HEADER IMMUNE SYSTEM 02-JUL-18 6A76 TITLE CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF B5209B, A MURINE MONOCLONAL TITLE 2 ANTIBODY SPECIFIC FOR THE FIFTH IMMUNOGLOBULIN DOMAIN (IG5) OF HUMAN TITLE 3 ROBO1 CAVEAT 6A76 THR H 48 HAS WRONG CHIRALITY AT ATOM CB THR H 114 HAS WRONG CAVEAT 2 6A76 CHIRALITY AT ATOM CB COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIGHT CHAIN OF THE ANTI-HUMAN ROBO1 ANTIBODY B5209B FAB; COMPND 3 CHAIN: L; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HEAVY CHAIN OF THE ANTI-HUMAN ROBO1 ANTIBODY B5209B FAB; COMPND 7 CHAIN: H; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_TAXID: 10090; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 6 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 9 ORGANISM_TAXID: 10090; SOURCE 10 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM_CELL_LINE: HEK293 KEYWDS HEPATOCELLULAR CARCINOMA ANTIGEN, ANGIOGENESIS, IMMUNE SYSTEM, KEYWDS 2 ANTIBODY DRUG EXPDTA X-RAY DIFFRACTION AUTHOR E.MIZOHATA,T.NAKAYAMA,Y.KADO,T.INOUE REVDAT 2 20-MAR-19 6A76 1 JRNL REVDAT 1 30-JAN-19 6A76 0 JRNL AUTH T.YAMASHITA,E.MIZOHATA,S.NAGATOISHI,T.WATANABE,M.NAKAKIDO, JRNL AUTH 2 H.IWANARI,Y.MOCHIZUKI,T.NAKAYAMA,Y.KADO,Y.YOKOTA, JRNL AUTH 3 H.MATSUMURA,T.KAWAMURA,T.KODAMA,T.HAMAKUBO,T.INOUE, JRNL AUTH 4 H.FUJITANI,K.TSUMOTO JRNL TITL AFFINITY IMPROVEMENT OF A CANCER-TARGETED ANTIBODY THROUGH JRNL TITL 2 ALANINE-INDUCED ADJUSTMENT OF ANTIGEN-ANTIBODY INTERFACE. JRNL REF STRUCTURE V. 27 519 2019 JRNL REFN ISSN 1878-4186 JRNL PMID 30595454 JRNL DOI 10.1016/J.STR.2018.11.002 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 70018 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.131 REMARK 3 R VALUE (WORKING SET) : 0.129 REMARK 3 FREE R VALUE : 0.165 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3752 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4804 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.2320 REMARK 3 BIN FREE R VALUE SET COUNT : 256 REMARK 3 BIN FREE R VALUE : 0.2470 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3227 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 359 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.60000 REMARK 3 B22 (A**2) : 1.23000 REMARK 3 B33 (A**2) : 0.37000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.063 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.058 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.039 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.484 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.968 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3410 ; 0.031 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 3014 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4645 ; 2.599 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7050 ; 1.956 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 440 ; 7.217 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 127 ;36.744 ;24.252 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 538 ;14.274 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;18.228 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 529 ; 0.338 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3778 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 671 ; 0.008 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1739 ; 4.855 ; 2.550 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1738 ; 4.848 ; 2.549 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2183 ; 5.262 ; 3.828 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2184 ; 5.263 ; 3.830 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1671 ; 6.128 ; 2.984 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1667 ; 6.134 ; 2.986 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2456 ; 6.695 ; 4.316 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 14020 ; 8.457 ;51.206 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 14020 ; 8.457 ;51.205 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 6424 ; 6.094 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 95 ;41.271 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 6606 ;21.352 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6A76 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1300008262. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAY-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL32XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 73816 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM CACODYLATE TRIHYDRATE REMARK 280 (PH 6.5), 29% (W/V) PEG 8000, 200 MM AMMONIUM SULFATE, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 21.21550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.74900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.97350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.74900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.21550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.97350 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: 5010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H 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 CYS H 134A REMARK 465 GLY H 134B REMARK 465 ASP H 134C REMARK 465 THR H 134D REMARK 465 THR H 134E REMARK 465 GLY H 134F REMARK 465 PRO H 217 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 L 80 O HOH L 401 2.12 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 O HOH L 414 O HOH H 486 4545 1.88 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 SER L 10 CB SER L 10 OG -0.082 REMARK 500 CYS L 23 CB CYS L 23 SG -0.171 REMARK 500 GLU L 27 CG GLU L 27 CD 0.097 REMARK 500 GLN L 45 CG GLN L 45 CD 0.139 REMARK 500 ASP L 57 CB ASP L 57 CG 0.127 REMARK 500 SER L 65 CB SER L 65 OG -0.085 REMARK 500 SER L 67 N SER L 67 CA -0.215 REMARK 500 SER L 67 C SER L 67 O 0.206 REMARK 500 PHE L 135 CG PHE L 135 CD2 -0.091 REMARK 500 ASP L 143 CG ASP L 143 OD1 0.142 REMARK 500 SER H 86 CB SER H 86 OG -0.082 REMARK 500 GLU H 87 CB GLU H 87 CG -0.126 REMARK 500 GLU H 87 CG GLU H 87 CD 0.110 REMARK 500 TYR H 104 N TYR H 104 CA -0.125 REMARK 500 TYR H 104 CB TYR H 104 CG -0.119 REMARK 500 TYR H 104 CZ TYR H 104 OH -0.211 REMARK 500 SER H 120 CB SER H 120 OG 0.126 REMARK 500 GLU H 153 CD GLU H 153 OE1 0.149 REMARK 500 SER H 154 CB SER H 154 OG 0.114 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 TYR L 36 CG - CD2 - CE2 ANGL. DEV. = 4.9 DEGREES REMARK 500 ASP L 57 CB - CG - OD1 ANGL. DEV. = 6.9 DEGREES REMARK 500 ASP L 57 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 GLY L 66 CA - C - N ANGL. DEV. = -14.2 DEGREES REMARK 500 GLY L 66 O - C - N ANGL. DEV. = 10.4 DEGREES REMARK 500 SER L 67 CA - C - O ANGL. DEV. = 14.5 DEGREES REMARK 500 SER L 67 CA - C - N ANGL. DEV. = -15.8 DEGREES REMARK 500 ARG L 69 NE - CZ - NH1 ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG L 69 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 ASP L 81 CB - CG - OD1 ANGL. DEV. = 11.2 DEGREES REMARK 500 TYR L 86 CB - CG - CD2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG L 108 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG L 108 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 LEU L 125 CB - CG - CD1 ANGL. DEV. = 11.4 DEGREES REMARK 500 ASP L 143 CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG H 36 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 MET H 81 CG - SD - CE ANGL. DEV. = -20.5 DEGREES REMARK 500 ARG H 