HEADER IMMUNE SYSTEM 07-JUN-16 5L88 TITLE AFAMIN ANTIBODY FRAGMENT, N14 FAB, L1- GLYCOSILATED, CRYSTAL FORM I, TITLE 2 NON-PARSIMONIOUS MODEL COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTI-AFAMIN ANTIBODY N14, FAB FRAGMENT, HEAVY CHAIN; COMPND 3 CHAIN: H; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: ANTI-AFAMIN ANTIBODY N14, FAB FRAGMENT, LIGHT CHAIN; COMPND 6 CHAIN: L SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_TAXID: 10090; SOURCE 4 STRAIN: BALB/C; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 7 ORGANISM_TAXID: 10090; SOURCE 8 STRAIN: BALB/C KEYWDS AFAMIN ANTIBODY, FAB FRAGMENT, IGG1-KAPPA, LIGHT CHAIN GLYCOSILATION, KEYWDS 2 IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR B.RUPP,A.NASCHBERGER REVDAT 7 10-JAN-24 5L88 1 HETSYN REVDAT 6 29-JUL-20 5L88 1 COMPND REMARK HETNAM LINK REVDAT 6 2 1 SITE ATOM REVDAT 5 06-SEP-17 5L88 1 REMARK REVDAT 4 21-DEC-16 5L88 1 JRNL REVDAT 3 07-DEC-16 5L88 1 JRNL REVDAT 2 16-NOV-16 5L88 1 REMARK REVDAT 1 03-AUG-16 5L88 0 JRNL AUTH A.NASCHBERGER,B.G.FURNROHR,T.LENAC ROVIS,S.MALIC, JRNL AUTH 2 K.SCHEFFZEK,H.DIEPLINGER,B.RUPP JRNL TITL THE N14 ANTI-AFAMIN ANTIBODY FAB: A RARE VL1 CDR JRNL TITL 2 GLYCOSYLATION, CRYSTALLOGRAPHIC RE-SEQUENCING, MOLECULAR JRNL TITL 3 PLASTICITY AND CONSERVATIVE VERSUS ENTHUSIASTIC MODELLING. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 72 1267 2016 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 27917827 JRNL DOI 10.1107/S205979831601723X REMARK 2 REMARK 2 RESOLUTION. 1.88 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 1.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.38 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 32346 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) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1659 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) : 1.88 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.93 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2299 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.69 REMARK 3 BIN R VALUE (WORKING SET) : 0.3260 REMARK 3 BIN FREE R VALUE SET COUNT : 122 REMARK 3 BIN FREE R VALUE : 0.3250 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3300 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 189 REMARK 3 SOLVENT ATOMS : 252 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.77000 REMARK 3 B22 (A**2) : -0.54000 REMARK 3 B33 (A**2) : -1.23000 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): 0.155 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.140 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.120 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.297 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3691 ; 0.009 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 3384 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4982 ; 1.377 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7923 ; 0.865 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 475 ; 6.436 ; 5.021 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 133 ;37.173 ;24.662 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 579 ;13.579 ;15.043 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;22.755 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 544 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4000 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 771 ; 0.002 ; 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): 1782 ; 2.102 ; 5.574 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1781 ; 2.089 ; 5.565 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2240 ; 3.136 ;10.381 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2241 ; 3.143 ;10.393 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1909 ; 3.171 ; 6.826 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1909 ; 3.169 ; 6.826 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2732 ; 4.647 ;12.077 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4013 ; 6.723 ;27.182 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4014 ; 6.722 ;27.194 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : L 1 L 107 REMARK 3 RESIDUE RANGE : L 301 L 302 REMARK 3 ORIGIN FOR THE GROUP (A): 3.9918 2.1770 22.7118 REMARK 3 T TENSOR REMARK 3 T11: 0.0992 T22: 0.0456 REMARK 3 T33: 0.0326 T12: -0.0208 REMARK 3 T13: -0.0479 T23: 0.0277 REMARK 3 L TENSOR REMARK 3 L11: 0.8754 L22: 0.1890 REMARK 3 L33: 0.6397 L12: 0.0792 REMARK 3 L13: 0.3491 L23: 0.0530 REMARK 3 S TENSOR REMARK 3 S11: 0.0680 S12: 0.0373 S13: -0.0476 REMARK 3 S21: 0.1236 S22: -0.0176 S23: -0.0570 REMARK 3 S31: 0.0428 S32: -0.0498 S33: -0.0503 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 108 L 213 REMARK 3 ORIGIN FOR THE GROUP (A): 23.4069 32.1215 32.3033 REMARK 3 T TENSOR REMARK 3 T11: 0.1024 T22: 0.0692 REMARK 3 T33: 0.0156 T12: 0.0031 REMARK 3 T13: -0.0064 T23: -0.0272 REMARK 3 L TENSOR REMARK 3 L11: 0.0594 L22: 1.2984 REMARK 3 L33: 0.6181 L12: 0.1568 REMARK 3 L13: -0.1233 L23: 0.0211 REMARK 3 S TENSOR REMARK 3 S11: 0.0336 S12: -0.0278 S13: 0.0222 REMARK 3 S21: -0.0154 S22: 0.0378 S23: 0.0254 REMARK 3 S31: 0.0230 S32: 0.0860 S33: -0.0715 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : H 1 H 113 REMARK 3 ORIGIN FOR THE GROUP (A): 6.6444 11.2690 2.2427 REMARK 3 T TENSOR REMARK 3 T11: 0.0383 T22: 0.0932 REMARK 3 T33: 0.0333 T12: 0.0103 REMARK 3 T13: 0.0092 T23: -0.0144 REMARK 3 L TENSOR REMARK 3 L11: 0.0468 L22: 0.5421 REMARK 3 L33: 0.6540 L12: 0.0532 REMARK 3 L13: -0.0557 L23: -0.0005 REMARK 3 S TENSOR REMARK 3 S11: 0.0126 S12: 0.0459 S13: 0.0128 REMARK 3 S21: 0.0138 S22: 0.0198 S23: -0.0481 REMARK 3 S31: 0.0434 S32: -0.0309 S33: -0.0324 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : H 114 H 214 REMARK 3 ORIGIN FOR THE GROUP (A): 29.4670 26.5172 19.2131 REMARK 3 T TENSOR REMARK 3 T11: 0.0700 T22: 0.1159 REMARK 3 T33: 0.0122 T12: 0.0202 REMARK 3 T13: -0.0083 T23: -0.0244 REMARK 3 L TENSOR REMARK 3 L11: 0.4453 L22: 0.0433 REMARK 3 L33: 0.9680 L12: 0.0768 REMARK 3 L13: 0.2065 L23: -0.0662 REMARK 3 S TENSOR REMARK 3 S11: 0.0362 S12: -0.0062 S13: -0.0261 REMARK 3 S21: 0.0164 S22: 0.0217 S23: 0.0002 REMARK 3 S31: -0.0329 S32: 0.1153 S33: -0.0579 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 5L88 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1200000282. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : TORROIDAL FOCUSSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AUTOPROC, SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34249 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.880 REMARK 200 RESOLUTION RANGE LOW (A) : 54.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.88 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.80000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: BALBES REMARK 200 STARTING MODEL: 1IL1 REMARK 200 REMARK 200 REMARK: BLOCK-SHAPED CRYSTALS WITH SHARP EDGES (0.15 X 0.15 X 0.3 REMARK 200 MM) REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200NL FAB 10MG/ML IN 20 MM HEPES PH REMARK 280 7.5, 150 MM NACL PLUS 200NL 30%W/V PEG 1K, 200MM KF, PH 5.8), REMARK 280 VAPOR DIFFUSION, TEMPERATURE 291K 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 33.89100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.90150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.62450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.90150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.89100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.62450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L, A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA H 130 REMARK 465 GLN H 131 REMARK 465 CYS H 215 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TYR H 96 -162.37 -112.51 REMARK 500 THR L 51 -48.16 74.02 REMARK 500 ALA L 84 174.50 179.79 REMARK 500 ASP L 151 48.06 39.45 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 L 519 DISTANCE = 9.37 ANGSTROMS REMARK 525 HOH L 520 DISTANCE = 9.99 ANGSTROMS 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 K H 310 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP H 55 OD1 REMARK 620 2 SER H 71 O 104.8 REMARK 620 3 ASP H 207 O 119.0 15.1 REMARK 620 4 ASP H 207 OD2 119.7 14.9 4.0 REMARK 620 5 HOH H 409 O 123.4 18.7 5.3 3.8 REMARK 620 6 HOH H 466 O 119.6 15.8 0.7 4.5 5.2 REMARK 620 7 HOH H 505 O 116.3 11.7 4.3 3.5 7.1 5.0 REMARK 620 8 HOH H 521 O 120.2 15.5 3.2 1.1 3.2 3.5 3.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5L7X RELATED DB: PDB REMARK 900 DIFFERENT, ALMOST ISOMORPHOUS CRYSTAL FORM DBREF 5L88 H 1 215 PDB 5L88 5L88 1 215 DBREF 5L88 L 1 214 PDB 5L88 5L88 1 214 SEQRES 1 H 220 GLU VAL LYS LEU GLU GLU SER GLY PRO GLU LEU VAL LYS SEQRES 2 H 220 PRO GLY ALA SER MET LYS MET SER CYS LYS ALA SER GLY SEQRES 3 H 220 TYR THR PHE THR SER TYR ILE ILE HIS TRP LEU LYS GLN SEQRES 4 H 220 LYS PRO GLY GLN GLY LEU GLU TRP ILE GLY TYR ILE ASN SEQRES 5 H 220 PRO TYR ASN ASP GLY SER LYS TYR ASN GLU LYS PHE LYS SEQRES 6 H 220 GLY LYS ALA THR LEU THR SER ASP LYS SER SER SER THR SEQRES 7 H 220 ALA TYR MET GLU LEU SER SER LEU ALA SER GLU ASP SER SEQRES 8 H 220 ALA VAL TYR TYR CYS THR ARG ASN TYR GLY SER ASP SER SEQRES 9 H 220 LEU ASP TYR TRP GLY GLN GLY THR THR LEU THR VAL SER SEQRES 10 H 220 SER ALA LYS THR THR PRO PRO SER VAL TYR PRO LEU ALA SEQRES 11 H 220 PRO GLY SER ALA ALA GLN THR ASN SER MET VAL THR LEU SEQRES 12 H 220 GLY CYS LEU VAL LYS GLY TYR PHE PRO GLU PRO VAL