSERVATIVE MUTATION. REMARK 1 REF J. MOL. BIOL. V. 245 261 1995 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 7531245 REMARK 1 REFERENCE 2 REMARK 1 AUTH S.SHERIFF,E.W.SILVERTON,E.A.PADLAN,G.H.COHEN,S.J.SMITH-GILL, REMARK 1 AUTH 2 B.C.FINZEL,D.R.DAVIES REMARK 1 TITL THREE-DIMENSIONAL STRUCTURE OF AN ANTIBODY-ANTIGEN COMPLEX. REMARK 1 REF PROC. NATL. ACAD. SCI. V. 84 8075 1987 REMARK 1 REF 2 U.S.A. REMARK 1 REFN ISSN 0027-8424 REMARK 1 PMID 2446316 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 55.0 REMARK 3 NUMBER OF REFLECTIONS : 15713 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.291 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4240 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 86 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 3.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BQL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172005. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18884 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 37.40000 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, Y 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 400 REMARK 400 COMPOUND REMARK 400 COMPND REMARK 400 FAB FRAGMENT OF AN ANTI-LYSOZYME IGG1 ANTIBODY HYHEL-5 - REMARK 400 BOBWHITE QUAIL LYSOZYME COMPLEX. 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 PCA H 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS L 187 NE2 HIS L 187 CD2 -0.077 REMARK 500 HIS L 196 NE2 HIS L 196 CD2 -0.087 REMARK 500 HIS H 61 NE2 HIS H 61 CD2 -0.069 REMARK 500 HIS H 98 NE2 HIS H 98 CD2 -0.078 REMARK 500 HIS H 167 NE2 HIS H 167 CD2 -0.074 REMARK 500 HIS H 202 NE2 HIS H 202 CD2 -0.075 REMARK 500 HIS Y 15 NE2 HIS Y 15 CD2 -0.067 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 L 23 CA - CB - SG ANGL. DEV. = 8.0 DEGREES REMARK 500 TRP L 34 CD1 - CG - CD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 TRP L 34 CE2 - CD2 - CG ANGL. DEV. = -5.2 DEGREES REMARK 500 TRP L 46 CD1 - CG - CD2 ANGL. DEV. = 6.8 DEGREES REMARK 500 TRP L 46 CE2 - CD2 - CG ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG L 60 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG L 60 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 TYR L 70 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 TRP L 90 CD1 - CG - CD2 ANGL. DEV. = 7.0 DEGREES REMARK 500 TRP L 90 CE2 - CD2 - CG ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG L 92 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 TRP L 146 CD1 - CG - CD2 ANGL. DEV. = 7.4 DEGREES REMARK 500 TRP L 146 CE2 - CD2 - CG ANGL. DEV. = -6.0 DEGREES REMARK 500 GLY L 150 C - N - CA ANGL. DEV. = -17.0 DEGREES REMARK 500 ARG L 153 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 TRP L 161 CD1 - CG - CD2 ANGL. DEV. = 6.8 DEGREES REMARK 500 TRP L 161 CE2 - CD2 - CG ANGL. DEV. = -5.8 DEGREES