101 CG - CD - NE ANGL. DEV. = -17.3 DEGREES REMARK 500 ARG H 101 NE - CZ - NH1 ANGL. DEV. = -7.1 DEGREES REMARK 500 GLU H 153 OE1 - CD - OE2 ANGL. DEV. = 8.9 DEGREES REMARK 500 GLU H 153 CG - CD - OE2 ANGL. DEV. = -17.1 DEGREES REMARK 500 GLU H 216 CA - C - O ANGL. DEV. = -17.1 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 ALA L 51 -31.59 61.84 REMARK 500 ASP L 57 8.77 59.59 REMARK 500 SER L 67 -18.69 -156.77 REMARK 500 ASP L 151 49.18 39.29 REMARK 500 ASN H 75 63.68 64.66 REMARK 500 TYR H 104 124.98 -178.11 REMARK 500 SER H 154 52.77 -164.58 REMARK 500 SER H 154 48.82 -161.64 REMARK 500 ASN H 160 47.82 34.85 REMARK 500 SER H 165 -72.19 20.73 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 H 103 -10.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL L 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL L 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL L 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL H 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL H 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL H 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 H 304 DBREF 6A76 L 1 211 PDB 6A76 6A76 1 211 DBREF 6A76 H -1 217 PDB 6A76 6A76 -1 217 SEQRES 1 L 211 ASP ILE GLN MET THR GLN SER PRO ALA SER LEU SER ALA SEQRES 2 L 211 SER VAL GLY GLU THR VAL THR ILE THR CYS GLY ALA SER SEQRES 3 L 211 GLU ASN ILE TYR GLY ALA LEU THR TRP TYR GLN ARG LYS SEQRES 4 L 211 GLN GLY LYS SER PRO GLN LEU LEU ILE TYR GLY ALA ILE SEQRES 5 L 211 ASN LEU ALA ASP ASP LYS SER SER ARG PHE SER GLY SER SEQRES 6 L 211 GLY SER GLY ARG GLN TYR SER LEU LYS ILE SER SER LEU SEQRES 7 L 211 HIS PRO ASP ASP VAL ALA THR TYR TYR CYS GLN ASN VAL SEQRES 8 L 211 LEU SER THR PRO PHE THR PHE GLY SER GLY THR LYS LEU SEQRES 9 L 211 GLU ILE LYS ARG ALA ASP ALA ALA PRO THR VAL SER ILE SEQRES 10 L 211 PHE PRO PRO SER SER GLU GLN LEU THR SER GLY GLY ALA SEQRES 11 L 211 SER VAL VAL CYS PHE LEU ASN ASN PHE TYR PRO LYS ASP SEQRES 12 L 211 ILE ASN VAL LYS TRP LYS ILE ASP GLY SER GLU ARG GLN SEQRES 13 L 211 ASN GLY VAL LEU ASN SER TRP THR ASP GLN ASP SER LYS SEQRES 14 L 211 ASP SER THR TYR SER MET SER SER THR LEU THR LEU THR SEQRES 15 L 211 LYS ASP GLU TYR GLU ARG HIS ASN SER TYR THR CYS GLU SEQRES 16 L 211 ALA THR HIS LYS THR SER THR SER PRO ILE VAL LYS SER SEQRES 17 L 211 PHE ASN ARG SEQRES 1 H 221 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY VAL VAL GLN SEQRES 2 H 221 PRO GLY GLY SER LEU LYS LEU SER CYS ALA ALA SER GLY SEQRES 3 H 221 PHE THR PHE SER THR TYR ASP MET SER TRP VAL ARG GLN SEQRES 4 H 221 THR PRO ASP LYS ARG LEU GLU LEU VAL ALA THR ILE ASN SEQRES 5 H 221 SER ASN GLY GLY SER THR TYR TYR PRO ASP SER VAL LYS SEQRES 6 H 221 GLY ARG PHE THR SER SER ARG ASP ASN ALA LYS ASN ILE SEQRES 7 H 221 LEU TYR LEU GLN MET SER SER LEU LYS SER GLU ASP THR SEQRES 8 H 221 ALA MET TYR TYR CYS ALA ARG GLU ALA LEU LEU ARG PRO SEQRES 9 H 221 PRO TYR TYR ALA LEU ASP TYR TRP GLY GLN GLY THR SER SEQRES 10 H 221 VAL THR VAL SER SER ALA LYS THR THR PRO PRO SER VAL SEQRES 11 H 221 TYR PRO LEU ALA PRO GLY CYS GLY ASP THR THR GLY SER SEQRES 12 H 221 SER VAL THR LEU GLY CYS LEU VAL LYS GLY TYR PHE PRO SEQRES 13 H 221 GLU SER VAL THR VAL THR TRP ASN SER GLY SER LEU SER SEQRES 14 H 221 SER SER VAL HIS THR PHE PRO ALA LEU LEU GLN SER GLY SEQRES 15 H 221 LEU TYR THR MET SER SER SER VAL THR VAL PRO SER SER SEQRES 16 H 221 THR TRP PRO SER GLN THR VAL THR CYS SER VAL ALA HIS SEQRES 17 H 221 PRO ALA SER SER THR THR VAL ASP LYS LYS LEU GLU PRO HET GOL L 301 6 HET GOL L 302 6 HET GOL L 303 6 HET GOL H 301 6 HET GOL H 302 6 HET GOL H 303 6 HET SO4 H 304 5 HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 6(C3 H8 O3) FORMUL 9 SO4 O4 