THR SEQRES 13 H 220 VAL THR TRP ASN SER GLY SER LEU SER SER GLY VAL HIS SEQRES 14 H 220 THR PHE PRO ALA VAL LEU GLN SER ASP LEU TYR THR LEU SEQRES 15 H 220 SER SER SER VAL THR VAL PRO SER SER THR TRP PRO SER SEQRES 16 H 220 GLU THR VAL THR CYS ASN VAL ALA HIS PRO ALA SER SER SEQRES 17 H 220 THR LYS VAL ASP LYS LYS ILE VAL PRO ARG ASP CYS SEQRES 1 L 215 ASP ILE VAL LEU THR GLN THR PRO ALA ILE MET SER ALA SEQRES 2 L 215 SER LEU GLY GLU ARG VAL THR MET THR CYS THR ALA ASN SEQRES 3 L 215 SER SER VAL SER SER ASN TYR PHE HIS TRP TYR GLN GLN SEQRES 4 L 215 LYS PRO GLY SER SER PRO LYS LEU TRP ILE TYR SER THR SEQRES 5 L 215 SER ASN LEU ALA SER GLY VAL PRO THR ARG PHE SER GLY SEQRES 6 L 215 SER GLY SER GLY THR SER TYR SER LEU THR LEU SER SER SEQRES 7 L 215 MET GLU ALA GLU ASP ALA ALA THR TYR TYR CYS HIS GLN SEQRES 8 L 215 TYR HIS ARG SER PRO PRO THR PHE GLY SER GLY THR LYS SEQRES 9 L 215 LEU LYS MET LYS ARG ALA ASP ALA ALA PRO THR VAL SER SEQRES 10 L 215 ILE PHE PRO PRO SER SER GLU GLN LEU THR SER GLY GLY SEQRES 11 L 215 ALA SER VAL VAL CYS PHE LEU ASN ASN PHE TYR PRO LYS SEQRES 12 L 215 ASP ILE ASN VAL LYS TRP LYS ILE ASP GLY SER GLU ARG SEQRES 13 L 215 GLN ASN GLY VAL LEU ASN SER TRP THR ASP GLN ASP SER SEQRES 14 L 215 LYS ASP SER THR TYR SER MET SER SER THR LEU THR LEU SEQRES 15 L 215 THR LYS ASP GLU TYR GLU ARG HIS ASN SER TYR THR CYS SEQRES 16 L 215 GLU ALA THR HIS LYS THR SER THR SER PRO ILE VAL LYS SEQRES 17 L 215 SER PHE ASN ARG ASN GLU CYS HET NAG A 1 14 HET FUC A 2 10 HET PG4 H 301 13 HET PG4 H 302 13 HET PG4 H 303 13 HET PE8 H 304 25 HET PGE H 305 10 HET PEG H 306 7 HET PEG H 307 7 HET PG4 H 308 13 HET PEG H 309 7 HET K H 310 1 HET PGE H 311 10 HET 1PE L 301 16 HET PGE L 304 10 HET PGE L 305 10 HET PGE L 306 10 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM PE8 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL HETNAM PGE TRIETHYLENE GLYCOL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM K POTASSIUM ION HETNAM 1PE PENTAETHYLENE GLYCOL 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 HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN 1PE PEG400 FORMUL 3 NAG C8 H15 N O6 FORMUL 3 FUC C6 H12 O5 FORMUL 4 PG4 4(C8 H18 O5) FORMUL 7 PE8 C16 H34 O9 FORMUL 8 PGE 5(C6 H14 O4) FORMUL 9 PEG 3(C4 H10 O3) FORMUL 13 K K 1+ FORMUL 15 1PE C10 H22 O6 FORMUL 19 HOH *252(H2 O) HELIX 1 AA1 THR H 28 TYR H 32 5 5 HELIX 2 AA2 GLU H 61 LYS H 64 5 4 HELIX 3 AA3 LYS H 73 SER H 75 5 3 HELIX 4 AA4 ALA H 83 SER H 87 5 5 HELIX 5 AA5 GLY H 97 ASP H 99 5 3 HELIX 6 AA6 PRO H 200 SER H 203 5 4 HELIX 7 AA7 SER L 29 ASN L 31 5 3 HELIX 8 AA8 GLU L 79 ALA L 83 5 5 HELIX 9 AA9 SER L 121 SER L 127 1 7 HELIX 10 AB1 LYS L 183 GLU L 187 1 5 HELIX 11 AB2 ASN L 212 CYS L 214 5 3 SHEET 1 AA1 4 LYS H 3 GLU H 6 0 SHEET 2 AA1 4 MET H 18 SER H 25 -1 O LYS H 23 N GLU H 5 SHEET 3 AA1 4 THR H 77 LEU H 82 -1 O LEU H 82 N MET H 18 SHEET 4 AA1 4 ALA H 67 ASP H 72 -1 N ASP H 72 O THR H 77 SHEET 1 AA2 6 GLU H 10 VAL H 12 0 SHEET 2 AA2 6 THR H 107 VAL H 111 1 O THR H 110 N VAL H 12 SHEET 3 AA2 6 ALA H 88 ASN H 95 -1 N ALA H 88 O LEU H 109 SHEET 4 AA2 6 ILE H 34 GLN H 39 -1 N HIS H 35 O THR H 93 