HEADER IMMUNE SYSTEM 30-NOV-10 2Y07 TITLE CRYSTAL STRUCTURE ANALYSIS OF THE ANTI-(4-HYDROXY-3- TITLE 2 NITROPHENYL) -ACETYL MURINE GERMLINE MONOCLONAL ANTIBODY TITLE 3 BBE6.12H3 FAB FRAGMENT IN COMPLEX WITH A PHAGE DISPLAY TITLE 4 DERIVED DODECAPEPTIDE PPYPAWHAPGNI COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTI-NP MURINE GERMLINE MONOCLONAL ANTIBODY BBE6.12H3, COMPND 3 HEAVY CHAIN; COMPND 4 CHAIN: H; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ANTI-NP MURINE GERMLINE MONOCLONAL ANTIBODY BBE6.12H3, COMPND 7 LIGHT CHAIN; COMPND 8 CHAIN: L; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: PHAGE DISPLAY DERIVED ANTIGEN; COMPND 11 CHAIN: P; COMPND 12 FRAGMENT: PEPTIDE, RESIDUES 1-12 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 STRAIN: C57BL/6; SOURCE 6 CELL_LINE: BBE6.12H3 MURINE HYBRIDOMA; SOURCE 7 ORGAN: SPLEEN; SOURCE 8 CELL: B-CELLS; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 11 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 12 ORGANISM_TAXID: 10090; SOURCE 13 STRAIN: C57BL/6; SOURCE 14 CELL_LINE: BBE6.12H3 MURINE HYBRIDOMA; SOURCE 15 ORGAN: SPLEEN; SOURCE 16 CELL: B-CELLS; SOURCE 17 MOL_ID: 3; SOURCE 18 SYNTHETIC: YES; SOURCE 19 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 20 ORGANISM_TAXID: 32630 KEYWDS IMMUNE SYSTEM, BETA-SANDWICH IMMUNOGLOBULIN FOLD, ANTIGEN BINDING, KEYWDS 2 SECRETED PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.KHAN,D.M.SALUNKE REVDAT 2 15-FEB-12 2Y07 1 JRNL REMARK REVDAT 1 28-DEC-11 2Y07 0 JRNL AUTH T.KHAN,D.M.SALUNKE JRNL TITL STRUCTURAL ELUCIDATION OF THE MECHANISTIC BASIS OF JRNL TITL 2 DEGENERACY IN THE PRIMARY HUMORAL RESPONSE. JRNL REF J.IMMUNOL. V. 188 1819 2012 JRNL REFN ISSN 0022-1767 JRNL PMID 22266283 JRNL DOI 10.4049/JIMMUNOL.1102701 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 184279.07 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.6 REMARK 3 NUMBER OF REFLECTIONS : 13136 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) : 0.2344 REMARK 3 FREE R VALUE : 0.2572 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.1 REMARK 3 FREE R VALUE TEST SET COUNT : 1310 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 2.4 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.6 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1859 REMARK 3 BIN R VALUE (WORKING SET) : 0.33 REMARK 3 BIN FREE R VALUE : 0.34 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.6 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 197 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.024 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3257 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 149 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.0 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.0 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.950 REMARK 3 B22 (A**2) : 7.319 REMARK 3 B33 (A**2) : -11.268 REMARK 3 B12 (A**2) : 0.000 REMARK 3 B13 (A**2) : 7.569 REMARK 3 B23 (A**2) : 0.000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.33 REMARK 3 ESD FROM SIGMAA (A) : 0.45 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.36 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.34 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009093 REMARK 3 BOND ANGLES (DEGREES) : 1.78250 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.7 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.9 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 : 0.3 REMARK 3 BSOL : 25.8733 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 : CNS_TOPPAR PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : TRIS.PARAM REMARK 3 PARAMETER FILE 4 : CNS_TOPPAR ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : CNS_TOPPAR PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : CNS_TOPPAR WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2Y07 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-DEC-10. REMARK 100 THE PDBE ID CODE IS EBI-46487. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 288 REMARK 200 PH : 7.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER CMF12 38CU-6 ( REMARK 200 OSMIC INC.) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14326 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.40 REMARK 200 RESOLUTION RANGE LOW (A) : 23.62 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 6.2 REMARK 200 R MERGE (I) : 0.10 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.00 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.0 REMARK 200 R MERGE FOR SHELL (I) : 0.12 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.60 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: NATIVE FAB STRUCTURE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.2 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM TRIS HCL, 0.025% SODIUM REMARK 280 AZIDE, PEG 3350 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 27.17950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.41450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 27.17950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.41450 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 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: 18910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L, P REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA H 136 REMARK 465 ALA H 137 REMARK 465 GLN H 138 REMARK 465 THR H 139 REMARK 465 ASN H 140 REMARK 465 HIS P 7 REMARK 465 ALA P 8 REMARK 465 PRO P 9 REMARK 465 GLY P 10 REMARK 465 ASN P 11 REMARK 465 ILE P 12 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 TYR L 143 CD1 TYR L 143 CE1 -0.242 REMARK 500 TYR L 143 CD2 TYR L 143 CE2 -0.159 REMARK 500 TYR L 143 CE1 TYR L 143 CZ -0.113 REMARK 500 TYR L 143 CE2 TYR L 143 CZ -0.161 REMARK 500 TYR L 143 CG TYR L 143 CD2 -0.079 REMARK 500 TYR L 143 C TYR L 143 O -0.154 REMARK 500 TYR L 143 CZ TYR L 143 OH -0.164 REMARK 500 PRO L 144 CA PRO L 144 CB -0.110 REMARK 500 PRO L 144 CB