S 2- FORMUL 10 HOH *359(H2 O) HELIX 1 AA1 HIS L 79 VAL L 83 5 5 HELIX 2 AA2 SER L 121 SER L 127 1 7 HELIX 3 AA3 LYS L 183 GLU L 187 1 5 HELIX 4 AA4 THR H 26 TYR H 30 5 5 HELIX 5 AA5 LYS H 85 THR H 89 5 5 HELIX 6 AA6 SER H 161 SER H 163 5 3 HELIX 7 AA7 LEU H 164 SER H 166 5 3 HELIX 8 AA8 PRO H 205 SER H 208 5 4 SHEET 1 AA1 4 MET L 4 SER L 7 0 SHEET 2 AA1 4 VAL L 19 ALA L 25 -1 O GLY L 24 N THR L 5 SHEET 3 AA1 4 GLN L 70 ILE L 75 -1 O TYR L 71 N CYS L 23 SHEET 4 AA1 4 PHE L 62 SER L 67 -1 N SER L 63 O LYS L 74 SHEET 1 AA2 6 SER L 10 ALA L 13 0 SHEET 2 AA2 6 THR L 102 ILE L 106 1 O GLU L 105 N LEU L 11 SHEET 3 AA2 6 ALA L 84 ASN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 AA2 6 LEU L 33 ARG L 38 -1 N ARG L 38 O THR L 85 SHEET 5 AA2 6 GLN L 45 TYR L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 AA2 6 ASN L 53 LEU L 54 -1 O ASN L 53 N TYR L 49 SHEET 1 AA3 4 THR L 114 PHE L 118 0 SHEET 2 AA3 4 GLY L 129 PHE L 139 -1 O ASN L 137 N THR L 114 SHEET 3 AA3 4 TYR L 173 THR L 182 -1 O LEU L 181 N ALA L 130 SHEET 4 AA3 4 VAL L 159 TRP L 163 -1 N LEU L 160 O THR L 178 SHEET 1 AA4 4 SER L 153 ARG L 155 0 SHEET 2 AA4 4 ASN L 145 ILE L 150 -1 N ILE L 150 O SER L 153 SHEET 3 AA4 4 SER L 191 THR L 197 -1 O GLU L 195 N LYS L 147 SHEET 4 AA4 4 ILE L 205 ASN L 210 -1 O PHE L 209 N TYR L 192 SHEET 1 AA5 4 GLN H 1 SER H 5 0 SHEET 2 AA5 4 LEU H 16 SER H 23 -1 O SER H 19 N SER H 5 SHEET 3 AA5 4 ILE H 76 MET H 81 -1 O MET H 81 N LEU H 16 SHEET 4 AA5 4 PHE H 66 ASP H 71 -1 N THR H 67 O GLN H 80 SHEET 1 AA6 6 GLY H 8 VAL H 10 0 SHEET 2 AA6 6 THR H 114 VAL H 118 1 O THR H 117 N VAL H 10 SHEET 3 AA6 6 ALA H 90 GLU H 97 -1 N TYR H 92 O THR H 114 SHEET 4 AA6 6 MET H 32 GLN H 37 -1 N VAL H 35 O TYR H 93 SHEET 5 AA6 6 LEU H 43 ILE H 49 -1 O GLU H 44 N ARG H 36 SHEET 6 AA6 6 THR H 56 TYR H 57 -1 O TYR H 57 N THR H 48 SHEET 1 AA7 4 GLY H 8 VAL H 10 0 SHEET 2 AA7 4 THR H 114 VAL H 118 1 O THR H 117 N VAL H 10 SHEET 3 AA7 4 ALA H 90 GLU H 97 -1 N TYR H 92 O THR H 114 SHEET 4 AA7 4 LEU H 107 TRP H 110 -1 O TYR H 109 N ARG H 96 SHEET 1 AA8 4 SER H 127 LEU H 131 0 SHEET 2 AA8 4 SER H 140 TYR H 150 -1 O GLY H 144 N LEU H 131 SHEET 3 AA8 4 LEU H 179 PRO H 189 -1 O TYR H 180 N TYR H 150 SHEET 4 AA8 4 VAL H 168 GLN H 176 -1 N GLN H 176 O LEU H 179 SHEET 1 AA9 3 THR H 156 TRP H 159 0 SHEET 2 AA9 3 THR H 199 HIS H 204 -1 O SER H 201 N THR H 158 SHEET 3 AA9 3 THR H 209 LYS H 214 -1 O VAL H 211 N VAL H 202 SSBOND 1 CYS L 23 CYS L 88 1555 1555 2.27 SSBOND 2 CYS L 134 CYS L 194 1555 1555 2.08 SSBOND 3 CYS H 20 CYS H 94 1555 1555 2.15 SSBOND 4 CYS H 145 CYS H 200 1555 1555 2.09 CISPEP 1 SER L 7 PRO L 8 0 -12.86 CISPEP 2 THR L 94 PRO L 95 0 -2.21 CISPEP 3 TYR L 140 PRO L 141 0 4.67 CISPEP 4 ARG H 101 PRO H 102 0 -9.82 CISPEP 5 PHE H 151 PRO H 152 0 -3.24 CISPEP 6 TRP H 193 PRO H 194 0 8.70 SITE 1 AC1 9 THR H 181 MET H 182 SER H 183 LEU L 160 SITE 2 AC1 9 SER L 176 SER L 177 THR L 178 HOH L 423 SITE 3 AC1 9 HOH L 469 SITE 1 AC2 3 SER L 59 ARG L 61 HOH L 471 SITE 1 AC3 5 LYS H 41 ARG L 38 GLN L 40 GLY L 41 SITE 2 AC3 5 ASP L 165 SITE 1 AC4 9 VAL H 3 ASN H 52 GLY H 54 HOH H 407 SITE 2 AC4 9 HOH H 415 HOH H 434 HOH H 459 HOH H 506 SITE 3 AC4 9 TYR L 30 SITE 1 AC5 4 ASP H 108 TYR L 49 ALA L 55 ASP L 56 SITE 1 AC6 7 ARG H 70 HOH H 413 HOH H 470 HOH H 471 SITE 2 AC6 7 HOH H 497 HOH H 540 HOH L 459 SITE 1 AC7 10 MET H 91 GLY H 113 SER H 115 HOH H 410 SITE 2 AC7 10 HOH H 446 HOH H 475 HOH H 498 HOH H 526 SITE 3 AC7 10 ASN L 28 ARG L 69 CRYST1 42.431 83.947 129.498 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 0.023568 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011912 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007722 0.00000