HEADER IMMUNE SYSTEM 06-JUL-12 4FZ8 TITLE CRYSTAL STRUCTURE OF C11 FAB, AN ADCC MEDIATING ANTI-HIV-1 ANTIBODY. COMPND MOL_ID: 1; COMPND 2 MOLECULE: FAB HEAVY CHAIN OF HUMAN ANTI-HIV-1 ENV ANTIBODY C11; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: FAB LIGHT CHAIN OF HUMAN ANTI-HIV-1 ENV ANTIBODY C11; COMPND 7 CHAIN: L; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK 293; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 14 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 16 EXPRESSION_SYSTEM_CELL_LINE: HEK 293 KEYWDS ADCC, ANTI-HIV-1 ENV ANTIBODY C11, CD4I ANTIBODY, FAB, VIRAL KEYWDS 2 GLYCOPROTEIN GP120, HIV-1 ENV, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR X.WU,W.D.TOLBERT,M.PAZGIER REVDAT 5 13-SEP-23 4FZ8 1 REMARK REVDAT 4 19-MAY-21 4FZ8 1 SOURCE HETSYN REVDAT 3 29-JUL-20 4FZ8 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 15-JUL-20 4FZ8 1 JRNL LINK REVDAT 1 10-JUL-13 4FZ8 0 JRNL AUTH W.D.TOLBERT,V.VAN,R.SHERBURN,M.TUYISHIME,F.YAN,D.N.NGUYEN, JRNL AUTH 2 S.STANFIELD-OAKLEY,D.EASTERHOFF,M.BONSIGNORI,B.F.HAYNES, JRNL AUTH 3 M.A.MOODY,K.RAY,G.FERRARI,G.K.LEWIS,M.PAZGIER JRNL TITL RECOGNITION PATTERNS OF THE C1/C2 EPITOPES INVOLVED IN JRNL TITL 2 FC-MEDIATED RESPONSE IN HIV-1 NATURAL INFECTION AND THE JRNL TITL 3 RV114 VACCINE TRIAL. JRNL REF MBIO V. 11 2020 JRNL REFN ESSN 2150-7511 JRNL PMID 32605979 JRNL DOI 10.1128/MBIO.00208-20 REMARK 2 REMARK 2 RESOLUTION. 2.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 13286 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) : 0.256 REMARK 3 R VALUE (WORKING SET) : 0.253 REMARK 3 FREE R VALUE : 0.313 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 708 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) : 2.66 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.73 REMARK 3 REFLECTION IN BIN (WORKING SET) : 697 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 69.35 REMARK 3 BIN R VALUE (WORKING SET) : 0.4750 REMARK 3 BIN FREE R VALUE SET COUNT : 43 REMARK 3 BIN FREE R VALUE : 0.5680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3323 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 10 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 96.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -10.27000 REMARK 3 B22 (A**2) : 21.40000 REMARK 3 B33 (A**2) : -8.63000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -3.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.432 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.467 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 53.222 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.904 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3418 ; 0.015 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3146 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4651 ; 1.964 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7249 ; 1.061 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 434 ; 9.422 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 137 ;36.487 ;24.161 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 538 ;22.416 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;23.420 