PDB Short entry for 3EYQ HEADER IMMUNE SYSTEM 21-OCT-08 3EYQ TITLE CRYSTAL STRUCTURE OF MJ5 FAB, A GERMLINE ANTIBODY VARIANT OF ANTI- TITLE 2 HUMAN CYTOMEGALOVIRUS ANTIBODY 8F9 CAVEAT 3EYQ 1. CHIRALITY ERRORS AT RESIDUES C115, C123, C130, D28, D147, CAVEAT 2 3EYQ AND D183. 2. VARIOUS CLOSE CONTACTS. COMPND MOL_ID: 1; COMPND 2 MOLECULE: M2J5 FAB; COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 8F9 FAB; COMPND 7 CHAIN: D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET40; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PET32B KEYWDS HUMAN CYTOMEGALOVIRUS, ANTIBODY, IMMUNOGLOBULIN DOMAIN, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR C.A.THOMSON,S.BRYSON,G.R.MCLEAN,A.L.CREAGH,E.F.PAI,J.W.SCHRADER REVDAT 3 06-SEP-23 3EYQ 1 SEQADV REVDAT 2 11-AUG-09 3EYQ 1 HEADER REVDAT 1 16-DEC-08 3EYQ 0 JRNL AUTH C.A.THOMSON,S.BRYSON,G.R.MCLEAN,A.L.CREAGH,E.F.PAI, JRNL AUTH 2 J.W.SCHRADER JRNL TITL GERMLINE V-GENES SCULPT THE BINDING SITE OF A FAMILY OF JRNL TITL 2 ANTIBODIES NEUTRALIZING HUMAN CYTOMEGALOVIRUS. JRNL REF EMBO J. V. 27 2592 2008 JRNL REFN ISSN 0261-4189 JRNL PMID 18772881 JRNL DOI 10.1038/EMBOJ.2008.179 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 19825 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.250 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1005 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 : 3206 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 88 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.30 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) : NULL 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) : 0.023 REMARK 3 BOND ANGLES (DEGREES) : NULL 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 3EYQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-OCT-08. REMARK 100 THE DEPOSITION ID IS D_1000049934. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-OCT-06 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 10.6 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 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROTEUM PLUS PLUS REMARK 200 DATA SCALING SOFTWARE : PROTEUM PLUS PLUS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19825 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.6 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.6000 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) : 2.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.40 REMARK 200 R MERGE FOR SHELL (I) : 0.43800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.410 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 3EYF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.6M AMMONIUM SULFATE, 2% PEG 400, REMARK 280 0.1M CAPS BUFFER, PH 10.