SHEET 5 AA2 6 LEU H 45 ASN H 52 -1 O GLU H 46 N LYS H 38 SHEET 6 AA2 6 GLY H 56 TYR H 59 -1 O GLY H 56 N ASN H 52 SHEET 1 AA3 4 GLU H 10 VAL H 12 0 SHEET 2 AA3 4 THR H 107 VAL H 111 1 O THR H 110 N VAL H 12 SHEET 3 AA3 4 ALA H 88 ASN H 95 -1 N ALA H 88 O LEU H 109 SHEET 4 AA3 4 LEU H 100A TRP H 103 -1 O TYR H 102 N ARG H 94 SHEET 1 AA4 4 SER H 120 LEU H 124 0 SHEET 2 AA4 4 MET H 135 TYR H 145 -1 O LYS H 143 N SER H 120 SHEET 3 AA4 4 LEU H 174 PRO H 184 -1 O LEU H 177 N VAL H 142 SHEET 4 AA4 4 VAL H 163 THR H 165 -1 N HIS H 164 O SER H 180 SHEET 1 AA5 4 SER H 120 LEU H 124 0 SHEET 2 AA5 4 MET H 135 TYR H 145 -1 O LYS H 143 N SER H 120 SHEET 3 AA5 4 LEU H 174 PRO H 184 -1 O LEU H 177 N VAL H 142 SHEET 4 AA5 4 VAL H 169 GLN H 171 -1 N VAL H 169 O THR H 176 SHEET 1 AA6 3 THR H 151 ASN H 155 0 SHEET 2 AA6 3 THR H 194 HIS H 199 -1 O ASN H 196 N THR H 153 SHEET 3 AA6 3 THR H 204 LYS H 209 -1 O LYS H 208 N CYS H 195 SHEET 1 AA7 4 LEU L 4 THR L 7 0 SHEET 2 AA7 4 VAL L 19 ALA L 25 -1 O THR L 24 N THR L 5 SHEET 3 AA7 4 SER L 70 LEU L 75 -1 O LEU L 75 N VAL L 19 SHEET 4 AA7 4 PHE L 62 SER L 67 -1 N SER L 63 O THR L 74 SHEET 1 AA8 6 ILE L 10 ALA L 13 0 SHEET 2 AA8 6 THR L 102 MET L 106 1 O LYS L 105 N MET L 11 SHEET 3 AA8 6 ALA L 84 GLN L 90 -1 N ALA L 84 O LEU L 104 SHEET 4 AA8 6 PHE L 33 GLN L 38 -1 N GLN L 38 O THR L 85 SHEET 5 AA8 6 LYS L 45 TYR L 49 -1 O TRP L 47 N TRP L 35 SHEET 6 AA8 6 ASN L 53 LEU L 54 -1 O ASN L 53 N TYR L 49 SHEET 1 AA9 4 ILE L 10 ALA L 13 0 SHEET 2 AA9 4 THR L 102 MET L 106 1 O LYS L 105 N MET L 11 SHEET 3 AA9 4 ALA L 84 GLN L 90 -1 N ALA L 84 O LEU L 104 SHEET 4 AA9 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 AB1 4 THR L 114 PHE L 118 0 SHEET 2 AB1 4 GLY L 129 PHE L 139 -1 O PHE L 135 N SER L 116 SHEET 3 AB1 4 TYR L 173 THR L 182 -1 O LEU L 179 N VAL L 132 SHEET 4 AB1 4 VAL L 159 TRP L 163 -1 N LEU L 160 O THR L 178 SHEET 1 AB2 4 SER L 153 ARG L 155 0 SHEET 2 AB2 4 ASN L 145 ILE L 150 -1 N ILE L 150 O SER L 153 SHEET 3 AB2 4 SER L 191 THR L 197 -1 O THR L 197 N ASN L 145 SHEET 4 AB2 4 ILE L 205 ASN L 210 -1 O ILE L 205 N ALA L 196 SSBOND 1 CYS H 22 CYS H 92 1555 1555 2.08 SSBOND 2 CYS H 140 CYS H 195 1555 1555 2.04 SSBOND 3 CYS L 23 CYS L 88 1555 1555 2.12 SSBOND 4 CYS L 134 CYS L 194 1555 1555 2.03 LINK ND2 ASN L 26 C1 NAG A 1 1555 1555 1.45 LINK O6 NAG A 1 C1 FUC A 2 1555 1555 1.45 LINK OD1 ASP H 55 K K H 310 1555 4455 2.89 LINK O SER H 71 K K H 310 1555 4455 2.71 LINK O ASP H 207 K K H 310 1555 1555 2.85 LINK OD2 ASP H 207 K K H 310 1555 1555 2.88 LINK K K H 310 O HOH H 409 1555 4555 3.44 LINK K K H 310 O HOH H 466 1555 1555 2.93 LINK K K H 310 O HOH H 505 1555 1555 2.96 LINK K K H 310 O HOH H 521 1555 4555 3.01 CISPEP 1 PHE H 146 PRO H 147 0 -9.29 CISPEP 2 GLU H 148 PRO H 149 0 0.42 CISPEP 3 TRP H 188 PRO H 189 0 6.79 CISPEP 4 THR L 7 PRO L 8 0 -6.37 CISPEP 5 SER L 94 PRO L 95 0 1.24 CISPEP 6 TYR L 140 PRO L 141 0 1.92 CRYST1 67.782 69.249 87.803 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 0.014753 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014441 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011389 0.00000