REMARK 500 SER L 169 N - CA - CB ANGL. DEV. = -15.1 DEGREES REMARK 500 TYR L 171 CB - CG - CD1 ANGL. DEV. = -4.4 DEGREES REMARK 500 MET L 173 CG - SD - CE ANGL. DEV. = -13.4 DEGREES REMARK 500 HIS L 196 CB - CG - CD2 ANGL. DEV. = -10.8 DEGREES REMARK 500 SER L 199 CA - C - N ANGL. DEV. = -14.9 DEGREES REMARK 500 PHE L 207 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 LYS H 23 CA - C - N ANGL. DEV. = -13.8 DEGREES REMARK 500 TRP H 33 CD1 - CG - CD2 ANGL. DEV. = 7.4 DEGREES REMARK 500 TRP H 33 CE2 - CD2 - CG ANGL. DEV. = -6.8 DEGREES REMARK 500 TRP H 36 CD1 - CG - CD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 TRP H 36 CB - CG - CD1 ANGL. DEV. = -10.6 DEGREES REMARK 500 TRP H 36 CE2 - CD2 - CG ANGL. DEV. = -6.3 DEGREES REMARK 500 TRP H 36 CG - CD2 - CE3 ANGL. DEV. = 8.0 DEGREES REMARK 500 TRP H 47 CD1 - CG - CD2 ANGL. DEV. = 6.8 DEGREES REMARK 500 TRP H 47 CE2 - CD2 - CG ANGL. DEV. = -5.6 DEGREES REMARK 500 TYR H 60 CB - CG - CD2 ANGL. DEV. = -4.1 DEGREES REMARK 500 HIS H 61 CB - CG - CD2 ANGL. DEV. = -11.5 DEGREES REMARK 500 ARG H 63 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 TRP H 106 CD1 - CG - CD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 TRP H 106 CE2 - CD2 - CG ANGL. DEV. = -5.9 DEGREES REMARK 500 ALA H 117 N - CA - CB ANGL. DEV. = -8.5 DEGREES REMARK 500 TYR H 125 CB - CG - CD2 ANGL. DEV. = -4.8 DEGREES REMARK 500 TYR H 148 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 TRP H 157 CD1 - CG - CD2 ANGL. DEV. = 7.1 DEGREES REMARK 500 TRP H 157 CE2 - CD2 - CG ANGL. DEV. = -6.7 DEGREES REMARK 500 TYR H 178 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 CYS H 198 CA - CB - SG ANGL. DEV. = 7.2 DEGREES REMARK 500 ARG Y 21 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG Y 21 CA - C - N ANGL. DEV. = 12.2 DEGREES REMARK 500 TYR Y 23 CB - CG - CD1 ANGL. DEV. = -4.0 DEGREES REMARK 500 TRP Y 28 CD1 - CG - CD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 TRP Y 28 CE2 - CD2 - CG ANGL. DEV. = -6.2 DEGREES REMARK 500 TRP Y 28 CG - CD2 - CE3 ANGL. DEV. = 6.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 72 ANGLE DEVIATIONS. 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 TRP L 46 -77.74 -112.09 REMARK 500 THR L 50 -64.10 54.40 REMARK 500 SER L 55 100.11 -53.55 REMARK 500 GLU L 80 12.21 -65.52 REMARK 500 ASP L 108 99.24 -59.26 REMARK 500 ASP L 149 83.42 32.30 REMARK 500 GLU L 152 -142.38 -177.75 REMARK 500 ARG L 153 -144.30 -176.35 REMARK 500 GLN L 154 150.75 175.92 REMARK 500 ASP L 165 -78.39 -18.99 REMARK 500 SER L 166 -46.99 124.03 REMARK 500 LYS L 167 31.36 -84.15 REMARK 500 ASP L 168 179.19 171.30 REMARK 500 HIS L 187 -145.12 -129.98 REMARK 500 ASN L 188 -78.23 -167.95 REMARK 500 ASN L 208 -36.37 -141.88 REMARK 500 TYR H 27 -168.42 -124.24 REMARK 500 SER H 30 -38.03 -39.17 REMARK 500 THR H 87 -168.69 -122.06 