HEADER IMMUNE SYSTEM 25-FEB-99 1QAC TITLE CHANGE IN DIMERIZATION MODE BY REMOVAL OF A SINGLE UNSATISFIED POLAR TITLE 2 RESIDUE COMPND MOL_ID: 1; COMPND 2 MOLECULE: IMMUNOGLOBULIN LIGHT CHAIN VARIABLE DOMAIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: VARIABLE DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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 KEYWDS BETA BARREL IMMUNOGLOBULIN VL DOMAIN DIMER, FLIPPED DOMAIN DIMER, KEYWDS 2 IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR P.R.POKKULURI,X.CAI,G.JOHNSON,F.J.STEVENS,M.SCHIFFER REVDAT 6 16-AUG-23 1QAC 1 REMARK REVDAT 5 04-OCT-17 1QAC 1 REMARK REVDAT 4 24-FEB-09 1QAC 1 VERSN REVDAT 3 01-APR-03 1QAC 1 JRNL REVDAT 2 28-MAR-01 1QAC 1 JRNL REMARK REVDAT 1 23-FEB-00 1QAC 0 JRNL AUTH P.R.POKKULURI,X.CAI,G.JOHNSON,F.J.STEVENS,M.SCHIFFER JRNL TITL CHANGE IN DIMERIZATION MODE BY REMOVAL OF A SINGLE JRNL TITL 2 UNSATISFIED POLAR RESIDUE LOCATED AT THE INTERFACE. JRNL REF PROTEIN SCI. V. 9 1852 2000 JRNL REFN ISSN 0961-8368 JRNL PMID 11045631 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.R.POKKULURI,D.-B.HUANG,R.RAFFEN,X.CAI,G.JOHNSON, REMARK 1 AUTH 2 P.WILKINS STEVENS,F.J.STEVENS,M.SCHIFFER REMARK 1 TITL A DOMAIN FLIP AS A RESULT OF A SINGLE AMINO-ACID REMARK 1 TITL 2 SUBSTITUTION. REMARK 1 REF STRUCTURE V. 6 1067 1998 REMARK 1 REFN ISSN 0969-2126 REMARK 1 DOI 10.1016/S0969-2126(98)00107-5 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.3 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.3 REMARK 3 NUMBER OF REFLECTIONS : 19236 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1925 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 18 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.83 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 69.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 748 REMARK 3 BIN R VALUE (WORKING SET) : 0.2020 REMARK 3 BIN FREE R VALUE : 0.2580 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 86 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.028 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1763 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 305 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.42000 REMARK 3 B22 (A**2) : 1.04000 REMARK 3 B33 (A**2) : 4.38000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.26000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.07 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.14 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.750 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.690 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.160 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.040 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.520 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT REMARK 3 KSOL : 0.46 REMARK 3 BSOL : 65.10 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 : PROTEIN_REP.PA REMARK 3 PARAMETER FILE 2 : WATER_REP.PARA REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 CONJUGATE-GRADIENT MINIMIZATION. MAXIMUM LIKELIHOOD BASED ON REMARK 3 AMPLITUDES TARGET REMARK 3 USED REMARK 4 REMARK 4 1QAC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-FEB-99. REMARK 100 THE DEPOSITION ID IS D_1000009005. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-NOV-98 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SOFTWARE AT APS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21776 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 8.600 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 9.20 REMARK 200 R MERGE FOR SHELL (I) : 0.17200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 3LVE WITH GLU-38 AND GLN-89 CHANGED TO ALA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 8000, 0.2M AMMONIUM SULPHATE REMARK 280 AT 4 DEG C, VAPOR DIFFUSION, TEMPERATURE 277K 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 41.80000 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: 1470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10640 