HEADER CELL ADHESION 09-DEC-15 5F9D TITLE BLOOD GROUP ANTIGEN BINDING ADHESIN BABA OF HELICOBACTER PYLORI STRAIN TITLE 2 P436 IN COMPLEX WITH LEWIS B BLOOD GROUP B HEPTASACCHARIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADHESIN BINDING FUCOSYLATED HISTO-BLOOD GROUP ANTIGEN, COMPND 3 ADHESIN,ADHESIN BINDING FUCOSYLATED HISTO-BLOOD GROUP ANTIGEN; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: IN THIS HYBRID CONSTRUCT THE INSERTION DOMAIN OF THE COMPND 7 PERUVIAN STRAIN P436 (RESIDUES 179 TO 258, RESPONSIBLE FOR COMPND 8 CARBOHYDRATE BINDING) WAS GRAFTED INTO THE FRAMEWORK OF THE COMPND 9 GENERALIST STRAIN 17875; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: NANOBODY NB-ER19; COMPND 12 CHAIN: C; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 210; SOURCE 4 GENE: BABA2, BABA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: TOP10; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 10 ORGANISM_COMMON: LLAMA; SOURCE 11 ORGANISM_TAXID: 9844; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 14 EXPRESSION_SYSTEM_VARIANT: WK6 KEYWDS ADHESIN, LECTIN, NANOBODY, COMPLEX, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR K.MOONENS,P.GIDEONSSON,S.SUBEDI,E.ROMAO,S.OSCARSON,S.MUYLDERMANS, AUTHOR 2 T.BOREN,H.REMAUT REVDAT 4 10-JAN-24 5F9D 1 HETSYN LINK REVDAT 3 29-JUL-20 5F9D 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 27-JAN-16 5F9D 1 JRNL REVDAT 1 20-JAN-16 5F9D 0 JRNL AUTH K.MOONENS,P.GIDEONSSON,S.SUBEDI,J.BUGAYTSOVA,E.ROMAO, JRNL AUTH 2 M.MENDEZ,J.NORDEN,M.FALLAH,L.RAKHIMOVA,A.SHEVTSOVA, JRNL AUTH 3 M.LAHMANN,G.CASTALDO,K.BRANNSTROM,F.COPPENS,A.W.LO,T.NY, JRNL AUTH 4 J.V.SOLNICK,G.VANDENBUSSCHE,S.OSCARSON,L.HAMMARSTROM, JRNL AUTH 5 A.ARNQVIST,D.E.BERG,S.MUYLDERMANS,T.BOREN,H.REMAUT JRNL TITL STRUCTURAL INSIGHTS INTO POLYMORPHIC ABO GLYCAN BINDING BY JRNL TITL 2 HELICOBACTER PYLORI. JRNL REF CELL HOST MICROBE V. 19 55 2016 JRNL REFN ESSN 1934-6069 JRNL PMID 26764597 JRNL DOI 10.1016/J.CHOM.2015.12.004 REMARK 2 REMARK 2 RESOLUTION. 2.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 2.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 73.15 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 30496 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1584 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) : 2.59 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2257 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.24 REMARK 3 BIN R VALUE (WORKING SET) : 0.4080 REMARK 3 BIN FREE R VALUE SET COUNT : 107 REMARK 3 BIN FREE R VALUE : 0.3910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3967 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 79 REMARK 3 SOLVENT ATOMS : 18 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 70.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.03000 REMARK 3 B22 (A**2) : -0.15000 REMARK 3 B33 (A**2) : -1.88000 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): 0.275 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.225 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.188 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 20.221 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4134 ; 0.016 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 3808 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5636 ; 1.792 