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 523 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3892 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 777 ; 0.003 ; 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): 2172 ; 4.075 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3504 ; 5.529 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1251 ; 4.868 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1153 ; 6.309 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 6562 ; 5.889 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 3 ; NULL ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 6491 ;36.204 ; 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : H 1 H 215 REMARK 3 ORIGIN FOR THE GROUP (A): -13.5772 -14.6561 -11.6408 REMARK 3 T TENSOR REMARK 3 T11: 0.8547 T22: 0.0253 REMARK 3 T33: 0.7658 T12: -0.0671 REMARK 3 T13: -0.0751 T23: 0.0345 REMARK 3 L TENSOR REMARK 3 L11: 1.9072 L22: 0.1434 REMARK 3 L33: 3.0989 L12: -0.1199 REMARK 3 L13: 0.4169 L23: 0.6116 REMARK 3 S TENSOR REMARK 3 S11: -0.0796 S12: 0.1980 S13: 0.1035 REMARK 3 S21: -0.0110 S22: -0.0101 S23: -0.0064 REMARK 3 S31: -0.1899 S32: 0.0274 S33: 0.0896 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : L 1 L 211 REMARK 3 ORIGIN FOR THE GROUP (A): -17.7301 -25.4997 3.3106 REMARK 3 T TENSOR REMARK 3 T11: 0.8301 T22: 0.3016 REMARK 3 T33: 0.8098 T12: 0.0031 REMARK 3 T13: -0.0247 T23: 0.0524 REMARK 3 L TENSOR REMARK 3 L11: 0.9827 L22: 0.4275 REMARK 3 L33: 1.2371 L12: -0.3595 REMARK 3 L13: -0.0120 L23: 0.5690 REMARK 3 S TENSOR REMARK 3 S11: -0.0934 S12: -0.5215 S13: -0.2812 REMARK 3 S21: -0.1380 S22: 0.1793 S23: -0.0370 REMARK 3 S31: -0.0841 S32: -0.0766 S33: -0.0859 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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 4FZ8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000073537. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JAN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03317 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : K-B FOCUSING MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14023 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.660 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 (%) : 97.3 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.14600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.75200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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: 3TNN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.14 M SODIUM CITRATE, 0.07 M HEPES REMARK 280 SODIUM PH 7.5, 14% ISOPROPANOL, AND 30% GLYCEROL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 294K 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 67.27350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.00550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 67.27350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.00550 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: 3730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -53.