PRO L 144 CG -0.316 REMARK 500 PRO L 144 CG PRO L 144 CD -0.261 REMARK 500 PRO L 144 C PRO L 144 O -0.145 REMARK 500 PRO L 144 N PRO L 144 CA -0.129 REMARK 500 PRO L 144 N PRO L 144 CD -0.094 REMARK 500 PRO L 157 CG PRO L 157 CD -0.243 REMARK 500 THR L 159 CB THR L 159 CG2 -0.352 REMARK 500 THR L 159 C THR L 159 O -0.117 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 H 96 CA - CB - SG ANGL. DEV. = 7.0 DEGREES REMARK 500 PRO H 156 C - N - CD ANGL. DEV. = -26.2 DEGREES REMARK 500 PRO L 144 C - N - CD ANGL. DEV. = -16.5 DEGREES REMARK 500 PRO L 144 N - CA - CB ANGL. DEV. = -6.9 DEGREES REMARK 500 THR L 159 CB - CA - C ANGL. DEV. = 22.2 DEGREES REMARK 500 PRO P 2 C - N - CA ANGL. DEV. = 14.6 DEGREES REMARK 500 PRO P 2 C - N - CD ANGL. DEV. = -21.3 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 TYR H 27 -175.64 -170.09 REMARK 500 SER H 84 -83.22 -95.45 REMARK 500 ALA H 92 -178.65 -170.48 REMARK 500 SER H 105 93.48 101.35 REMARK 500 TYR H 106 175.56 174.86 REMARK 500 ASP H 108 -94.50 20.83 REMARK 500 ASN H 162 36.03 39.58 REMARK 500 SER H 197 -88.66 7.32 REMARK 500 SER H 210 68.04 37.68 REMARK 500 THR L 30 -166.40 -106.86 REMARK 500 ALA L 35 128.59 -34.23 REMARK 500 ASP L 43 40.43 76.17 REMARK 500 THR L 53 -48.90 70.16 REMARK 500 SER L 67 -156.05 -163.52 REMARK 500 ASP L 71 31.30 -100.00 REMARK 500 GLU L 84 99.06 -60.68 REMARK 500 ASN L 96 10.03 160.46 REMARK 500 THR L 159 -117.14 61.17 REMARK 500 ASN L 173 6.19 89.19 REMARK 500 PRO P 2 -165.31 45.98 REMARK 500 TYR P 3 -18.56 169.17 REMARK 500 PRO P 4 -102.88 -133.06 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 TYR L 143 PRO L 144 30.26 REMARK 500 VAL L 158 THR L 159 99.44 REMARK 500 THR L 159 GLN L 160 -131.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ASP H 108 24.3 L L OUTSIDE RANGE REMARK 500 THR L 159 17.2 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2XZQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF THE ANTI-(4-HYDROXY-3- REMARK 900 NITROPHENYL)-ACETYL MURINE GERMLINE MONOCLONAL ANTIBODY REMARK 900 BBE6.12H3 FAB FRAGMENT IN COMPLEX WITH A PHAGE REMARK 900 DISPLAY DERIVED DODECAPEPTIDE YQLRPNAETLRF REMARK 900 RELATED ID: 4A6Y RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF FAB FRAGMENT OF ANTI-(4-HYDROXY- REMARK 900 3-NITROPHENYL)-ACETYL MURINE GERMLINE ANTIBODY BBE6.12H3 REMARK 900 RELATED ID: 2Y06 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF THE ANTI-(4-HYDROXY-3- REMARK 900 NITROPHENYL) -ACETYL MURINE GERMLINE ANTIBODY BBE6.12H3 REMARK 900 FAB FRAGMENT IN COMPLEX WITH A PHAGE DISPLAY DERIVED REMARK 900 DODECAPEPTIDE GDPRPSYISHLL REMARK 900 RELATED ID: 2Y36 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF THE ANTI-(4-HYDROXY-3- REMARK 900 NITROPHENYL)- ACETYL MURINE GERMLINE ANTIBODY BBE6.12H3 REMARK 900 FAB FRAGMENT IN COMPLEX WITH A PHAGE DISPLAY DERIVED REMARK 900 DODECAPEPTIDE DLWTTAIPTIPS DBREF 2Y07 H 1 220 PDB 2Y07 2Y07 1 220 DBREF 2Y07 L 1 211 PDB 2Y07 2Y07 1 211 DBREF 