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8745 ; 0.877 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 529 ; 6.281 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 179 ;39.693 ;25.978 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 639 ;17.314 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;21.209 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 659 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4790 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 937 ; 0.001 ; 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): 2122 ; 4.457 ; 5.491 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2121 ; 4.458 ; 5.489 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2646 ; 6.542 ; 8.223 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2647 ; 6.542 ; 8.225 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2012 ; 6.042 ; 6.322 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2013 ; 6.040 ; 6.324 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2990 ; 8.838 ; 9.263 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4311 ;10.145 ;44.251 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4312 ;10.146 ;44.261 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 : 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 : A 34 A 460 REMARK 3 ORIGIN FOR THE GROUP (A): -14.6683 -26.0860 11.5507 REMARK 3 T TENSOR REMARK 3 T11: 0.0632 T22: 0.1630 REMARK 3 T33: 0.0144 T12: 0.0650 REMARK 3 T13: 0.0061 T23: 0.0352 REMARK 3 L TENSOR REMARK 3 L11: 0.1516 L22: 1.3250 REMARK 3 L33: 0.7442 L12: -0.2245 REMARK 3 L13: -0.2396 L23: 0.8401 REMARK 3 S TENSOR REMARK 3 S11: 0.0600 S12: 0.0697 S13: -0.0017 REMARK 3 S21: -0.1665 S22: -0.0681 S23: -0.0148 REMARK 3 S31: -0.1862 S32: -0.1157 S33: 0.0082 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 : C 3 C 116 REMARK 3 ORIGIN FOR THE GROUP (A): -21.6727 -47.3443 -15.0324 REMARK 3 T TENSOR REMARK 3 T11: 0.0903 T22: 0.2391 REMARK 3 T33: 0.0416 T12: 0.0688 REMARK 3 T13: -0.0392 T23: -0.0128 REMARK 3 L TENSOR REMARK 3 L11: 0.9585 L22: 2.0036 REMARK 3 L33: 1.7734 L12: -0.0696 REMARK 3 L13: -0.1314 L23: 1.7809 REMARK 3 S TENSOR REMARK 3 S11: -0.0368 S12: 0.0162 S13: -0.0946 REMARK 3 S21: -0.2710 S22: -0.1705 S23: 0.1552 REMARK 3 S31: -0.2853 S32: -0.1166 S33: 0.2073 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 5F9D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1000216230. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-SEP-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32091 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.590 REMARK 200 RESOLUTION RANGE LOW (A) : 73.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 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: 5F7K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 M SODIUM ACETATE, 100 MM IMIDAZOLE REMARK 280 PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 63.66500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.66500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 59.59000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 67.54500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 59.59000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 67.54500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 63.66500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 59.59000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 67.54500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 63.66500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 59.59000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 67.54500 REMARK 290 SMTRY3 8 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: 4040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 22.