HEADER IMMUNE SYSTEM 24-NOV-10 2XZC TITLE CRYSTAL STRUCTURE OF PHOSPHONATE-MODIFIED RECOMBINANT A.17 ANTIBODY TITLE 2 FAB FRAGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: FAB A.17 HEAVY CHAIN; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: FAB A.17 LIGHT CHAIN; 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: CRICETULUS GRISEUS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: CHO; 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: CRICETULUS GRISEUS; SOURCE 14 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 16 EXPRESSION_SYSTEM_CELL_LINE: CHO KEYWDS IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR E.CARLETTI,F.NACHON,Y.NICOLET,P.MASSON,I.KURKOVA,I.SMIRNOV, AUTHOR 2 A.FRIBOULET,A.TRAMONTANO,A.GABIBOV REVDAT 3 11-MAR-20 2XZC 1 SEQRES LINK REVDAT 2 05-OCT-11 2XZC 1 JRNL REVDAT 1 21-SEP-11 2XZC 0 JRNL AUTH I.SMIRNOV,E.CARLETTI,I.KURKOVA,F.NACHON,Y.NICOLET, JRNL AUTH 2 V.A.MITKEVICH,H.DEBAT,B.AVALLE,A.A.BELOGUROV,N.KUZNETSOV, JRNL AUTH 3 A.RESHETNYAK,P.MASSON,A.G.TONEVITSKY,N.PONOMARENKO, JRNL AUTH 4 A.A.MAKAROV,A.FRIBOULET,A.TRAMONTANO,A.GABIBOV JRNL TITL REACTIBODIES GENERATED BY KINETIC SELECTION COUPLE CHEMICAL JRNL TITL 2 REACTIVITY WITH FAVORABLE PROTEIN DYNAMICS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 15954 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 21896761 JRNL DOI 10.1073/PNAS.1108460108 REMARK 2 REMARK 2 RESOLUTION. 1.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 89715 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) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2749 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) : 1.36 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.40 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6019 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.16 REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE SET COUNT : 168 REMARK 3 BIN FREE R VALUE : 0.2910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3199 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 19 REMARK 3 SOLVENT ATOMS : 779 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 61.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.053 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.057 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.037 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.898 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3445 ; 0.032 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4747 ; 2.578 ; 1.968 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 473 ; 7.172 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 126 ;35.718 ;25.397 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 539 ;12.185 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;22.652 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 540 ; 0.215 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2628 ; 0.016 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2219 ; 1.612 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3624 ; 2.665 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1226 ; 3.418 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1100 ; 5.051 ; 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): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 2XZC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1290046370. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUN-09 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 : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 92464 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.360 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.40000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M ADA BUFFER PH 6.5, 0.1M MGCL2, REMARK 280 20% PEG6000 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 33.47500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.3 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 SER H 134 REMARK 465 LYS H 135 REMARK 465 SER H 136 REMARK 465 THR H 137 REMARK 465 SER H 138 REMARK 465 GLY H 139 REMARK 465 SER H 221 REMARK 465 CYS H 222 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 SER H 133 CA C O CB OG REMARK 470 LYS H 220 CA C O CB CG CD CE REMARK 470 LYS H 220 NZ REMARK 470 CYS L 216 CA C O CB SG 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 H 42 O HOH H 2129 1.24 REMARK 500 O HOH H 2314 O HOH H 2315 1.26 REMARK 500 OD1 ASN L 97 O HOH L 2180 1.34 REMARK 500 O THR L 70 O HOH L 2140 1.47 REMARK 500 O HOH H 2226 O HOH H 2230 1.51 REMARK 500 O HOH H 2180 O HOH H 2369 1.52 REMARK 500 O HOH H 2263 O HOH H 2264 1.52 REMARK 500 O HOH H 2347 O HOH H 2369 1.52 REMARK 500 O HOH L 2308 O HOH L 2310 1.55 REMARK 500 N GLY H 43 O HOH H 2135 1.55 REMARK 500 O HOH H 2180 O HOH H 2367 1.58 REMARK 500 O HOH H 2029 O HOH H 2093 1.58 REMARK 500 O HOH H 2132 O HOH H 2135 1.63 REMARK 500 OE1 GLN L 16 O HOH L 2028 1.68 REMARK 500 O PCA H 1 O HOH H 2002 1.69 REMARK 500 O HOH L 2021 O HOH L 2081 1.69 REMARK 500 O HOH H 2179 O HOH L 2179 1.70 REMARK 500 O HOH H 2180 O HOH L 2308 1.73 REMARK 500 O HOH H 2301 O HOH L 2214 1.74 REMARK 500 O HOH H 2299 O HOH H 2300 1.76 REMARK 500 O HOH L 2214 O HOH L 2215 1.76 REMARK 500 O HOH L 2081 O HOH L 2083 1.77 REMARK 500 CB GLU L 125 O HOH L 2224 1.78 REMARK 500 O HOH L 2030 O HOH L 2032 1.81 REMARK 500 OE1 GLN H 5 O HOH H 2020 1.82 REMARK 500 O HOH H 2348 O HOH H 2350 1.82 REMARK 500 NE2 GLN L 149 CD1 LEU L 156 1.86 REMARK 500 O HOH L 2151 O HOH L 2367 1.88 REMARK 500 NE2 GLN L 16 O HOH L 2027 1.88 REMARK 500 ND2 ASN L 140 O HOH L 2238 1.89 REMARK 500 O HOH L 2237 O HOH L 2239 1.89 REMARK 500 N GLY L 24 O HOH L 2140 1.90 REMARK 500 O HOH H 2164 O HOH H 2210 1.91 REMARK 500 CD GLN L 149 CD1 LEU L 156 1.92 REMARK 500 O HOH H 2212 O HOH H 2213 1.93 REMARK 500 O HOH L 2126 O HOH L 2152 1.96 REMARK 500 O HOH H 2399 O HOH L 2224 2.01 REMARK 500 OG1 THR L 131 O HOH L 2231 2.02 REMARK 500 NZ LYS L 54 O HOH L 2096 2.02 REMARK 500 OE1 GLU H 154 O HOH H 2315 2.02 REMARK 500 ND2 ASN L 140 O HOH L 2239 2.03 REMARK 500 OE1 GLN L 149 O HOH L 2250 2.04 REMARK 500 O HOH H 2253 O HOH H 2257 2.05 REMARK 500 CB PRO H 9 O HOH H 2043 2.07 REMARK 500 N PCA H 1 O HOH H 2004 2.07 REMARK 500 O HOH L 2083 O HOH L 2107 2.08 REMARK 500 O HOH L 2345 O HOH L 2346 2.08 REMARK 500 O HOH H 2105 O HOH H 2124 2.09 REMARK 500 O HOH H 2087 O HOH H 2214 