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 32.69000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.77000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.02500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.77000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.69000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.02500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 MET C 0 REMARK 465 GLY C 213 REMARK 465 GLU C 214 REMARK 465 CYS C 215 REMARK 465 CYS D 102 REMARK 465 GLY D 103 REMARK 465 GLY D 104 REMARK 465 GLY D 105 REMARK 465 SER D 106 REMARK 465 CYS D 107 REMARK 465 TYR D 108 REMARK 465 PRO D 138 REMARK 465 SER D 139 REMARK 465 SER D 140 REMARK 465 LYS D 141 REMARK 465 SER D 142 REMARK 465 THR D 143 REMARK 465 SER D 144 REMARK 465 GLY D 145 REMARK 465 GLY D 146 REMARK 465 PRO D 225 REMARK 465 LYS D 226 REMARK 465 SER D 227 REMARK 465 CYS D 228 REMARK 465 ASP D 229 REMARK 465 LYS D 230 REMARK 465 THR D 231 REMARK 465 HIS D 232 REMARK 465 THR D 233 REMARK 465 GLY D 234 REMARK 465 LEU D 235 REMARK 465 GLU D 236 REMARK 465 HIS D 237 REMARK 465 HIS D 238 REMARK 465 HIS D 239 REMARK 465 HIS D 240 REMARK 465 HIS D 241 REMARK 465 HIS D 242 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 OG SER C 12 OE2 GLU C 106 1.91 REMARK 500 OG1 THR D 177 OG SER D 192 1.94 REMARK 500 NH2 ARG D 67 OD2 ASP D 90 1.96 REMARK 500 OG SER D 124 O HOH D 255 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OH TYR D 53 ND2 ASN D 216 4546 0.45 REMARK 500 OH TYR D 53 CG ASN D 216 4546 1.12 REMARK 500 CZ TYR D 53 ND2 ASN D 216 4546 1.27 REMARK 500 OH TYR D 53 OD1 ASN D 216 4546 1.82 REMARK 500 CE1 TYR D 53 ND2 ASN D 216 4546 2.00 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 TYR C 32 CD1 TYR C 32 CE1 -0.165 REMARK 500 TYR C 32 CE2 TYR C 32 CD2 -0.163 REMARK 500 TYR C 36 CD1 TYR C 36 CE1 -0.125 REMARK 500 TYR C 36 CE2 TYR C 36 CD2 -0.121 REMARK 500 TYR C 49 CD1 TYR C 49 CE1 -0.132 REMARK 500 SER C 67 CB SER C 67 OG -0.091 REMARK 500 ASP C 70 CB ASP C 70 CG -0.141 REMARK 500 PHE C 71 CZ PHE C 71 CE2 -0.119 REMARK 500 VAL C 85 CB VAL C 85 CG1 -0.136 REMARK 500 VAL C 85 CB VAL C 85 CG2 -0.142 REMARK 500 TYR C 86 CD1 TYR C 86 CE1 -0.114 REMARK 500 TYR C 86 CE2 TYR C 86 CD2 -0.102 REMARK 500 PHE C 119 CD1 PHE C 119 CE1 -0.155 REMARK 500 PHE C 119 CE2 PHE C 119 CD2 -0.141 REMARK 500 LYS C 127 CB LYS C 127 CG -0.195 REMARK 500 VAL C 133 CB VAL C 133 CG2 -0.127 REMARK 500 VAL C 134 CB VAL C 134 CG1 -0.192 REMARK 500 VAL C 134 CB VAL C 134 CG2 -0.214 REMARK 500 PHE C 140 CD1 PHE C 140 CE1 -0.141 REMARK 500 PHE C 140 CE2 PHE C 140 CD2 -0.140 REMARK 500 ALA C 154 CA ALA C 154 CB -0.137 REMARK 500 GLU C 162 CD GLU C 162 OE1 -0.066 REMARK 500 VAL C 164 CB VAL C 164 CG1 -0.152 REMARK 500 VAL C 164 CB VAL C 164 CG2 -0.193 REMARK 500 ASP C 171 CB ASP C 171 CG -0.165 REMARK 500 TYR C 174 CD1 TYR C 174 CE1 -0.150 REMARK 500 TYR C 174 