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L 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 PRO H 123 REMARK 465 LEU H 124 REMARK 465 ALA H 125 REMARK 465 PRO H 126 REMARK 465 SER H 127 REMARK 465 SER H 128 REMARK 465 LYS H 129 REMARK 465 SER H 130 REMARK 465 THR H 131 REMARK 465 SER H 132 REMARK 465 GLY H 133 REMARK 465 CYS H 216 REMARK 465 ASP H 217 REMARK 465 LYS H 218 REMARK 465 THR H 219 REMARK 465 GLY L 212 REMARK 465 GLU L 213 REMARK 465 CYS L 214 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 TYR H 100K CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR H 100K OH 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 TYR H 100L OD2 ASP L 34 2.11 REMARK 500 NH2 ARG L 54 O VAL L 58 2.14 REMARK 500 O LYS H 201 N SER H 203 2.14 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 OE1 GLU L 79 OE1 GLU L 79 2555 2.00 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 PRO H 119 C - N - CA ANGL. DEV. = 10.8 DEGREES REMARK 500 ARG L 24 NE - CZ - NH1 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG L 24 NE - CZ - NH2 ANGL. DEV. = 3.0 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 CYS H 22 114.61 -161.77 REMARK 500 SER H 30 -19.12 -46.92 REMARK 500 VAL H 48 -88.87 -117.15 REMARK 500 TYR H 56 57.65 83.43 REMARK 500 GLU H 64 151.96 -43.33 REMARK 500 TYR H 79 107.83 42.52 REMARK 500 GLU H 85 -15.51 -46.47 REMARK 500 ALA H 88 -163.53 -174.36 REMARK 500 ASN H 96 173.37 -58.86 REMARK 500 GLN H 97 -109.08 -116.21 REMARK 500 HIS H 98 105.81 89.69 REMARK 500 ASP H 100 -156.22 49.48 REMARK 500 LEU H 100C -166.90 -75.70 REMARK 500 SER H 100D -140.04 -40.43 REMARK 500 LEU H 100F 107.92 42.08 REMARK 500 HIS H 100J 90.87 -59.98 REMARK 500 TYR H 100K 88.21 81.04 REMARK 500 SER H 112 -179.31 -176.96 REMARK 500 ALA H 114 -139.68 -83.14 REMARK 500 SER H 115 -154.59 -124.37 REMARK 500 THR H 116 134.15 65.92 REMARK 500 LYS H 117 171.34 -7.24 REMARK 500 PRO H 119 156.65 -45.52 REMARK 500 SER H 120 -67.41 -103.09 REMARK 500 VAL H 121 115.95 63.05 REMARK 500 LEU H 138 -178.57 172.84 REMARK 500 SER H 156 -6.25 64.49 REMARK 500 SER H 173 -10.68 -49.29 REMARK 500 SER H 186 -81.82 -45.90 REMARK 500 SER H 187 -69.18 17.74 REMARK 500 THR H 191 -67.36 -91.26 REMARK 500 PRO H 202 47.25 -52.84 REMARK 500 SER H 203 -28.67 -168.13 REMARK 500 GLU H 212 83.31 -156.40 REMARK 500 LYS H 214 103.88 49.33 REMARK 500 HIS L 27D 123.51 70.43 REMARK 500 ASN L 28 132.36 71.36 REMARK 500 TYR L 30 169.28 50.05 REMARK 500 TYR L 32 78.86 -103.53 REMARK 500 SER L 56 127.15 -36.42 REMARK 500 ARG L 77 72.97 68.65 REMARK 500 ASP L 82 1.39 -69.67 REMARK 500 LEU L 92 -86.69 -76.91 REMARK 500 ALA L 94 -132.90 54.95 REMARK 500 THR L 109 41.11 -93.22 REMARK 500 VAL L 110 -174.55 59.11 REMARK 500 ALA L 111 126.24 146.78 REMARK 500 SER L 121 125.97 88.77 REMARK 500 GLU L 123 -45.19 -158.09 REMARK 500 ASP L 151 74.42 39.95 REMARK 500 REMARK 500 THIS ENTRY HAS 52 RAMACHANDRAN OUTLIERS. 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 H 100K TYR H 100L 149.03 REMARK 500 LYS L 107 ARG L 108 -149.