2Y07 P 1 12 PDB 2Y07 2Y07 1 12 SEQRES 1 H 220 GLN VAL GLN LEU GLN GLN PRO GLY ALA GLU LEU VAL LYS SEQRES 2 H 220 PRO GLY ALA SER VAL LYS LEU SER CYS LYS ALA SER GLY SEQRES 3 H 220 TYR THR PHE THR SER TYR TRP MET HIS TRP VAL LYS GLN SEQRES 4 H 220 ARG PRO GLY ARG GLY LEU GLU TRP ILE GLY ARG ILE ASP SEQRES 5 H 220 PRO ASN SER GLY GLY THR ALA TYR ASN GLU LYS PHE LYS SEQRES 6 H 220 SER LYS ALA THR LEU THR VAL ASP LYS PRO SER SER THR SEQRES 7 H 220 ALA TYR MET ALA LEU SER SER LEU THR SER ALA ASP SER SEQRES 8 H 220 ALA VAL TYR TYR CYS ALA ARG TYR ASP TYR TYR GLY GLY SEQRES 9 H 220 SER TYR PHE ASP TYR TRP GLY GLN GLY THR THR LEU THR SEQRES 10 H 220 VAL SER SER GLY GLY THR THR PRO PRO SER VAL TYR PRO SEQRES 11 H 220 LEU ALA PRO GLY SER ALA ALA GLN THR ASN SER MET VAL SEQRES 12 H 220 THR LEU GLY CYS LEU VAL LYS GLY TYR PHE PRO GLU PRO SEQRES 13 H 220 VAL THR VAL THR TRP ASN SER GLY SER LEU SER SER GLY SEQRES 14 H 220 VAL HIS THR PHE PRO ALA VAL LEU GLN SER ASP LEU TYR SEQRES 15 H 220 THR LEU SER SER SER VAL THR VAL PRO SER SER PRO TRP SEQRES 16 H 220 PRO SER GLU THR VAL THR CYS ASN VAL ALA HIS PRO ALA SEQRES 17 H 220 SER SER THR ALA VAL ASP LYS ALA ILE VAL PRO ARG SEQRES 1 L 211 GLN ALA VAL VAL THR GLN GLU SER ALA LEU THR THR SER SEQRES 2 L 211 PRO GLY GLU THR VAL THR LEU THR CYS ARG SER SER THR SEQRES 3 L 211 GLY ALA VAL THR THR SER ASN TYR ALA ASN TRP VAL GLN SEQRES 4 L 211 GLU LYS PRO ASP HIS LEU PHE THR GLY LEU ILE GLY GLY SEQRES 5 L 211 THR ASN ASN ARG ALA PRO GLY VAL PRO ALA ARG PHE SER SEQRES 6 L 211 GLY SER LEU ILE GLY ASP LYS ALA ALA LEU THR ILE THR SEQRES 7 L 211 GLY GLY GLN THR GLU ASP GLU ALA ILE TYR PHE CYS ALA SEQRES 8 L 211 LEU TRP TYR SER ASN HIS TRP VAL PHE GLY GLY GLY THR SEQRES 9 L 211 ALA LEU THR VAL LEU GLY GLN PRO LYS SER SER PRO SER SEQRES 10 L 211 VAL THR LEU PHE PRO PRO SER SER GLU GLU LEU GLU THR SEQRES 11 L 211 ASN THR ALA THR LEU VAL CYS THR ILE THR ASP PHE TYR SEQRES 12 L 211 PRO GLY VAL VAL THR VAL ASP TRP THR VAL ASP GLY THR SEQRES 13 L 211 PRO VAL THR GLN GLY MET GLU THR THR GLN PRO SER LYS SEQRES 14 L 211 GLN SER ASN ASN LYS TYR MET ALA SER SER TYR LEU THR SEQRES 15 L 211 LEU THR ALA ALA ALA TRP GLU ARG HIS SER SER TYR SER SEQRES 16 L 211 CYS GLN VAL THR HIS GLU GLY HIS THR VAL GLU LYS SER SEQRES 17 L 211 LEU SER ARG SEQRES 1 P 12 PRO PRO TYR PRO ALA TRP HIS ALA PRO GLY ASN ILE FORMUL 4 HOH *149(H2 O) HELIX 1 1 THR H 28 TYR H 32 5 5 HELIX 2 2 GLU H 62 LYS H 65 5 4 HELIX 3 3 THR H 87 SER H 91 5 5 HELIX 4 4 SER H 163 SER H 165 5 3 HELIX 5 5 PRO H 207 SER H 210 5 4 HELIX 6 6 GLN L 80 GLU L 84 5 5 HELIX 7 7 SER L 124 GLU L 129 1 6 HELIX 8 8 ALA L 185 HIS L 191 1 7 SHEET 1 HA 4 GLN H 3 GLN H 5 0 SHEET 2 HA 4 VAL H 18 SER H 25 -1 O LYS H 23 N GLN H 5 SHEET 3 HA 4 THR H 78 LEU H 83 -1 O ALA H 79 N CYS H 22 SHEET 4 HA 4 ALA H 68 ASP H 73 -1 O THR H 69 N ALA H 82 SHEET 1 HB 6 ALA H 9 VAL H 12 0 SHEET 2 HB 6 THR H 114 VAL H 118 1 O THR H 115 N GLU H 10 SHEET 3 HB 6 ALA H 92 TYR H 99 -1 O