REMARK 500 ASP H 104 21.42 -152.81 REMARK 500 ALA H 132 83.64 -58.80 REMARK 500 PRO H 150 -169.19 -77.04 REMARK 500 HIS H 167 88.09 -151.90 REMARK 500 GLN H 174 -125.47 -125.60 REMARK 500 SER H 175 51.38 -59.10 REMARK 500 SER H 188 63.79 -68.32 REMARK 500 SER H 189 -36.07 -154.51 REMARK 500 PRO H 190 -76.17 -59.59 REMARK 500 ALA H 204 -8.71 -57.32 REMARK 500 SER H 205 50.46 -147.33 REMARK 500 SER H 206 58.35 11.13 REMARK 500 ARG Y 5 -88.04 -31.84 REMARK 500 HIS Y 15 22.68 -77.79 REMARK 500 ARG Y 21 -130.44 60.36 REMARK 500 THR Y 47 3.81 -65.75 REMARK 500 LYS Y 68 -4.43 -141.01 REMARK 500 LEU Y 84 44.24 -106.32 REMARK 500 ILE Y 88 18.22 -59.72 REMARK 500 ASP Y 101 30.83 -76.29 REMARK 500 TRP Y 123 -8.12 -59.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR L 171 0.07 SIDE CHAIN 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 ILE L 104 10.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE LIGHT CHAIN OF THE FAB HAS THE CHAIN INDICATOR L. THE REMARK 999 HEAVY CHAIN OF THE FAB HAS THE CHAIN INDICATOR H. THE REMARK 999 LYSOZYME HAS THE CHAIN INDICATOR Y. THE NUMBERING SYSTEM REMARK 999 USED IS SEQUENTIAL, FROM 1 - 212 FOR THE LIGHT CHAIN AND REMARK 999 FROM 1 - 215 FOR THE HEAVY CHAIN. THE CONVERSION TO KABAT REMARK 999 NUMBERING (E.A. KABAT, T.T. WU, M. REID-MILLER, H.M. REMARK 999 PERRY, K.S. GOTTESMAN (1991) SEQUENCES OF PROTEINS OF REMARK 999 IMMUNOLOGICAL INTEREST, 5TH ED, NATIONAL INSTITUTES OF REMARK 999 HEALTH, BETHESDA, MD) FOR THE VARIABLE REGIONS OF THE REMARK 999 LIGHT AND HEAVY CHAINS IS GIVEN BELOW. THE NUMBERING REMARK 999 SYSTEM USED IS THE SAME AS IN THE PDB COORDINATE FILE FOR REMARK 999 THE WILD-TYPE HYHEL-5-LYSOZYME COMPLEX. REMARK 999 REMARK 999 SEQUENTIAL NUMBERING KABAT NUMBERING REMARK 999 L1 - L27 1 - 27 REMARK 999 L28 - L94 29 - 95 REMARK 999 L95 - L106 97 - 108 REMARK 999 H2 - H52 2 - 52 REMARK 999 H53 52A REMARK 999 H54 - H83 53 - 82 REMARK 999 H84 - H86 82A - 82C REMARK 999 H87 - H102 83 - 98 REMARK 999 H103 - H116 100 - 113 DBREF 1BQL L 2 212 GB 1042224 AAB34980 2 213 DBREF 1BQL Y 1 129 UNP P00700 LYSC_COLVI 1 129 DBREF 1BQL H 1 215 PDB 1BQL 1BQL 1 215 SEQADV 1BQL LYS L 18 GB 1042224 ARG 18 CONFLICT SEQADV 1BQL SER L 26 GB 1042224 ASN 26 CONFLICT SEQADV 1BQL ASN L 30 GB 1042224 SER 30 CONFLICT SEQADV 1BQL TYR L 33 GB 1042224 HIS 33 CONFLICT SEQADV 1BQL VAL L 59 GB 1042224 ALA 59 CONFLICT SEQADV 1BQL THR L 79 GB 1042224 ALA 79 CONFLICT SEQADV 1BQL GLY L 91 GB 1042224 SER 91 CONFLICT SEQADV 1BQL ARG L 92 GB 1042224 SER 92 CONFLICT SEQADV 1BQL ASN L 93 GB 1042224 HIS 93 CONFLICT SEQADV 1BQL L GB 1042224 TYR 95 DELETION SEQADV 1BQL PRO L 111 GB 1042224 GLN 112 CONFLICT SEQRES 1 L 212 ASP ILE VAL LEU THR GLN SER PRO ALA ILE MET SER ALA SEQRES 2 L 212 SER PRO GLY GLU LYS VAL THR MET THR CYS SER ALA SER SEQRES 3 L 212 SER SER VAL ASN TYR MET TYR