HEADER IMMUNE SYSTEM, SUGAR BINDING PROTEIN 28-AUG-01 1JV5 TITLE ANTI-BLOOD GROUP A FV COMPND MOL_ID: 1; COMPND 2 MOLECULE: IG KAPPA CHAIN PRECURSOR V REGION; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ANTI-BLOOD GROUP A FV; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: IG CHAIN HEAVY CHAIN PRECURSOR V REGION; COMPND 8 CHAIN: B; COMPND 9 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: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: TG1; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PUCE8; 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: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 EXPRESSION_SYSTEM_STRAIN: TG1; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PUCE8 KEYWDS IMMUNOGLOBULIN, IMMUNE SYSTEM, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.THOMAS,S.I.PATENAUDE,C.R.MACKENZIE,R.TO,T.HIRAMA,N.M.YOUNG, AUTHOR 2 S.V.EVANS REVDAT 5 18-APR-18 1JV5 1 REMARK REVDAT 4 04-OCT-17 1JV5 1 REMARK REVDAT 3 24-FEB-09 1JV5 1 VERSN REVDAT 2 30-JAN-02 1JV5 1 JRNL REVDAT 1 09-JAN-02 1JV5 0 JRNL AUTH R.THOMAS,S.I.PATENAUDE,C.R.MACKENZIE,R.TO,T.HIRAMA, JRNL AUTH 2 N.M.YOUNG,S.V.EVANS JRNL TITL STRUCTURE OF AN ANTI-BLOOD GROUP A FV AND IMPROVEMENT OF ITS JRNL TITL 2 BINDING AFFINITY WITHOUT LOSS OF SPECIFICITY. JRNL REF J.BIOL.CHEM. V. 277 2059 2002 JRNL REFN ISSN 0021-9258 JRNL PMID 11679577 JRNL DOI 10.1074/JBC.M104364200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.I.PATENAUDE,C.R.MACKENZIE,D.BILOUS,R.J.TO,S.E.RYAN, REMARK 1 AUTH 2 N.M.YOUNG,S.V.EVANS REMARK 1 TITL PRODUCTION, CRYSTALLIZATION AND DIFFRACTION TO ATOMIC REMARK 1 TITL 2 RESOLUTION OF AN ANTIBODY FV SPECIFIC FOR THE BLOOD-GROUP A REMARK 1 TITL 3 OLIGOSACCHARIDE ANTIGEN REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 54 1456 1998 REMARK 1 REFN ISSN 0907-4449 REMARK 1 DOI 10.1107/S0907444998005824 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 9440 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1266 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.21 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 71.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2030 REMARK 3 BIN FREE R VALUE : 0.2560 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 59 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1740 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 62 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.412 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1JV5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-AUG-01. REMARK 100 THE DEPOSITION ID IS D_1000014218. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-94 REMARK 200 TEMPERATURE (KELVIN) : 300 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : ENRAF-NONIUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : ENRAF-NONIUS FAST REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ROTAVATA, CAD4 REMARK 200 DATA SCALING SOFTWARE : CCP4 (AGROVATA, ROTAVATA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12350 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.07300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MERLOT REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, HEPES, CALCIUM CHLORIDE, PH REMARK 280 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 300K 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 25.85500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.79000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.98000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.79000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.85500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.98000 