CE1 TYR C 174 CZ -0.143 REMARK 500 TYR C 174 CE2 TYR C 174 CD2 -0.153 REMARK 500 VAL C 192 CB VAL C 192 CG2 -0.165 REMARK 500 GLU C 196 CD GLU C 196 OE1 -0.081 REMARK 500 VAL C 197 CB VAL C 197 CG1 -0.148 REMARK 500 THR C 198 CB THR C 198 CG2 -0.219 REMARK 500 VAL C 206 CB VAL C 206 CG1 -0.209 REMARK 500 VAL D 5 CB VAL D 5 CG1 -0.136 REMARK 500 VAL D 11 CB VAL D 11 CG1 -0.141 REMARK 500 VAL D 11 CB VAL D 11 CG2 -0.208 REMARK 500 VAL D 12 CB VAL D 12 CG1 -0.146 REMARK 500 ALA D 40 CA ALA D 40 CB -0.145 REMARK 500 GLU D 46 CD GLU D 46 OE1 -0.066 REMARK 500 VAL D 48 CB VAL D 48 CG1 -0.161 REMARK 500 TYR D 59 CD1 TYR D 59 CE1 -0.099 REMARK 500 ALA D 61 CA ALA D 61 CB -0.156 REMARK 500 TYR D 114 CD1 TYR D 114 CE1 -0.092 REMARK 500 TYR D 114 CZ TYR D 114 CE2 -0.085 REMARK 500 TYR D 114 CE2 TYR D 114 CD2 -0.114 REMARK 500 TRP D 115 CE3 TRP D 115 CZ3 -0.137 REMARK 500 VAL D 121 CB VAL D 121 CG2 -0.164 REMARK 500 VAL D 123 CB VAL D 123 CG1 -0.176 REMARK 500 ALA D 137 CA ALA D 137 CB -0.154 REMARK 500 THR D 147 CB THR D 147 CG2 -0.213 REMARK 500 REMARK 500 THIS ENTRY HAS 69 BOND DEVIATIONS. 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 ALA C 51 N - CA - C ANGL. DEV. = 17.5 DEGREES REMARK 500 ARG C 61 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ASP C 123 CB - CG - OD2 ANGL. DEV. = 8.8 DEGREES REMARK 500 THR C 130 N - CA - C ANGL. DEV. = 16.8 DEGREES REMARK 500 ASP C 168 CB - CG - OD2 ANGL. DEV. = 7.3 DEGREES REMARK 500 LEU C 176 CA - CB - CG ANGL. DEV. = 17.2 DEGREES REMARK 500 ASP C 186 CB - CG - OD2 ANGL. DEV. = 8.6 DEGREES REMARK 500 LEU D 20 CA - CB - CG ANGL. DEV. = 13.9 DEGREES REMARK 500 THR D 28 N - CA - C ANGL. DEV. = 17.5 DEGREES REMARK 500 PRO D 41 C - N - CD ANGL. DEV. = -13.2 DEGREES REMARK 500 TYR D 53 CA - CB - CG ANGL. DEV. = 13.8 DEGREES REMARK 500 TYR D 53 CB - CG - CD2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ASP D 62 CB - CG - OD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG D 67 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP D 73 CB - CG - OD2 ANGL. DEV. = 7.5 DEGREES REMARK 500 CYS D 96 CA - CB - SG ANGL. DEV. = 7.9 DEGREES REMARK 500 LEU D 171 CA - CB - CG ANGL. DEV. = 14.0 DEGREES REMARK 500 LEU D 190 CA - CB - CG ANGL. DEV. = 13.9 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 SER C 30 -118.97 59.51 REMARK 500 PRO C 44 138.38 -31.81 REMARK 500 LEU C 47 -69.94 -98.51 REMARK 500 ALA C 51 -34.34 70.53 REMARK 500 SER C 52 -15.30 -146.06 REMARK 500 THR C 56 120.66 -36.47 REMARK 500 SER C 67 139.04 -174.90 REMARK 500 GLU C 81 -35.84 -11.64 REMARK 500 SER C 115 86.26 6.98 REMARK 500 ASP C 123 -75.14 20.00 REMARK 500 LEU C 126 -12.55 -44.52 REMARK 500 SER C 128 -4.54 -54.33 REMARK 500 ASN C 139 82.57 45.13 REMARK 500 PRO C 142 -162.81 -75.65 REMARK 500 ASP C 152 46.91 35.60 REMARK 500 GLU