TRP TYR GLN GLN LYS SER SEQRES 4 L 212 GLY THR SER PRO LYS ARG TRP ILE TYR ASP THR SER LYS SEQRES 5 L 212 LEU ALA SER GLY VAL PRO VAL ARG PHE SER GLY SER GLY SEQRES 6 L 212 SER GLY THR SER TYR SER LEU THR ILE SER SER MET GLU SEQRES 7 L 212 THR GLU ASP ALA ALA THR TYR TYR CYS GLN GLN TRP GLY SEQRES 8 L 212 ARG ASN PRO THR PHE GLY GLY GLY THR LYS LEU GLU ILE SEQRES 9 L 212 LYS ARG ALA ASP ALA ALA PRO THR VAL SER ILE PHE PRO SEQRES 10 L 212 PRO SER SER GLU GLN LEU THR SER GLY GLY ALA SER VAL SEQRES 11 L 212 VAL CYS PHE LEU ASN ASN PHE TYR PRO LYS ASP ILE ASN SEQRES 12 L 212 VAL LYS TRP LYS ILE ASP GLY SER GLU ARG GLN ASN GLY SEQRES 13 L 212 VAL LEU ASN SER TRP THR ASP GLN ASP SER LYS ASP SER SEQRES 14 L 212 THR TYR SER MET SER SER THR LEU THR LEU THR LYS ASP SEQRES 15 L 212 GLU TYR GLU ARG HIS ASN SER TYR THR CYS GLU ALA THR SEQRES 16 L 212 HIS LYS THR SER THR SER PRO ILE VAL LYS SER PHE ASN SEQRES 17 L 212 ARG ASN GLU CYS SEQRES 1 H 215 PCA VAL GLN LEU GLN GLN SER GLY ALA GLU LEU MET LYS SEQRES 2 H 215 PRO GLY ALA SER VAL LYS ILE SER CYS LYS ALA SER GLY SEQRES 3 H 215 TYR THR PHE SER ASP TYR TRP ILE GLU TRP VAL LYS GLN SEQRES 4 H 215 ARG PRO GLY HIS GLY LEU GLU TRP ILE GLY GLU ILE LEU SEQRES 5 H 215 PRO GLY SER GLY SER THR ASN TYR HIS GLU ARG PHE LYS SEQRES 6 H 215 GLY LYS ALA THR PHE THR ALA ASP THR SER SER SER THR SEQRES 7 H 215 ALA TYR MET GLN LEU ASN SER LEU THR SER GLU ASP SER SEQRES 8 H 215 GLY VAL TYR TYR CYS LEU HIS GLY ASN TYR ASP PHE ASP SEQRES 9 H 215 GLY TRP GLY GLN GLY THR THR LEU THR VAL SER SER ALA SEQRES 10 H 215 LYS THR THR PRO PRO SER VAL TYR PRO LEU ALA PRO GLY SEQRES 11 H 215 SER ALA ALA GLN THR ASN SER MET VAL THR LEU GLY CYS SEQRES 12 H 215 LEU VAL LYS GLY TYR PHE PRO GLU PRO VAL THR VAL THR SEQRES 13 H 215 TRP ASN SER GLY SER LEU SER SER GLY VAL HIS THR PHE SEQRES 14 H 215 PRO ALA VAL LEU GLN SER ASP LEU TYR THR LEU SER SER SEQRES 15 H 215 SER VAL THR VAL PRO SER SER PRO ARG PRO SER GLU THR SEQRES 16 H 215 VAL THR CYS ASN VAL ALA HIS PRO ALA SER SER THR LYS SEQRES 17 H 215 VAL ASP LYS LYS ILE VAL PRO SEQRES 1 Y 129 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS SEQRES 2 Y 129 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY SEQRES 3 Y 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN SEQRES 4 Y 129 SER GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP SEQRES 5 Y 129 TYR GLY VAL LEU GLN ILE ASN SER ARG TRP TRP CYS ASN SEQRES 6 Y 129 ASP GLY LYS THR PRO GLY SER ARG ASN LEU CYS ASN ILE SEQRES 7 Y 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA THR SEQRES 8 Y 129 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY SEQRES 9 Y 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY SEQRES 10 Y 129 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU FORMUL 4 HOH *86(H2 O) HELIX 1 1 THR L 79 ASP L 81 5 3 HELIX 2 2 SER L 120 