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN L 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS H 164 NE2 REMARK 620 2 ASN L 137 ND2 118.8 REMARK 620 3 ASN L 137 OD1 66.2 54.2 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3TNM RELATED DB: PDB REMARK 900 RELATED ID: 3TNN RELATED DB: PDB REMARK 900 RELATED ID: 4FZE RELATED DB: PDB DBREF 4FZ8 H 1 219 PDB 4FZ8 4FZ8 1 219 DBREF 4FZ8 L 1 214 PDB 4FZ8 4FZ8 1 214 SEQRES 1 H 237 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL LYS SEQRES 2 H 237 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 237 PHE THR PHE SER SER TYR SER MET ASN TRP VAL ARG GLN SEQRES 4 H 237 ALA PRO GLY ARG GLY LEU GLU TRP VAL SER SER ILE SER SEQRES 5 H 237 ASN THR SER THR TYR ILE TYR TYR ALA ASP SER VAL GLU SEQRES 6 H 237 GLY ARG PHE THR LEU SER ARG ASP ASN ALA LYS ASN SER SEQRES 7 H 237 LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 H 237 ALA VAL TYR TYR CYS ALA ARG ALA ASN GLN HIS PHE ASP SEQRES 9 H 237 TRP LEU LEU SER LEU LEU GLY GLY TYR HIS TYR TYR GLY SEQRES 10 H 237 MET ASP VAL TRP GLY GLN GLY THR THR VAL THR VAL SER SEQRES 11 H 237 SER ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU ALA SEQRES 12 H 237 PRO SER SER LYS SER THR SER GLY GLY THR ALA ALA LEU SEQRES 13 H 237 GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL THR SEQRES 14 H 237 VAL SER TRP ASN SER GLY ALA LEU THR SER GLY VAL HIS SEQRES 15 H 237 THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SER SEQRES 16 H 237 LEU SER SER VAL VAL THR VAL PRO SER SER SER LEU GLY SEQRES 17 H 237 THR GLN THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SER SEQRES 18 H 237 ASN THR LYS VAL ASP LYS ARG VAL GLU PRO LYS SER CYS SEQRES 19 H 237 ASP LYS THR SEQRES 1 L 218 ASP ILE VAL MET THR GLN SER PRO LEU SER LEU PRO VAL SEQRES 2 L 218 THR PRO GLY GLU PRO ALA SER ILE SER CYS ARG SER SER SEQRES 3 L 218 GLN SER LEU LEU HIS SER ASN GLY TYR ASN TYR LEU ASP SEQRES 4 L 218 TRP TYR LEU GLN LYS PRO GLY GLN SER PRO GLN LEU LEU SEQRES 5 L 218 ILE TYR LEU GLY SER ASN ARG ALA SER GLY VAL PRO ASP SEQRES 6 L 218 ARG PHE ILE GLY SER GLY SER GLY THR ASP PHE THR LEU SEQRES 7 L 218 LYS ILE SER ARG VAL GLU ALA GLU ASP VAL GLY VAL PHE SEQRES 8 L 218 TYR CYS MET GLN ALA LEU GLN ALA VAL GLY PHE GLY PRO SEQRES 9 L 218 GLY THR LYS VAL GLU ILE LYS ARG THR VAL ALA ALA PRO SEQRES 10 L 218 SER VAL PHE ILE PHE PRO PRO SER ASP GLU GLN LEU LYS SEQRES 11 L 218 SER GLY THR ALA SER VAL VAL CYS LEU LEU ASN ASN PHE SEQRES 12 L 218 TYR PRO ARG GLU ALA LYS VAL GLN TRP LYS VAL ASP ASN SEQRES 13 L 218 ALA LEU GLN SER GLY ASN SER GLN GLU SER VAL THR GLU SEQRES 14 L 218 GLN ASP SER LYS ASP SER THR TYR SER LEU SER SER THR SEQRES 15 L 218 LEU THR LEU SER LYS ALA ASP TYR GLU LYS HIS LYS VAL SEQRES 16 L 218 TYR ALA CYS GLU VAL THR HIS GLN GLY LEU SER SER PRO SEQRES 17 L 218 VAL THR LYS SER PHE ASN ARG GLY GLU CYS MODRES 4FZ8 ASN H 52A ASN GLYCOSYLATION SITE HET NAG H 300 14 HET ZN L 301 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM ZN ZINC ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 3 NAG C8 H15 N O6 FORMUL 4 ZN ZN 2+ FORMUL 5 HOH *10(H2 O) HELIX 1 1 THR H 28 TYR H 32 5 5 HELIX 2 2 ARG H 83 THR H 87 5 5 HELIX 3 3 TRP H 154 ALA H 158 5 5 HELIX 4 4 SER H 187 LEU H 189 5 3 HELIX 5 5 LYS L 183 GLU L 187 1 5 SHEET 1 