2.10 REMARK 500 O HOH L 2103 O HOH L 2281 2.10 REMARK 500 REMARK 500 THIS ENTRY HAS 64 CLOSE CONTACTS 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 H 2095 O HOH H 2139 2545 1.31 REMARK 500 O HOH L 2032 O HOH L 2122 1455 1.78 REMARK 500 O HOH H 2298 O HOH L 2267 2646 1.85 REMARK 500 O HOH H 2092 O HOH H 2238 2545 1.86 REMARK 500 O HOH L 2180 O HOH L 2333 1454 1.96 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 GLY H 10 C GLY H 10 O -0.140 REMARK 500 TYR H 60 CD1 TYR H 60 CE1 0.092 REMARK 500 GLN H 78 CB GLN H 78 CG -0.179 REMARK 500 VAL H 156 CB VAL H 156 CG2 -0.258 REMARK 500 SER H 179 CB SER H 179 OG 0.090 REMARK 500 SER L 27 CB SER L 27 OG -0.092 REMARK 500 GLU L 145 CD GLU L 145 OE1 0.068 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 LEU H 11 CB - CG - CD2 ANGL. DEV. = -11.8 DEGREES REMARK 500 ARG H 39 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG H 67 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ASP H 150 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ASP H 150 CB - CG - OD2 ANGL. DEV. = -6.7 DEGREES REMARK 500 CYS H 202 CA - CB - SG ANGL. DEV. = 7.5 DEGREES REMARK 500 ARG L 55 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ASP L 61 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG L 110 NE - CZ - NH1 ANGL. DEV. = 9.3 DEGREES REMARK 500 ARG L 110 NE - CZ - NH2 ANGL. DEV. = -8.4 DEGREES REMARK 500 ASP L 124 CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ASP L 153 CB - CG - OD2 ANGL. DEV. = -6.6 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 H 15 -10.48 82.13 REMARK 500 ASN L 28 -94.40 -107.76 REMARK 500 ASN L 52 -40.76 73.61 REMARK 500 ASN L 53 10.97 -151.12 REMARK 500 ALA L 85 170.09 177.80 REMARK 500 GLU L 215 -157.50 -109.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR L 37 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH H2006 DISTANCE = 7.83 ANGSTROMS REMARK 525 HOH H2015 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH L2039 DISTANCE = 6.13 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 8-METHYL-8-AZABICYCLO[3.2.1]OCTAN-3-YL PHENYLPHOSPHONATE REMARK 600 (XOP): THE LIGAND XOP IS COVALENTLY BOND TO TYR37 OF THE L REMARK 600 CHAIN. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL H 1221 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XOP L 1217 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2XZA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RECOMBINANT A.17 ANTIBODY FAB FRAGMENT DBREF 2XZC H 1 222 PDB 2XZC 2XZC 1 222 DBREF 2XZC L 1 216 PDB 2XZC 2XZC 1 216 SEQRES 1 H 222 PCA VAL GLN LEU GLN GLU SER GLY PRO GLY LEU VAL LYS SEQRES 2 H 222 PRO SER GLU THR LEU SER LEU THR CYS ALA VAL SER GLY SEQRES 3 H 222 TYR SER ILE SER SER GLY TYR TYR TRP GLY TRP ILE ARG SEQRES 4 H 222 GLN PRO PRO GLY LYS GLY LEU GLU TRP ILE GLY SER ILE SEQRES 5 H 222 TYR HIS SER GLY SER THR TYR TYR ASN PRO SER LEU LYS SEQRES 6 H 222 SER ARG VAL THR ILE SER VAL ASP THR SER LYS ASN GLN SEQRES 7 H 222 PHE SER LEU LYS LEU SER SER VAL THR ALA ALA ASP THR SEQRES 8 H 222 ALA VAL TYR TYR CYS ALA GLY LEU THR GLN SER SER HIS SEQRES 9 H 222 ASN ASP ALA ASN TRP GLY GLN GLY THR LEU THR THR VAL SEQRES 10 H 222 SER SER ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU SEQRES 11 H 222 ALA PRO SER SER LYS SER THR SER GLY GLY THR ALA ALA SEQRES 12 H 222 LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL SEQRES 13 H 222 THR VAL SER TRP ASN SER GLY ALA LEU THR SER GLY VAL SEQRES 14 H 222 HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SEQRES 15 H 222 SER LEU SER SER VAL VAL THR VAL PRO SER SER SER LEU SEQRES 16 H 222 GLY THR GLN THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SEQRES 17 H 222 SER ASN THR LYS VAL ASP LYS LYS VAL GLU PRO LYS SER SEQRES 18 H 222 CYS SEQRES 1 L 216 PCA SER VAL LEU THR GLN PRO PRO SER VAL SER ALA ALA SEQRES 2 L 216 PRO GLY GLN LYS VAL THR ILE SER CYS SER GLY SER SER SEQRES 3 L 216 SER ASN ILE GLY ASN ASN TYR VAL SER TRP TYR GLN GLN SEQRES 4 L 216 LEU PRO GLY THR ALA PRO LYS LEU LEU ILE TYR ASP ASN SEQRES 5 L 216 ASN LYS ARG PRO SER GLY ILE PRO ASP ARG PHE SER GLY SEQRES 6 L 216 SER LYS SER GLY THR SER ALA THR LEU GLY ILE THR GLY SEQRES 7 L 216 LEU GLN THR GLY ASP GLU ALA ASP TYR TYR CYS GLY THR SEQRES 8 L 216 TRP ASP SER SER LEU ASN PRO VAL PHE GLY GLY GLY THR SEQRES 9 L 216 LYS LEU GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL SEQRES 10 L 216 PHE ILE PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY SEQRES 11 L 216 THR ALA SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO SEQRES 12 L 216 ARG GLU ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU SEQRES 13 L 216 GLN SER GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SEQRES 14 L 216 SER LYS ASP SER THR TYR SER LEU SER SER THR LEU THR SEQRES 15 L 216 LEU SER LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA SEQRES 16 L 216 CYS GLU VAL THR HIS GLN GLY LEU SER SER PRO VAL THR SEQRES 17 L 216 LYS SER PHE ASN ARG GLY GLU CYS MODRES 2XZC PCA H 1 GLU PYROGLUTAMIC ACID MODRES 2XZC PCA L 1 GLU PYROGLUTAMIC ACID HET PCA H 1 8 HET PCA L 1 8 HET CL H1221 1 HET XOP L1217 18 HETNAM PCA PYROGLUTAMIC ACID HETNAM CL CHLORIDE ION HETNAM XOP 8-METHYL-8-AZABICYCLO[3.2.1]OCTAN-3-YL HETNAM 2 XOP PHENYLPHOSPHONATE FORMUL 1 PCA 2(C5 H7 N O3) FORMUL 3 CL CL 1- FORMUL 4 XOP C14 H20 N O3 P FORMUL 5 HOH *779(H2 O) HELIX 1 1 SER H 28 GLY H 32 5 5 HELIX 2 2 LEU H 64 SER H 66 5 3 HELIX 3 3 THR H 87 THR H 91 5 5 HELIX 4 4 SER H 162 ALA H 164 5 3 HELIX 5 5 SER H 193 THR H 197 5 5 HELIX 6 6 LYS H 207 ASN H 210 5 4 HELIX 7 7 ASN L 28 ASN L 32 5 5 HELIX 8 8 GLN L 80 GLU L 84 5 5 HELIX 9 9 SER L 123 SER L 129 1 7 HELIX 10 10 LYS L 185 GLU L 189 1 5 SHEET 1 HA 4 GLN H 3 GLU H 6 0 SHEET 2 HA 4 LEU H 18 SER H 25 -1 O ALA H 23 N GLN H 5 SHEET 3 HA 4 GLN H 78 LEU H 83 -1 O PHE H 79 N CYS H 22 SHEET 4 HA 4 VAL H 68 ASP H 73 -1 O THR H 69 N LYS H 82 SHEET 1 HB 4 GLY H 10 VAL H 12 0 SHEET 2 HB 4 THR H 113 VAL H 117 1 O LEU H 114 N GLY H 10 SHEET 3 HB 4 ALA H 92 LEU H 99 -1 O ALA H 92 N THR H 115 SHEET 4 HB 4 ASN H 108 TRP H 109 -1 O ASN H 108 N GLY H 98 SHEET 1 HC 6 GLY H 10 VAL H 12 0 SHEET 2 HC 6 THR H 113 VAL H 117 1 O LEU H 114 N GLY H 10 SHEET 3 HC 6 ALA H 92 LEU H 99 -1 O ALA H 92 N THR H 115 SHEET 4 HC 6 TYR H 34 GLN H 40 -1 O TYR H 34 N LEU H 99 SHEET 5 HC 6 GLU H 47 TYR H 53 -1 O GLU H 47 N ARG H 39 SHEET 6 HC 6 THR H 58 TYR H 60 -1 O TYR