C 166 150.66 -43.89 REMARK 500 LEU C 182 128.50 -176.06 REMARK 500 GLN C 200 -55.35 -16.68 REMARK 500 SER C 203 -76.95 -36.43 REMARK 500 ARG D 16 -164.35 -114.56 REMARK 500 THR D 28 66.40 -54.25 REMARK 500 TYR D 32 -65.94 -103.48 REMARK 500 TYR D 53 -68.54 17.70 REMARK 500 ASP D 54 -17.85 -141.25 REMARK 500 ARG D 72 112.62 -166.43 REMARK 500 SER D 85 37.10 76.08 REMARK 500 ALA D 88 -42.58 -8.62 REMARK 500 ALA D 92 150.43 174.39 REMARK 500 ASP D 156 59.45 76.44 REMARK 500 PRO D 159 -161.68 -103.09 REMARK 500 PRO D 161 -168.94 -117.67 REMARK 500 LEU D 182 86.83 -68.45 REMARK 500 GLN D 183 106.81 31.21 REMARK 500 SER D 185 -44.21 -23.63 REMARK 500 SER D 199 -95.36 -20.02 REMARK 500 SER D 200 146.98 -16.71 REMARK 500 LEU D 201 -24.84 126.02 REMARK 500 THR D 203 -28.31 -177.85 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 ALA C 51 SER C 52 -147.46 REMARK 500 ARG C 54 ALA C 55 149.41 REMARK 500 PRO C 80 GLU C 81 131.92 REMARK 500 PHE C 99 GLY C 100 147.45 REMARK 500 PRO C 114 SER C 115 91.97 REMARK 500 SER C 122 ASP C 123 128.82 REMARK 500 GLY C 129 THR C 130 142.36 REMARK 500 THR C 181 LEU C 182 -146.15 REMARK 500 GLY D 9 GLY D 10 -125.71 REMARK 500 GLY D 10 VAL D 11 148.94 REMARK 500 PHE D 29 SER D 30 -145.97 REMARK 500 SER D 52 TYR D 53 142.62 REMARK 500 TYR D 53 ASP D 54 -109.51 REMARK 500 SER D 75 LYS D 76 136.13 REMARK 500 PRO D 131 SER D 132 141.46 REMARK 500 LYS D 155 ASP D 156 145.98 REMARK 500 VAL D 181 LEU D 182 142.33 REMARK 500 LEU D 182 GLN D 183 108.30 REMARK 500 SER D 184 SER D 185 145.39 REMARK 500 SER D 198 SER D 199 145.52 REMARK 500 SER D 199 SER D 200 139.37 REMARK 500 GLY D 202 THR D 203 -107.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3EYF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ANTI-HUMAN CYTOMEGALOVIRUS ANTIBODY 8F9 PLUS REMARK 900 GB PEPTIDE REMARK 900 RELATED ID: 3EYO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ANTI-HUMAN CYTOMEGALOVIRUS ANTIBODY 8F9 REMARK 900 RELATED ID: 3F12 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MJ1 FAB, A GERMLINE ANTIBODY OF ANTI-HUMAN REMARK 900 CYTOMEGALOVIRUS ANTIBODY 8F9 DBREF 3EYQ C 1 215 PDB 3EYQ 3EYQ 1 215 DBREF 3EYQ D 1 234 PDB 3EYQ 3EYQ 1 234 SEQADV 3EYQ MET C 0 PDB 3EYQ EXPRESSION TAG SEQADV 3EYQ LEU D 235 PDB 3EYQ EXPRESSION TAG SEQADV 3EYQ GLU D 236 PDB 3EYQ EXPRESSION TAG SEQADV 3EYQ HIS D 237 PDB 3EYQ EXPRESSION TAG SEQADV 3EYQ HIS D 238 PDB 3EYQ EXPRESSION TAG SEQADV 3EYQ HIS D 239 PDB 3EYQ EXPRESSION TAG SEQADV 3EYQ HIS D 240 PDB 3EYQ EXPRESSION TAG SEQADV 3EYQ HIS D 241 PDB 3EYQ EXPRESSION TAG SEQADV 3EYQ HIS D 242 PDB 3EYQ EXPRESSION TAG SEQRES 1 C 216 MET GLU ILE VAL LEU THR GLN SER PRO ALA THR LEU SER SEQRES 2 C 216 LEU SER PRO GLY GLU ARG ALA THR LEU SER CYS ARG ALA SEQRES 3 C 216 SER GLN SER VAL SER SER TYR LEU ALA TRP TYR GLN