LEU L 123 1 4 HELIX 3 3 LYS L 181 GLU L 185 1 5 HELIX 4 4 PHE H 29 ASP H 31 5 3 HELIX 5 5 GLU H 62 PHE H 64 5 3 HELIX 6 6 SER H 88 ASP H 90 5 3 HELIX 7 7 ASN H 158 GLY H 160 5 3 HELIX 8 8 PRO H 203 SER H 205 5 3 HELIX 9 9 ARG Y 5 ARG Y 14 1 10 HELIX 10 10 LEU Y 25 SER Y 36 1 12 HELIX 11 11 CYS Y 80 LEU Y 84 5 5 HELIX 12 12 THR Y 89 VAL Y 99 1 11 HELIX 13 13 GLY Y 104 ALA Y 107 5 4 HELIX 14 14 VAL Y 109 ARG Y 114 1 6 HELIX 15 15 VAL Y 120 ILE Y 124 5 5 SHEET 1 A 4 LEU L 4 SER L 7 0 SHEET 2 A 4 VAL L 19 ALA L 25 -1 N SER L 24 O THR L 5 SHEET 3 A 4 SER L 69 ILE L 74 -1 N ILE L 74 O VAL L 19 SHEET 4 A 4 PHE L 61 SER L 66 -1 N SER L 66 O SER L 69 SHEET 1 B 2 ILE L 10 ALA L 13 0 SHEET 2 B 2 LYS L 101 ILE L 104 1 N LYS L 101 O MET L 11 SHEET 1 C 2 TYR L 33 GLN L 37 0 SHEET 2 C 2 THR L 84 GLN L 88 -1 N GLN L 88 O TYR L 33 SHEET 1 D 3 THR L 112 PHE L 116 0 SHEET 2 D 3 GLY L 127 ASN L 135 -1 N ASN L 135 O THR L 112 SHEET 3 D 3 MET L 173 THR L 180 -1 N LEU L 179 O ALA L 128 SHEET 1 E 3 ILE L 142 ILE L 148 0 SHEET 2 E 3 TYR L 190 HIS L 196 -1 N THR L 195 O ASN L 143 SHEET 3 E 3 ILE L 203 PHE L 207 -1 N PHE L 207 O TYR L 190 SHEET 1 F 4 LEU H 4 GLN H 6 0 SHEET 2 F 4 VAL H 18 ALA H 24 -1 N LYS H 23 O GLN H 5 SHEET 3 F 4 THR H 78 LEU H 83 -1 N LEU H 83 O VAL H 18 SHEET 4 F 4 ALA H 68 ASP H 73 -1 N ASP H 73 O THR H 78 SHEET 1 G 6 GLU H 10 MET H 12 0 SHEET 2 G 6 THR H 110 VAL H 114 1 N THR H 113 O GLU H 10 SHEET 3 G 6 GLY H 92 LEU H 97 -1 N TYR H 94 O THR H 110 SHEET 4 G 6 TRP H 33 ARG H 40 -1 N GLN H 39 O VAL H 93 SHEET 5 G 6 GLY H 44 LEU H 52 -1 N ILE H 51 O ILE H 34 SHEET 6 G 6 SER H 57 TYR H 60 -1 N ASN H 59 O GLU H 50 SHEET 1 H 3 SER H 123 PRO H 126 0 SHEET 2 H 3 MET H 138 TYR H 148 -1 N LYS H 146 O SER H 123 SHEET 3 H 3 TYR H 178 PRO H 187 -1 N VAL H 186 O VAL H 139 SHEET 1 I 3 THR H 154 TRP H 157 0 SHEET 2 I 3 THR H 197 HIS H 202 -1 N ALA H 201 O THR H 154 SHEET 3 I 3 THR H 207 LYS H 212 -1 N LYS H 211 O CYS H 198 SHEET 1 J 2 THR Y 43 ARG Y 45 0 SHEET 2 J 2 THR Y 51 TYR Y 53 -1 N ASP Y 52 O ASN Y 44 SSBOND 1 CYS L 23 CYS L 87 1555 1555 2.02 SSBOND 2 CYS L 132 CYS L 192 1555 1555 2.03 SSBOND 3 CYS H 22 CYS H 96 1555 1555 2.04 SSBOND 4 CYS H 143 CYS H 198 1555 1555 2.04 SSBOND 5 CYS Y 6 CYS Y 127 1555 1555 1.93 SSBOND 6 CYS Y 30 CYS Y 115 1555 1555 2.04 SSBOND 7 CYS Y 64 CYS Y 80 1555 1555 2.02 SSBOND 8 CYS Y 76 CYS Y 94 1555 1555 2.04 CISPEP 1 SER L 7 PRO L 8 0 -2.93 CISPEP 2 TYR L 138 PRO L 139 0 -21.86 CISPEP 3 PHE H 149 PRO H 150 0 -23.68 CISPEP 4 GLU H 151 PRO H 152 0 8.62 CISPEP 5 ARG H 191 PRO H 192 0 -11.57 CRYST1 54.800 74.800 79.000 90.00 101.80 90.00 P 1 21 1 2 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 0.018248 0.000000 0.003812 0.00000 SCALE2 0.000000 0.013369 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012932 0.00000 MASTER 427 0 0 15 32 0 0 6 0 0 0 44 END