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 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 GLU B 317 CG CD OE1 OE2 REMARK 470 SER B 377 OG REMARK 470 GLN B 400 CG CD OE1 NE2 REMARK 470 LYS B 403 CG CD CE NZ REMARK 470 LYS B 407 CG CD CE NZ 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 ALA A 51 -35.84 72.22 REMARK 500 SER A 77 70.18 45.59 REMARK 500 ALA A 84 -176.60 -179.87 REMARK 500 ALA B 351 -37.95 66.99 REMARK 500 REMARK 500 REMARK: NULL DBREF 1QAC A 1 108 PDB 1QAC 1QAC 1 108 DBREF 1QAC B 301 408 PDB 1QAC 1QAC 301 408 SEQRES 1 A 114 ASP ILE VAL MET THR GLN SER PRO ASP SER LEU ALA VAL SEQRES 2 A 114 SER LEU GLY GLU ARG ALA THR ILE ASN CYS LYS SER SER SEQRES 3 A 114 GLN SER VAL LEU TYR SER SER ASN SER LYS ASN TYR LEU SEQRES 4 A 114 ALA TRP TYR GLN GLN LYS PRO GLY GLN PRO PRO LYS LEU SEQRES 5 A 114 LEU ILE TYR TRP ALA SER THR ARG GLU SER GLY VAL PRO SEQRES 6 A 114 ASP ARG PHE SER GLY SER GLY SER GLY THR ASP PHE THR SEQRES 7 A 114 LEU THR ILE SER SER LEU GLN ALA GLU ASP VAL ALA VAL SEQRES 8 A 114 TYR TYR CYS LEU GLN TYR TYR SER THR PRO TYR SER PHE SEQRES 9 A 114 GLY GLN GLY THR LYS LEU GLU ILE LYS ARG SEQRES 1 B 114 ASP ILE VAL MET THR GLN SER PRO ASP SER LEU ALA VAL SEQRES 2 B 114 SER LEU GLY GLU ARG ALA THR ILE ASN CYS LYS SER SER SEQRES 3 B 114 GLN SER VAL LEU TYR SER SER ASN SER LYS ASN TYR LEU SEQRES 4 B 114 ALA TRP TYR GLN GLN LYS PRO GLY GLN PRO PRO LYS LEU SEQRES 5 B 114 LEU ILE TYR TRP ALA SER THR ARG GLU SER GLY VAL PRO SEQRES 6 B 114 ASP ARG PHE SER GLY SER GLY SER GLY THR ASP PHE THR SEQRES 7 B 114 LEU THR ILE SER SER LEU GLN ALA GLU ASP VAL ALA VAL SEQRES 8 B 114 TYR TYR CYS LEU GLN TYR TYR SER THR PRO TYR SER PHE SEQRES 9 B 114 GLY GLN GLY THR LYS LEU GLU ILE LYS ARG FORMUL 3 HOH *305(H2 O) HELIX 1 1 ALA A 80 ASP A 82 5 3 HELIX 2 2 ALA B 380 ASP B 382 5 3 SHEET 1 A 4 MET A 4 SER A 7 0 SHEET 2 A 4 ALA A 19 SER A 25 -1 N ASN A 22 O SER A 7 SHEET 3 A 4 ASP A 70 ILE A 75 -1 N PHE A 71 O CYS A 23 SHEET 4 A 4 PHE A 62 SER A 67 -1 O SER A 63 N THR A 74 SHEET 1 B 5 THR A 53 ARG A 54 0 SHEET 2 B 5 LYS A 45 TYR A 49 -1 O TYR A 49 N THR A 53 SHEET 3 B 5 LEU A 33 GLN A 38 -1 O TRP A 35 N LEU A 47 SHEET 4 B 5 ALA A 84 GLN A 90 -1 O VAL A 85 N GLN A 38 SHEET 5 B 5 SER A 97 PHE A 98 -1 O SER A 97 N GLN A 90 SHEET 1 C 6 THR A 53 ARG A 54 0 SHEET 2 C 6 LYS A 45 TYR A 49 -1 O TYR A 49 N THR A 53 SHEET 3 C 6 LEU A 33 GLN A 38 -1 O TRP A 35 N LEU A 47 SHEET 4 C 6 ALA A 84 GLN A 90 -1 O VAL A 85 N GLN A 38 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 VAL A 13 1 N LEU A 11 O LYS A 103 SHEET 1 D 2 LEU A 27C TYR A 27D 0 SHEET 2 D 2 LYS A 30 ASN A 31 -1 O LYS A 30 N TYR A 27D SHEET 1 E 4 MET B 304 SER B 307 0 SHEET 2 E 4 ALA B 319 SER B 325 -1 N ASN B 322 O SER B 307 SHEET 3 E 4 ASP B 370 ILE B 375 -1 N PHE B 371 O CYS B 323 SHEET 4 E 4 PHE B 362 SER B 365 -1 O SER B 363 N THR B 374 SHEET 1 F 5 THR B 353 ARG B 354 0 SHEET 2 F 5 LYS B 345 TYR B 349 -1 N TYR B 349 O THR B 353 SHEET 3 F 5 LEU B 333 GLN B 338 -1 O TRP B 335 N LEU B 347 SHEET 4 F 5 VAL B 385 GLN B 390 -1 O VAL B 385 N GLN B 338 SHEET 5 F 5 SER B 397 PHE B 398 -1 O SER B 397 N GLN B 390 SHEET 1 G 6 THR B 353 ARG B 354 0 SHEET 2 G 6 LYS B 345 TYR B 349 -1 N TYR B 349 O THR B 353 SHEET 3 G 6 LEU B 333 GLN B 338 -1 O TRP B 335 N LEU B 347 SHEET 4 G 6 VAL B 385 GLN B 390 -1 O VAL B 385 N GLN B 338 SHEET 5 G 6 THR B 402 ILE B 406 -1 O THR B 402 N TYR B 386 SHEET 6 G 6 SER B 310 VAL B 313 1 N LEU B 311 O LYS B 403 SHEET 1 H 2 LEU B 327C TYR B 327D 0 SHEET 2 H 2 LYS B 330 ASN B 331 -1 O LYS B 330 N TYR B 327D SSBOND 1 CYS A 23 CYS A 88 1555 1555 2.04 SSBOND 2 CYS B 323 CYS B 388 1555 1555 2.04 CISPEP 1 SER A 7 PRO A 8 0 -0.09 CISPEP 2 THR A 94 PRO A 95 0 -0.15 CISPEP 3 SER B 307 PRO B 308 0 -0.41 CISPEP 4 THR B 394 PRO B 395 0 -0.12 CRYST1 35.300 83.600 42.800 90.00 109.00 90.00 P 1 21 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 0.028329 0.000000 0.009754 0.00000 SCALE2 0.000000 0.011962 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024711 0.00000