ALA H 92 N LEU H 116 SHEET 4 HB 6 TRP H 33 GLN H 39 -1 O TRP H 33 N TYR H 99 SHEET 5 HB 6 LEU H 45 ILE H 51 -1 O GLU H 46 N LYS H 38 SHEET 6 HB 6 THR H 58 TYR H 60 -1 O ALA H 59 N ARG H 50 SHEET 1 HC 4 SER H 127 LEU H 131 0 SHEET 2 HC 4 MET H 142 TYR H 152 -1 O GLY H 146 N LEU H 131 SHEET 3 HC 4 LEU H 181 PRO H 191 -1 O TYR H 182 N TYR H 152 SHEET 4 HC 4 VAL H 176 GLN H 178 1 O VAL H 176 N THR H 183 SHEET 1 HD 4 SER H 127 LEU H 131 0 SHEET 2 HD 4 MET H 142 TYR H 152 -1 O GLY H 146 N LEU H 131 SHEET 3 HD 4 LEU H 181 PRO H 191 -1 O TYR H 182 N TYR H 152 SHEET 4 HD 4 VAL H 170 THR H 172 -1 O HIS H 171 N SER H 187 SHEET 1 HE 2 VAL H 176 GLN H 178 0 SHEET 2 HE 2 LEU H 181 PRO H 191 1 O LEU H 181 N GLN H 178 SHEET 1 HF 3 THR H 158 TRP H 161 0 SHEET 2 HF 3 VAL H 200 HIS H 206 -1 O ASN H 203 N THR H 160 SHEET 3 HF 3 THR H 211 ILE H 217 -1 O THR H 211 N HIS H 206 SHEET 1 LA 4 VAL L 4 THR L 5 0 SHEET 2 LA 4 VAL L 18 SER L 24 -1 O ARG L 23 N THR L 5 SHEET 3 LA 4 ALA L 73 ILE L 76 -1 O ALA L 73 N CYS L 22 SHEET 4 LA 4 PHE L 64 LEU L 68 -1 O SER L 65 N THR L 75A SHEET 1 LB 4 ALA L 9 THR L 12 0 SHEET 2 LB 4 THR L 104 VAL L 108 1 O ALA L 105 N LEU L 10 SHEET 3 LB 4 ILE L 86 TRP L 93 -1 O TYR L 87 N THR L 104 SHEET 4 LB 4 TRP L 98 PHE L 100 -1 O VAL L 99 N LEU L 92 SHEET 1 LC 6 ALA L 9 THR L 12 0 SHEET 2 LC 6 THR L 104 VAL L 108 1 O ALA L 105 N LEU L 10 SHEET 3 LC 6 ILE L 86 TRP L 93 -1 O TYR L 87 N THR L 104 SHEET 4 LC 6 ASN L 36 LYS L 41 -1 O ASN L 36 N ALA L 91 SHEET 5 LC 6 LEU L 45 GLY L 51 -1 O LEU L 45 N LYS L 41 SHEET 6 LC 6 ASN L 55 ARG L 56 -1 O ASN L 55 N GLY L 51 SHEET 1 LD 2 TRP L 98 PHE L 100 0 SHEET 2 LD 2 ILE L 86 TRP L 93 -1 O LEU L 92 N VAL L 99 SHEET 1 LE 4 SER L 117 PHE L 121 0 SHEET 2 LE 4 THR L 132 PHE L 142 -1 O VAL L 136 N PHE L 121 SHEET 3 LE 4 TYR L 175 THR L 184 -1 O TYR L 175 N PHE L 142 SHEET 4 LE 4 SER L 168 LYS L 169 1 O SER L 168 N MET L 176 SHEET 1 LF 4 SER L 117 PHE L 121 0 SHEET 2 LF 4 THR L 132 PHE L 142 -1 O VAL L 136 N PHE L 121 SHEET 3 LF 4 TYR L 175 THR L 184 -1 O TYR L 175 N PHE L 142 SHEET 4 LF 4 MET L 162 THR L 164 -1 O GLU L 163 N TYR L 180 SHEET 1 LG 2 SER L 168 LYS L 169 0 SHEET 2 LG 2 TYR L 175 THR L 184 1 O MET L 176 N SER L 168 SHEET 1 LH 4 THR L 156 PRO L 157 0 SHEET 2 LH 4 THR L 148 VAL L 153 -1 O VAL L 153 N THR L 156 SHEET 3 LH 4 SER L 193 THR L 199 -1 O SER L 195 N THR L 152 SHEET 4 LH 4 THR L 204 SER L 210 -1 O VAL L 205 N VAL L 198 SSBOND 1 CYS H 22 CYS H 96 1555 1555 2.02 SSBOND 2 CYS H 147 CYS H 202 1555 1555 2.04 SSBOND 3 CYS L 22 CYS L 90 1555 1555 2.02 SSBOND 4 CYS L 137 CYS L 196 1555 1555 2.03 CISPEP 1 PHE H 153 PRO H 154 0 0.00 CISPEP 2 GLU H 155 PRO H 156 0 12.28 CISPEP 3 TRP H 195 PRO H 196 0 0.31 CISPEP 4 TYR L 143 PRO L 144 0 30.26 CRYST1 54.359 60.829 111.724 90.00 94.79 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.018396 0.000000 0.001542 0.00000 SCALE2 0.000000 0.016440 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008982 0.00000