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, B 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 A 3 REMARK 465 SER A 4 REMARK 465 TRP A 5 REMARK 465 SER A 6 REMARK 465 HIS A 7 REMARK 465 PRO A 8 REMARK 465 GLN A 9 REMARK 465 PHE A 10 REMARK 465 GLU A 11 REMARK 465 LYS A 12 REMARK 465 SER A 13 REMARK 465 GLY A 14 REMARK 465 GLY A 15 REMARK 465 GLY A 16 REMARK 465 GLY A 17 REMARK 465 GLY A 18 REMARK 465 LEU A 19 REMARK 465 VAL A 20 REMARK 465 PRO A 21 REMARK 465 ARG A 22 REMARK 465 GLY A 23 REMARK 465 SER A 24 REMARK 465 GLY A 25 REMARK 465 ILE A 26 REMARK 465 GLN A 27 REMARK 465 ASP A 28 REMARK 465 LEU A 29 REMARK 465 SER A 30 REMARK 465 ASP A 31 REMARK 465 ASN A 32 REMARK 465 TYR A 33 REMARK 465 LYS A 282 REMARK 465 SER A 283 REMARK 465 THR A 397 REMARK 465 ALA A 398 REMARK 465 GLY A 399 REMARK 465 THR A 400 REMARK 465 SER A 401 REMARK 465 GLY A 402 REMARK 465 THR A 403 REMARK 465 GLN A 404 REMARK 465 HIS A 461 REMARK 465 HIS A 462 REMARK 465 HIS A 463 REMARK 465 HIS A 464 REMARK 465 HIS A 465 REMARK 465 GLN C 2 REMARK 465 HIS C 117 REMARK 465 HIS C 118 REMARK 465 HIS C 119 REMARK 465 HIS C 120 REMARK 465 HIS C 121 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 CYS C 96 CA - CB - SG ANGL. DEV. = 9.7 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 TYR A 43 78.05 -118.91 REMARK 500 THR A 77 -77.31 -121.21 REMARK 500 SER A 117 65.68 -152.24 REMARK 500 SER A 136 22.04 -142.03 REMARK 500 LEU A 137 99.36 -66.03 REMARK 500 ARG A 139 -47.72 81.52 REMARK 500 TYR A 145 31.84 37.67 REMARK 500 ASP A 207 -179.75 -59.97 REMARK 500 SER A 239 169.69 158.29 REMARK 500 PHE A 388 -59.99 -134.24 REMARK 500 ALA A 390 31.56 -95.45 REMARK 500 CYS A 420 42.90 39.32 REMARK 500 ALA C 92 169.69 172.40 REMARK 500 REMARK 500 REMARK: NULL DBREF 5F9D A 25 180 UNP O52269 O52269_HELPX 45 200 DBREF 5F9D A 181 260 UNP Q6DT10 Q6DT10_HELPX 50 129 DBREF 5F9D A 261 457 UNP O52269 O52269_HELPX 284 480 DBREF 5F9D C 2 121 PDB 5F9D 5F9D 2 121 SEQADV 5F9D ALA A 3 UNP O52269 EXPRESSION TAG SEQADV 5F9D SER A 4 UNP O52269 EXPRESSION TAG SEQADV 5F9D TRP A 5 UNP O52269 EXPRESSION TAG SEQADV 5F9D SER A 6 UNP O52269 EXPRESSION TAG SEQADV 5F9D HIS A 7 UNP O52269 EXPRESSION TAG SEQADV 5F9D PRO A 8 UNP O52269 EXPRESSION TAG SEQADV 5F9D GLN A 9 UNP O52269 EXPRESSION TAG SEQADV 5F9D PHE A 10 UNP O52269 EXPRESSION TAG SEQADV 5F9D GLU A 11 UNP O52269 EXPRESSION TAG SEQADV 5F9D LYS A 12 UNP O52269 EXPRESSION TAG SEQADV 5F9D SER A 13 UNP O52269 EXPRESSION TAG SEQADV 5F9D GLY A 14 UNP O52269 EXPRESSION TAG SEQADV 5F9D GLY A 15 UNP O52269 EXPRESSION TAG SEQADV 5F9D GLY A 16 UNP O52269 EXPRESSION TAG SEQADV 5F9D GLY A 17 UNP O52269 EXPRESSION TAG SEQADV 5F9D GLY A 18 UNP O52269 EXPRESSION TAG SEQADV 5F9D LEU A 19 UNP O52269 EXPRESSION TAG SEQADV 5F9D VAL A 20 UNP O52269 EXPRESSION TAG SEQADV 5F9D PRO A 21 UNP O52269 EXPRESSION TAG SEQADV 5F9D ARG A 22 UNP O52269 EXPRESSION TAG SEQADV 5F9D GLY A 23 UNP