GLN SEQRES 4 C 216 LYS PRO GLY GLN ALA PRO ARG LEU LEU ILE TYR ASP ALA SEQRES 5 C 216 SER ASN ARG ALA THR GLY ILE PRO ALA ARG PHE SER GLY SEQRES 6 C 216 SER GLY SER GLY THR ASP PHE THR LEU THR ILE SER SER SEQRES 7 C 216 LEU GLU PRO GLU ASP PHE ALA VAL TYR TYR CYS GLN GLN SEQRES 8 C 216 ARG SER ASN TRP PRO PRO ILE THR PHE GLY GLN GLY THR SEQRES 9 C 216 ARG LEU GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL SEQRES 10 C 216 PHE ILE PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY SEQRES 11 C 216 THR ALA SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO SEQRES 12 C 216 ARG GLU ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU SEQRES 13 C 216 GLN SER GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SEQRES 14 C 216 SER LYS ASP SER THR TYR SER LEU SER SER THR LEU THR SEQRES 15 C 216 LEU SER LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA SEQRES 16 C 216 CYS GLU VAL THR HIS GLN GLY LEU SER SER PRO VAL THR SEQRES 17 C 216 LYS SER PHE ASN ARG GLY GLU CYS SEQRES 1 D 242 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY VAL VAL GLN SEQRES 2 D 242 PRO GLY ARG SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 D 242 PHE THR PHE SER SER TYR GLY MET HIS TRP VAL ARG GLN SEQRES 4 D 242 ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA VAL ILE SER SEQRES 5 D 242 TYR ASP GLY SER ASN LYS TYR TYR ALA ASP SER VAL LYS SEQRES 6 D 242 GLY ARG PHE THR ILE SER ARG ASP ASN SER LYS ASN THR SEQRES 7 D 242 LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 D 242 ALA VAL TYR TYR CYS ALA LYS ASP GLY LYS CYS GLY GLY SEQRES 9 D 242 GLY SER CYS TYR SER GLY LEU LEU ASP TYR TRP GLY GLN SEQRES 10 D 242 GLY THR LEU VAL THR VAL SER SER ALA SER PHE LYS GLY SEQRES 11 D 242 PRO SER VAL PHE PRO LEU ALA PRO SER SER LYS SER THR SEQRES 12 D 242 SER GLY GLY THR ALA ALA LEU GLY CYS LEU VAL LYS ASP SEQRES 13 D 242 TYR PHE PRO GLU PRO VAL THR VAL SER TRP ASN SER GLY SEQRES 14 D 242 ALA LEU THR SER GLY VAL HIS THR PHE PRO ALA VAL LEU SEQRES 15 D 242 GLN SER SER GLY LEU TYR SER LEU SER SER VAL VAL THR SEQRES 16 D 242 VAL PRO SER SER SER LEU GLY THR GLN THR TYR ILE CYS SEQRES 17 D 242 ASN VAL ASN HIS LYS PRO SER ASN THR LYS VAL ASP LYS SEQRES 18 D 242 LYS VAL GLU PRO LYS SER CYS ASP LYS THR HIS THR GLY SEQRES 19 D 242 LEU GLU HIS HIS HIS HIS HIS HIS FORMUL 3 HOH *88(H2 O) HELIX 1 1 GLU C 79 PHE C 83 5 5 HELIX 2 2 SER C 183 HIS C 190 1 8 HELIX 3 3 THR D 28 GLY D 33 1 6 HELIX 4 4 ASP D 62 LYS D 65 5 4 HELIX 5 5 ASN D 74 LYS D 76 5 3 HELIX 6 6 ARG D 87 THR D 91 5 5 HELIX 7 7 SER D 168 ALA D 170 5 3 HELIX 8 8 LYS D 213 ASN D 216 5 4 SHEET 1 A 4 THR C 5 SER C 7 0 SHEET 2 A 4 ALA C 19 ARG C 24 -1 O ARG C 24 N THR C 5 SHEET 3 A 4 ASP C 70 ILE C 75 -1 O LEU C 73 N LEU C 21 SHEET 4 A 4 PHE C 62 SER C 67 -1 N SER C 63 O THR C 74 SHEET 1 B 6 THR C 10 