A 2 GLN H 3 GLU H 6 0 SHEET 2 A 2 CYS H 22 SER H 25 -1 O ALA H 23 N VAL H 5 SHEET 1 B 5 GLY H 10 LEU H 11 0 SHEET 2 B 5 THR H 108 THR H 110 1 O THR H 108 N GLY H 10 SHEET 3 B 5 ALA H 88 ALA H 95 -1 N ALA H 88 O VAL H 109 SHEET 4 B 5 SER H 33 GLN H 39 -1 N VAL H 37 O TYR H 91 SHEET 5 B 5 LEU H 45 ILE H 51 -1 O GLU H 46 N ARG H 38 SHEET 1 C 3 LEU H 18 LEU H 20 0 SHEET 2 C 3 LEU H 80 MET H 82 -1 O MET H 82 N LEU H 18 SHEET 3 C 3 PHE H 67 LEU H 69 -1 N THR H 68 O GLN H 81 SHEET 1 D 3 THR H 135 TYR H 145 0 SHEET 2 D 3 TYR H 176 PRO H 185 -1 O LEU H 178 N VAL H 142 SHEET 3 D 3 VAL H 163 THR H 165 -1 N HIS H 164 O VAL H 181 SHEET 1 E 3 THR H 135 TYR H 145 0 SHEET 2 E 3 TYR H 176 PRO H 185 -1 O LEU H 178 N VAL H 142 SHEET 3 E 3 VAL H 169 LEU H 170 -1 N VAL H 169 O SER H 177 SHEET 1 F 2 TYR H 194 ILE H 195 0 SHEET 2 F 2 ARG H 210 VAL H 211 -1 O VAL H 211 N TYR H 194 SHEET 1 G 2 VAL H 198 HIS H 200 0 SHEET 2 G 2 THR H 205 VAL H 207 -1 O VAL H 207 N VAL H 198 SHEET 1 H 4 MET L 4 SER L 7 0 SHEET 2 H 4 ALA L 19 SER L 25 -1 O ARG L 24 N THR L 5 SHEET 3 H 4 ASP L 70 ILE L 75 -1 O LEU L 73 N ILE L 21 SHEET 4 H 4 PHE L 62 SER L 67 -1 N SER L 65 O THR L 72 SHEET 1 I 6 SER L 10 VAL L 13 0 SHEET 2 I 6 LYS L 103 ILE L 106 1 O GLU L 105 N VAL L 13 SHEET 3 I 6 GLY L 84 GLN L 90 -1 N GLY L 84 O VAL L 104 SHEET 4 I 6 LEU L 33 GLN L 38 -1 N ASP L 34 O MET L 89 SHEET 5 I 6 GLN L 45 TYR L 49 -1 O GLN L 45 N LEU L 37 SHEET 6 I 6 ASN L 53 ARG L 54 -1 O ASN L 53 N TYR L 49 SHEET 1 J 4 SER L 10 VAL L 13 0 SHEET 2 J 4 LYS L 103 ILE L 106 1 O GLU L 105 N VAL L 13 SHEET 3 J 4 GLY L 84 GLN L 90 -1 N GLY L 84 O VAL L 104 SHEET 4 J 4 GLY L 97 PHE L 98 -1 O GLY L 97 N GLN L 90 SHEET 1 K 4 SER L 114 ILE L 117 0 SHEET 2 K 4 THR L 129 PHE L 139 -1 O LEU L 135 N PHE L 116 SHEET 3 K 4 THR L 178 SER L 182 -1 O LEU L 181 N ALA L 130 SHEET 4 K 4 SER L 159 GLN L 160 -1 N GLN L 160 O THR L 178 SHEET 1 L 3 SER L 114 ILE L 117 0 SHEET 2 L 3 THR L 129 PHE L 139 -1 O LEU L 135 N PHE L 116 SHEET 3 L 3 TYR L 173 LEU L 175 -1 O TYR L 173 N PHE L 139 SHEET 1 M 4 ALA L 153 LEU L 154 0 SHEET 2 M 4 ALA L 144 VAL L 150 -1 N VAL L 150 O ALA L 153 SHEET 3 M 4 VAL L 191 HIS L 198 -1 O THR L 197 N LYS L 145 SHEET 4 M 4 VAL L 205 ASN L 210 -1 O PHE L 209 N TYR L 192 SSBOND 1 CYS H 22 CYS H 92 1555 1555 2.03 SSBOND 2 CYS H 140 CYS H 196 1555 1555 2.04 SSBOND 3 CYS L 23 CYS L 88 1555 1555 2.14 SSBOND 4 CYS L 134 CYS L 194 1555 1555 2.03 LINK ND2 ASN H 52A C1 NAG H 300 1555 1555 1.49 LINK NE2 HIS H 164 ZN ZN L 301 1555 1555 1.79 LINK ND2 ASN L 137 ZN ZN L 301 1555 1555 2.32 LINK OD1 ASN L 137 ZN ZN L 301 1555 1555 2.52 CISPEP 1 ASN H 82A SER H 82B 0 -29.39 CISPEP 2 ASP H 100 TRP H 100A 0 -22.43 CISPEP 3 SER H 113 ALA H 114 0 -10.21 CISPEP 4 PHE H 146 PRO H 147 0 -13.73 CISPEP 5 GLU H 148 PRO H 149 0 0.23 CISPEP 6 SER L 7 PRO L 8 0 2.93 CISPEP 7 HIS L 27D SER L 27E 0 25.76 CISPEP 8 TYR L 140 PRO L 141 0 0.80 CRYST1 134.547 56.011 70.708 90.00 106.87 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 0.007432 0.000000 0.002254 0.00000 SCALE2 0.000000 0.017854 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014779 0.00000