O52269 EXPRESSION TAG SEQADV 5F9D SER A 24 UNP O52269 EXPRESSION TAG SEQADV 5F9D SER A 255 UNP Q6DT10 ASN 124 CONFLICT SEQADV 5F9D GLY A 458 UNP O52269 EXPRESSION TAG SEQADV 5F9D SER A 459 UNP O52269 EXPRESSION TAG SEQADV 5F9D HIS A 460 UNP O52269 EXPRESSION TAG SEQADV 5F9D HIS A 461 UNP O52269 EXPRESSION TAG SEQADV 5F9D HIS A 462 UNP O52269 EXPRESSION TAG SEQADV 5F9D HIS A 463 UNP O52269 EXPRESSION TAG SEQADV 5F9D HIS A 464 UNP O52269 EXPRESSION TAG SEQADV 5F9D HIS A 465 UNP O52269 EXPRESSION TAG SEQRES 1 A 463 ALA SER TRP SER HIS PRO GLN PHE GLU LYS SER GLY GLY SEQRES 2 A 463 GLY GLY GLY LEU VAL PRO ARG GLY SER GLY ILE GLN ASP SEQRES 3 A 463 LEU SER ASP ASN TYR GLU ASN LEU SER LYS LEU LEU THR SEQRES 4 A 463 ARG TYR SER THR LEU ASN THR LEU ILE LYS LEU SER ALA SEQRES 5 A 463 ASP PRO SER ALA ILE ASN ALA ALA ARG GLU ASN LEU GLY SEQRES 6 A 463 ALA SER ALA LYS ASN LEU ILE GLY ASP THR LYS ASN SER SEQRES 7 A 463 PRO ALA TYR GLN ALA VAL LEU LEU ALA ILE ASN ALA ALA SEQRES 8 A 463 VAL GLY PHE TRP ASN VAL LEU GLY TYR ALA THR GLN CYS SEQRES 9 A 463 GLY GLY ASN ALA ASN GLY GLN GLU SER THR SER SER THR SEQRES 10 A 463 THR ILE PHE ASN ASN GLU PRO GLY TYR ARG SER THR SER SEQRES 11 A 463 ILE THR CYS SER LEU ASN ARG TYR LYS PRO GLY TYR TYR SEQRES 12 A 463 GLY PRO MET SER ILE GLU ASN PHE LYS LYS LEU ASN GLU SEQRES 13 A 463 ALA TYR GLN ILE LEU GLN THR ALA LEU ASN LYS GLY LEU SEQRES 14 A 463 PRO ALA LEU LYS GLU ASN ASN GLY THR ILE ASN VAL GLU SEQRES 15 A 463 TYR THR TYR THR CYS SER GLY GLY GLY ASN THR ASN CYS SEQRES 16 A 463 ASP PRO SER LEU PHE GLY ILE GLY GLY ASP GLY ARG ASN SEQRES 17 A 463 GLY GLY SER VAL THR LYS THR GLN THR ILE ASP GLY LYS SEQRES 18 A 463 GLN VAL ASN THR THR ILE SER SER LYS VAL VAL GLN PRO SEQRES 19 A 463 PRO HIS SER ALA ALA TYR THR GLU ILE THR ASN ALA LEU SEQRES 20 A 463 ASN GLY VAL PRO ASP SER ALA GLN ALA LEU LEU ALA GLN SEQRES 21 A 463 ALA SER THR LEU ILE ASN THR ILE ASN THR ALA CYS PRO SEQRES 22 A 463 TYR PHE SER VAL THR ASN LYS SER GLY GLY PRO GLN MET SEQRES 23 A 463 GLU PRO THR ARG GLY LYS LEU CYS GLY PHE THR GLU GLU SEQRES 24 A 463 ILE SER ALA ILE GLN LYS MET ILE THR ASP ALA GLN GLU SEQRES 25 A 463 LEU VAL ASN GLN THR SER VAL ILE ASN GLU HIS GLU GLN SEQRES 26 A 463 SER THR PRO VAL GLY GLY ASN ASN GLY LYS PRO PHE ASN SEQRES 27 A 463 PRO PHE THR ASP ALA SER PHE ALA GLN GLY MET LEU ALA SEQRES 28 A 463 ASN ALA SER ALA GLN ALA LYS MET LEU ASN LEU ALA HIS SEQRES 29 A 463 GLN VAL GLY GLN THR ILE ASN PRO ASP ASN LEU THR GLY SEQRES 30 A 463 THR PHE LYS ASN PHE VAL THR GLY PHE LEU ALA THR CYS SEQRES 31 A 463 ASN ASN LYS SER THR ALA GLY THR SER GLY THR GLN GLY SEQRES 32 A 463 SER PRO PRO GLY THR VAL THR THR GLN THR PHE ALA SER SEQRES 33 A 463 GLY CYS ALA TYR VAL GLU GLN THR ILE THR ASN LEU ASN SEQRES 34 A 463 ASN SER ILE ALA HIS PHE GLY THR GLN GLU GLN GLN ILE SEQRES 35 A 463 GLN GLN ALA GLU ASN ILE ALA ASP THR LEU VAL ASN PHE SEQRES 36 A 463 GLY SER HIS HIS HIS HIS HIS HIS SEQRES 1 C 120 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 C 120 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 C 120 SER ILE PHE SER GLY ASN VAL MET GLY TRP TYR ARG GLN SEQRES 4 C 120 ALA PRO GLY LYS LEU ARG GLU TRP VAL ALA ALA ILE THR SEQRES 5 C 120 PRO GLN GLY VAL PRO ASN TYR ALA ASP SER VAL LYS GLY SEQRES 6 C 120 ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN MET LEU SEQRES 7 C 120 TYR LEU GLN MET SER SER LEU LYS PRO GLU ASP THR ALA SEQRES 8 C 120 LEU TYR TYR CYS ASN ARG LEU PRO ASN TYR ARG SER TRP SEQRES 9 C 120 GLY GLN GLY THR GLN VAL THR VAL SER SER HIS HIS HIS SEQRES 10 C 120 HIS HIS HIS MODRES 5F9D GAL B 2 GAL -D MODRES 5F9D NAG B 3 NAG -D MODRES 5F9D GAL B 4 GAL -D MODRES 5F9D FUC B 5 FUC -L MODRES 5F9D FUC B 7 FUC -L HET BGC B 1 12 HET GAL B 2 11 HET NAG B 3 14 HET GAL B 4 11 HET FUC B 5 10 HET GLA B 6 11 HET FUC B 7 10 HETNAM BGC BETA-D-GLUCOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM GLA ALPHA-D-GALACTOPYRANOSE HETSYN BGC BETA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE 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 GLA ALPHA-D-GALACTOSE; D-GALACTOSE; GALACTOSE; ALPHA D- HETSYN 2 GLA GALACTOSE FORMUL 3 BGC C6 H12 O6 FORMUL 3 GAL 2(C6 H12 O6) FORMUL 3 NAG C8 H15 N O6 FORMUL 3 FUC 2(C6 H12 O5) FORMUL 3 GLA C6 H12 O6 FORMUL 4 HOH *18(H2 O) HELIX 1 AA1 ASN A 35 TYR A 43 1 9 HELIX 2 AA2 TYR A 43 ALA A 54 1 12 HELIX 3 AA3 ASP A 55 ASP A 76 1 22 HELIX 4 AA4 SER A 80 GLY A 101 1 22 HELIX 5 AA5 TYR A 102 THR A 104 5 3 HELIX 6 AA6 SER A 149 GLY A 170 1 22 HELIX 7 AA7 ASP A 198 GLY A 203 5 6 HELIX 8 AA8 SER A 255 CYS A 274 1 20 HELIX 9 AA9 PHE A 298 ASN A 317 1 20 HELIX 10 AB1 ASN A 317 GLU A 324 1 8 HELIX 11 AB2 PHE A 347 ASN A 373 1 27 HELIX 12 AB3 PRO A 374 LEU A 377 5 4 HELIX 13 AB4 THR A 378 PHE A 388 1 11 HELIX 14 AB5 TYR A 422 HIS A 436 1 15 HELIX 15 AB6 PHE A 437 GLY A 458 1 22 HELIX 16 AB7 SER C 26 SER C 31 1 6 HELIX 17 AB8 LYS C 87 THR C 91 5 5 SHEET 1 AA1 6 SER A 130 CYS A 135 0 SHEET 2 AA1 6 THR A 119 GLY A 127 -1 N PHE A 122 O ILE A 133 SHEET 3 AA1 6 THR A 180 SER A 190 -1 O SER A 190 N THR A 119 SHEET 4 AA1 6 TYR A 242 PRO A 253 -1 O LEU A 249 N VAL A 183 SHEET 5 AA1 6 LYS A 223 VAL A 234 -1 N ASN A 226 O ASN A 250 SHEET 6 AA1 6 SER A 213 ILE A 220 -1 N GLN A 218 O VAL A 225 SHEET 1 AA2 2 TYR A 276 SER A 278 0 SHEET 2 AA2 2 ARG A 292 LYS A 294 -1 O GLY A 293 N PHE A 277 SHEET 1 AA3 4 LEU C 5 SER C 8 0 SHEET 2 AA3 4 LEU C 19 ALA C 25 -1 O ALA C 24 N GLN C 6 SHEET 3 AA3 4 MET C 78 MET C 83 -1 O MET C 83 N LEU C 19 SHEET 4 AA3 4 PHE C 68 ASP C 73 -1 N SER C 71 O TYR C 80 SHEET 1 AA4 6 LEU C 12 VAL C 13 0 SHEET 2 AA4 6 THR C 109 VAL C 113 1 O THR C 112 N VAL C 13 SHEET 3 AA4 6 ALA C 92 LEU C 99 -1 N TYR C 94 O THR C 109 SHEET 4 AA4 6 VAL C 34 GLN C 40 -1 N TYR C 38 O TYR C 95 SHEET 5 AA4 6 GLU C 47 ILE C 52 -1 O GLU C 47 N ARG C 39 SHEET 6 AA4 6 PRO C 58 TYR C 60 -1 O ASN C 59 N ALA C 51 SSBOND 1 CYS A 106 CYS A 135 1555 1555 2.11 SSBOND 2 CYS A 189 CYS A 197 1555 1555 2.04 SSBOND 3 CYS A 274 CYS A 296 1555 1555 2.12 SSBOND 4 CYS A 392 CYS A 420 1555 1555 2.21 SSBOND 5 CYS C 23 CYS C 96 1555 1555 2.08 LINK O4 BGC B 1 C1 GAL B 2 1555 1555 1.44 LINK O3 GAL B 2 C1 NAG B 3 1555 1555 1.45 LINK O3 NAG B 3 C1 GAL B 4 1555 1555 1.46 LINK O4 NAG B 3 C1 FUC B 7 1555 1555 1.46 LINK O2 GAL B 4 C1 FUC B 5 1555 1555 1.48 LINK O3 GAL B 4 C1 GLA B 6 1555 1555 1.47 CISPEP 1 GLU A 289 PRO A 290 0 -4.05 CISPEP 2 LEU C 99 PRO C 100 0 -15.78 CRYST1 119.180 135.090 127.330 90.00 90.00 90.00 C 2 2 21 8 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 0.008391 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007402 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007854 0.00000