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: 1450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 LEU A 47 -62.68 -100.71 REMARK 500 THR A 51 -51.57 74.90 REMARK 500 ALA A 84 -167.38 -171.18 REMARK 500 SER B 325 -96.06 -105.35 REMARK 500 GLU B 362 -6.33 -54.77 REMARK 500 TYR B 400 137.03 -172.77 REMARK 500 REMARK 500 REMARK: NULL DBREF 1JV5 A 1 107 UNP P01594 KV1B_HUMAN 15 121 DBREF 1JV5 B 301 417 GB 90683 E29380 20 136 SEQRES 1 A 107 ASP ILE GLN MET THR GLN THR THR SER SER LEU SER ALA SEQRES 2 A 107 SER LEU GLY ASP ARG VAL THR ILE SER CYS ARG ALA SER SEQRES 3 A 107 GLN ASP ILE ASN ASN TYR LEU ASN TRP TYR GLN GLN LYS SEQRES 4 A 107 PRO ASP GLY THR VAL LYS LEU LEU ILE HIS TYR THR SER SEQRES 5 A 107 ARG LEU HIS SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 A 107 GLY SER GLY THR ASP TYR SER LEU THR ILE SER ASN LEU SEQRES 7 A 107 GLU GLN GLU ASP ILE ALA THR TYR PHE CYS GLN GLN GLY SEQRES 8 A 107 ASN THR LEU PRO TRP THR PHE GLY GLY GLY THR LYS LEU SEQRES 9 A 107 GLU ILE LYS SEQRES 1 B 117 GLN VAL GLN LEU GLN GLN PRO GLY ALA GLU LEU VAL LYS SEQRES 2 B 117 PRO GLY THR SER VAL LYS LEU SER CYS LYS ALA SER GLY SEQRES 3 B 117 TYR ASN PHE THR SER TYR TRP ILE ASN TRP VAL LYS LEU SEQRES 4 B 117 ARG PRO GLY GLN GLY LEU GLU TRP ILE GLY ASP ILE TYR SEQRES 5 B 117 PRO GLY SER GLY ILE THR ASN TYR ASN GLU LYS PHE LYS SEQRES 6 B 117 SER LYS ALA THR LEU THR VAL ASP THR SER SER SER THR SEQRES 7 B 117 ALA TYR MET GLN LEU SER SER LEU ALA SER GLU ASP SER SEQRES 8 B 117 ALA LEU TYR TYR CYS ALA GLY GLN TYR GLY ASN LEU TRP SEQRES 9 B 117 PHE ALA TYR TRP GLY GLN GLY THR LEU VAL THR VAL SER FORMUL 3 HOH *62(H2 O) HELIX 1 2 ASN B 328 TYR B 332 5 5 HELIX 2 3 ALA B 387 SER B 391 5 5 SHEET 1 A 4 MET A 4 THR A 5 0 SHEET 2 A 4 VAL A 19 ALA A 25 -1 O ARG A 24 N THR A 5 SHEET 3 A 4 ASP A 70 ILE A 75 -1 O TYR A 71 N CYS A 23 SHEET 4 A 4 PHE A 62 SER A 67 -1 N SER A 63 O THR A 74 SHEET 1 B 5 ARG A 53 LEU A 54 0 SHEET 2 B 5 VAL A 44 HIS A 49 -1 N HIS A 49 O ARG A 53 SHEET 3 B 5 LEU A 33 GLN A 38 -1 N TRP A 35 O LEU A 47 SHEET 4 B 5 THR A 85 GLN A 90 -1 O PHE A 87 N TYR A 36 SHEET 5 B 5 THR A 97 PHE A 98 -1 O THR A 97 N GLN A 90 SHEET 1 C 6 ARG A 53 LEU A 54 0 SHEET 2 C 6 VAL A 44 HIS A 49 -1 N HIS A 49 O ARG A 53 SHEET 3 C 6 LEU A 33 GLN A 38 -1 N TRP A 35 O LEU A 47 SHEET 4 C 6 THR A 85 GLN A 90 -1 O PHE A 87 N TYR A 36 SHEET 5 C 6 THR A 102 ILE A 106 -1 O THR A 102 N TYR A 86 SHEET 6 C 6 SER A 10 ALA A 13 1 N LEU A 11 O LYS A 103 SHEET 1 D 4 LEU B 304 GLN B 305 0 SHEET 2 D 4 VAL B 318 ALA B 324 -1 O LYS B 323 N GLN B 305 SHEET 3 D 4 THR B 378 LEU B 383 -1 O ALA B 379 N CYS B 322 SHEET 4 D 4 ALA B 368 ASP B 373 -1 N THR B 371 O TYR B 380 SHEET 1 E 5 LEU B 403 TRP B 408 0 SHEET 2 E 5 ALA B 392 TYR B 400 -1 N GLY B 398 O TYR B 407 SHEET 3 E 5 ILE B 334 LEU B 339 -1 N ASN B 335 O ALA B 397 SHEET 4 E 5 LEU B 345 ILE B 351 -1 O ILE B 348 N TRP B 336 SHEET 5 E 5 THR B 358 TYR B 360 -1 O ASN B 359 N ASP B 350 SHEET 1 F 4 LEU B 403 TRP B 408 0 SHEET 2 F 4 ALA B 392 TYR B 400 -1 N GLY B 398 O TYR B 407 SHEET 3 F 4 THR B 412 VAL B 416 -1 O VAL B 414 N ALA B 392 SHEET 4 F 4 ALA B 309 VAL B 312 1 N VAL B 312 O THR B 415 SSBOND 1 CYS A 23 CYS A 88 1555 1555 2.03 SSBOND 2 CYS B 322 CYS B 396 1555 1555 2.03 CISPEP 1 LEU A 94 PRO A 95 0 0.02 CRYST1 51.710 57.960 83.580 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 0.019339 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017253 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011965 0.00000