LEU C 13 0 SHEET 2 B 6 THR C 103 ILE C 107 1 O ARG C 104 N LEU C 11 SHEET 3 B 6 VAL C 85 GLN C 90 -1 N TYR C 86 O THR C 103 SHEET 4 B 6 LEU C 33 GLN C 38 -1 N ALA C 34 O GLN C 89 SHEET 5 B 6 ARG C 45 TYR C 49 -1 O LEU C 47 N TRP C 35 SHEET 6 B 6 ASN C 53 ARG C 54 -1 O ASN C 53 N TYR C 49 SHEET 1 C 4 THR C 10 LEU C 13 0 SHEET 2 C 4 THR C 103 ILE C 107 1 O ARG C 104 N LEU C 11 SHEET 3 C 4 VAL C 85 GLN C 90 -1 N TYR C 86 O THR C 103 SHEET 4 C 4 THR C 98 PHE C 99 -1 O THR C 98 N GLN C 90 SHEET 1 D 4 SER C 115 PHE C 119 0 SHEET 2 D 4 SER C 132 PHE C 140 -1 O ASN C 138 N SER C 115 SHEET 3 D 4 TYR C 174 THR C 181 -1 O LEU C 180 N VAL C 133 SHEET 4 D 4 SER C 160 VAL C 164 -1 N GLN C 161 O THR C 179 SHEET 1 E 4 ALA C 154 LEU C 155 0 SHEET 2 E 4 LYS C 146 VAL C 151 -1 N VAL C 151 O ALA C 154 SHEET 3 E 4 VAL C 192 THR C 198 -1 O GLU C 196 N GLN C 148 SHEET 4 E 4 VAL C 206 ASN C 211 -1 O VAL C 206 N VAL C 197 SHEET 1 F 4 GLN D 3 SER D 7 0 SHEET 2 F 4 LEU D 18 SER D 25 -1 O SER D 25 N GLN D 3 SHEET 3 F 4 THR D 78 MET D 83 -1 O LEU D 79 N CYS D 22 SHEET 4 F 4 PHE D 68 ASP D 73 -1 N THR D 69 O GLN D 82 SHEET 1 G 6 VAL D 11 VAL D 12 0 SHEET 2 G 6 THR D 119 VAL D 123 1 O THR D 122 N VAL D 12 SHEET 3 G 6 ALA D 92 ASP D 99 -1 N TYR D 94 O THR D 119 SHEET 4 G 6 MET D 34 GLN D 39 -1 N HIS D 35 O ALA D 97 SHEET 5 G 6 GLU D 46 ILE D 51 -1 O ILE D 51 N MET D 34 SHEET 6 G 6 LYS D 58 TYR D 60 -1 O TYR D 59 N VAL D 50 SHEET 1 H 4 VAL D 11 VAL D 12 0 SHEET 2 H 4 THR D 119 VAL D 123 1 O THR D 122 N VAL D 12 SHEET 3 H 4 ALA D 92 ASP D 99 -1 N TYR D 94 O THR D 119 SHEET 4 H 4 LEU D 112 TRP D 115 -1 O TYR D 114 N LYS D 98 SHEET 1 I 4 SER D 132 LEU D 136 0 SHEET 2 I 4 ALA D 148 TYR D 157 -1 O LEU D 153 N PHE D 134 SHEET 3 I 4 TYR D 188 VAL D 196 -1 O LEU D 190 N VAL D 154 SHEET 4 I 4 VAL D 175 THR D 177 -1 N HIS D 176 O VAL D 193 SHEET 1 J 4 SER D 132 LEU D 136 0 SHEET 2 J 4 ALA D 148 TYR D 157 -1 O LEU D 153 N PHE D 134 SHEET 3 J 4 TYR D 188 VAL D 196 -1 O LEU D 190 N VAL D 154 SHEET 4 J 4 VAL D 181 LEU D 182 -1 N VAL D 181 O SER D 189 SHEET 1 K 3 THR D 163 TRP D 166 0 SHEET 2 K 3 TYR D 206 HIS D 212 -1 O ASN D 209 N SER D 165 SHEET 3 K 3 THR D 217 VAL D 223 -1 O LYS D 221 N CYS D 208 SSBOND 1 CYS C 23 CYS C 88 1555 1555 2.08 SSBOND 2 CYS C 135 CYS C 195 1555 1555 2.03 SSBOND 3 CYS D 22 CYS D 96 1555 1555 2.05 SSBOND 4 CYS D 152 CYS D 208 1555 1555 2.05 CISPEP 1 SER C 7 PRO C 8 0 -25.37 CISPEP 2 TRP C 94 PRO C 95 0 1.14 CISPEP 3 PRO C 95 PRO C 96 0 -1.20 CISPEP 4 TYR C 141 PRO C 142 0 -9.72 CISPEP 5 PHE D 158 PRO D 159 0 -1.88 CISPEP 6 GLU D 160 PRO D 161 0 0.40 CRYST1 65.380 76.050 111.540 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015295 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013149 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008965 0.00000