H 59 N SER H 51 SHEET 1 HD 2 ASN H 108 TRP H 109 0 SHEET 2 HD 2 ALA H 92 LEU H 99 -1 O GLY H 98 N ASN H 108 SHEET 1 HE 4 SER H 126 LEU H 130 0 SHEET 2 HE 4 THR H 141 TYR H 151 -1 O GLY H 145 N LEU H 130 SHEET 3 HE 4 TYR H 182 PRO H 191 -1 O TYR H 182 N TYR H 151 SHEET 4 HE 4 VAL H 175 LEU H 176 1 O VAL H 175 N SER H 183 SHEET 1 HF 4 SER H 126 LEU H 130 0 SHEET 2 HF 4 THR H 141 TYR H 151 -1 O GLY H 145 N LEU H 130 SHEET 3 HF 4 TYR H 182 PRO H 191 -1 O TYR H 182 N TYR H 151 SHEET 4 HF 4 VAL H 169 THR H 171 -1 O HIS H 170 N VAL H 187 SHEET 1 HG 2 VAL H 175 LEU H 176 0 SHEET 2 HG 2 TYR H 182 PRO H 191 1 O SER H 183 N VAL H 175 SHEET 1 HH 3 THR H 157 TRP H 160 0 SHEET 2 HH 3 ILE H 201 HIS H 206 -1 O ASN H 203 N SER H 159 SHEET 3 HH 3 THR H 211 LYS H 216 -1 O THR H 211 N HIS H 206 SHEET 1 LA 4 SER L 9 ALA L 12 0 SHEET 2 LA 4 THR L 104 ILE L 108 1 O LYS L 105 N VAL L 10 SHEET 3 LA 4 ALA L 85 TRP L 92 -1 O ALA L 85 N LEU L 106 SHEET 4 LA 4 PRO L 98 PHE L 100 1 O VAL L 99 N THR L 91 SHEET 1 LB 5 SER L 9 ALA L 12 0 SHEET 2 LB 5 THR L 104 ILE L 108 1 O LYS L 105 N VAL L 10 SHEET 3 LB 5 ALA L 85 TRP L 92 -1 O ALA L 85 N LEU L 106 SHEET 4 LB 5 SER L 35 GLN L 39 -1 O SER L 35 N GLY L 90 SHEET 5 LB 5 LYS L 46 ILE L 49 -1 O LYS L 46 N GLN L 38 SHEET 1 LC 2 PRO L 98 PHE L 100 0 SHEET 2 LC 2 ALA L 85 TRP L 92 1 O THR L 91 N VAL L 99 SHEET 1 LD 3 VAL L 18 SER L 23 0 SHEET 2 LD 3 SER L 71 ILE L 76 -1 O ALA L 72 N CYS L 22 SHEET 3 LD 3 PHE L 63 SER L 68 -1 O SER L 64 N GLY L 75 SHEET 1 LE 4 SER L 116 PHE L 120 0 SHEET 2 LE 4 THR L 131 PHE L 141 -1 O VAL L 135 N PHE L 120 SHEET 3 LE 4 TYR L 175 SER L 184 -1 O TYR L 175 N PHE L 141 SHEET 4 LE 4 SER L 161 VAL L 165 -1 O GLN L 162 N THR L 180 SHEET 1 LF 4 ALA L 155 LEU L 156 0 SHEET 2 LF 4 LYS L 147 VAL L 152 -1 O VAL L 152 N ALA L 155 SHEET 3 LF 4 VAL L 193 THR L 199 -1 O ALA L 195 N LYS L 151 SHEET 4 LF 4 VAL L 207 ASN L 212 -1 O VAL L 207 N VAL L 198 SSBOND 1 CYS H 22 CYS H 96 1555 1555 2.16 SSBOND 2 CYS H 146 CYS H 202 1555 1555 2.03 SSBOND 3 CYS L 22 CYS L 89 1555 1555 2.08 SSBOND 4 CYS L 136 CYS L 196 1555 1555 1.96 LINK C PCA H 1 N VAL H 2 1555 1555 1.32 LINK C PCA L 1 N SER L 2 1555 1555 1.33 LINK OH TYR L 37 P XOP L1217 1555 1555 1.63 CISPEP 1 PHE H 152 PRO H 153 0 -16.72 CISPEP 2 GLU H 154 PRO H 155 0 -1.18 CISPEP 3 TYR L 142 PRO L 143 0 7.75 SITE 1 AC1 3 ALA H 107 TRP H 109 HOH L2084 SITE 1 AC2 12 TYR H 34 HIS H 104 ASN H 105 HOH H2265 SITE 2 AC2 12 SER L 35 TYR L 37 GLY L 90 THR L 91 SITE 3 AC2 12 TRP L 92 PRO L 98 VAL L 99 PHE L 100 CRYST1 52.560 66.950 66.210 90.00 107.65 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.019026 0.000000 0.006054 0.00000 SCALE2 0.000000 0.014937 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015850 0.00000 HETATM 1 N PCA H 1 -9.202 -20.262 5.728 1.00 36.79 N HETATM 2 CA PCA H 1 -9.691 -18.933 5.291 0.60 33.12 C HETATM 3 CB PCA H 1 -9.843 -18.084 6.558 1.00 34.51 C HETATM 4 CG PCA H 1 -8.791 -18.666 7.513 0.60 36.81 C HETATM 5 CD PCA H 1 -8.212 -19.831 6.750 1.00 36.71 C HETATM 6 OE PCA H 1 -7.054 -20.324 6.967 1.00 39.84 O HETATM 7 C PCA H 1 -8.753 -18.294 4.219 1.00 28.13 C HETATM 8 O PCA H 1 -7.693 -18.827 3.958 1.00 25.57 O