HEADER IMMUNE SYSTEM 06-AUG-99 1CQK TITLE CRYSTAL STRUCTURE OF THE CH3 DOMAIN FROM THE MAK33 ANTIBODY COMPND MOL_ID: 1; COMPND 2 MOLECULE: CH3 DOMAIN OF MAK33 ANTIBODY; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CH3 DOMAIN OF MAK33 ANTIBODY; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CONSTANT DOMAIN, C1-SUBSET, IMMUNOGLOBULIN, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR M.J.THIES,J.MAYER,J.G.AUGUSTINE,C.A.FREDERICK,H.LILIE,J.BUCHNER REVDAT 8 16-OCT-24 1CQK 1 REMARK SEQADV REVDAT 7 29-AUG-18 1CQK 1 COMPND SOURCE REMARK REVDAT 6 14-MAR-18 1CQK 1 SEQADV REVDAT 5 31-JAN-18 1CQK 1 REMARK REVDAT 4 24-FEB-09 1CQK 1 VERSN REVDAT 3 29-MAR-05 1CQK 1 COMPND AUTHOR JRNL REMARK REVDAT 3 2 1 CRYST1 MASTER REVDAT 2 11-SEP-99 1CQK 1 REMARK REVDAT 1 11-SEP-99 1CQK 0 JRNL AUTH M.J.THIES,J.MAYER,J.G.AUGUSTINE,C.A.FREDERICK,H.LILIE, JRNL AUTH 2 J.BUCHNER JRNL TITL FOLDING AND ASSOCIATION OF THE ANTIBODY DOMAIN CH3: PROLYL JRNL TITL 2 ISOMERIZATION PRECEEDS DIMERIZATION. JRNL REF J.MOL.BIOL. V. 293 67 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10512716 JRNL DOI 10.1006/JMBI.1999.3128 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) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 9447 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) : 0.196 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 496 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 1622 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 77 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.80 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) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.350 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 1CQK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-AUG-99. REMARK 100 THE DEPOSITION ID IS D_1000009489. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUL-98 REMARK 200 TEMPERATURE (KELVIN) : 20 REMARK 200 PH : 8.5 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 : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10340 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 200 DATA REDUNDANCY : 5.580 REMARK 200 R MERGE (I) : 0.10400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1000 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) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.27300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS, AMMONIUM SULFATE, PH 8.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 18K, TEMPERATURE 291.0K 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 21.40000 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A DIMER. 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: 2260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 56 CB CG CD OE1 NE2 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 B 47 DISTANCE = 9.45 ANGSTROMS REMARK 525 HOH B 79 DISTANCE = 6.31 ANGSTROMS DBREF 1CQK A 4 104 UNP Q9R1A4 Q9R1A4_MOUSE 353 453 DBREF 1CQK B 204 304 UNP Q9R1A4 Q9R1A4_MOUSE 353 453 SEQADV 1CQK ALA A 5 UNP Q9R1A4 LYS 354 ENGINEERED MUTATION SEQADV 1CQK LEU A 16 UNP Q9R1A4 LYS 365 ENGINEERED MUTATION SEQADV 1CQK LEU A 23 UNP Q9R1A4 LYS 372 ENGINEERED MUTATION SEQADV 1CQK ALA B 205 UNP Q9R1A4 LYS 354 ENGINEERED MUTATION SEQADV 1CQK LEU B 216 UNP Q9R1A4 LYS 365 ENGINEERED MUTATION SEQADV 1CQK LEU B 223 UNP Q9R1A4 LYS 372 ENGINEERED MUTATION SEQRES 1 A 101 PRO ALA ALA PRO GLN VAL TYR THR ILE PRO PRO PRO LEU SEQRES 2 A 101 GLU GLN MET ALA LYS ASP LEU VAL SER LEU THR CYS MET SEQRES 3 A 101 ILE THR ASP PHE PHE PRO GLU ASP ILE THR VAL GLU TRP SEQRES 4 A 101 GLN TRP ASN GLY GLN PRO ALA GLU ASN TYR LYS ASN THR SEQRES 5 A 101 GLN PRO ILE MET ASP THR ASP GLY SER TYR PHE VAL TYR SEQRES 6 A 101 SER LYS LEU ASN VAL GLN LYS SER ASN TRP GLU ALA GLY SEQRES 7 A 101 ASN THR PHE THR CYS SER VAL LEU HIS GLU GLY LEU HIS SEQRES 8 A 101 ASN HIS HIS THR GLU LYS SER LEU SER HIS SEQRES 1 B 101 PRO ALA ALA PRO GLN VAL TYR THR ILE PRO PRO PRO LEU SEQRES 2 B 101 GLU GLN MET ALA LYS ASP LEU VAL SER LEU THR CYS MET SEQRES 3 B 101 ILE THR ASP PHE PHE PRO GLU ASP ILE THR VAL GLU TRP SEQRES 4 B 101 GLN TRP ASN GLY GLN PRO ALA GLU ASN TYR LYS ASN THR SEQRES 5 B 101 GLN PRO ILE MET ASP THR ASP GLY SER TYR PHE VAL TYR SEQRES 6 B 101 SER LYS LEU ASN VAL GLN LYS SER ASN TRP GLU ALA GLY SEQRES 7 B 101 ASN THR PHE THR CYS SER VAL LEU HIS GLU GLY LEU HIS SEQRES 8 B 101 ASN HIS HIS THR GLU LYS SER LEU SER HIS FORMUL 3 HOH *77(H2 O) HELIX 1 1 PRO A 15 MET A 19 5 5 HELIX 2 2 LYS A 75 ALA A 80 1 6 HELIX 3 3 LEU A 93 ASN A 95 5 3 HELIX 4 4 PRO B 215 MET B 219 5 5 HELIX 5 5 LYS B 275 ALA B 280 1 6 HELIX 6 6 LEU B 293 ASN B 295 5 3 SHEET 1 A 4 GLN A 8 ILE A 12 0 SHEET 2 A 4 LEU A 23 PHE A 33 -1 O THR A 27 N ILE A 12 SHEET 3 A 4 TYR A 65 GLN A 74 -1 N TYR A 65 O PHE A 33 SHEET 4 A 4 TYR A 52 ASN A 54 -1 O LYS A 53 N LYS A 70 SHEET 1 A1 4 GLN A 8 ILE A 12 0 SHEET 2 A1 4 LEU A 23 PHE A 33 -1 O THR A 27 N ILE A 12 SHEET 3 A1 4 TYR A 65 GLN A 74 -1 N TYR A 65 O PHE A 33 SHEET 4 A1 4 ILE A 58 MET A 59 -1 N ILE A 58 O PHE A 66 SHEET 1 B 4 GLN A 47 PRO A 48 0 SHEET 2 B 4 THR A 39 TRP A 44 -1 N TRP A 44 O GLN A 47 SHEET 3 B 4 PHE A 84 LEU A 89 -1 O THR A 85 N GLN A 43 SHEET 4 B 4 HIS A 97 LEU A 102 -1 O THR A 98 N VAL A 88 SHEET 1 C 4 GLN B 208 ILE B 212 0 SHEET 2 C 4 LEU B 223 PHE B 233 -1 O THR B 227 N ILE B 212 SHEET 3 C 4 TYR B 265 GLN B 274 -1 N TYR B 265 O PHE B 233 SHEET 4 C 4 TYR B 252 ASN B 254 -1 O LYS B 253 N LYS B 270 SHEET 1 C1 4 GLN B 208 ILE B 212 0 SHEET 2 C1 4 LEU B 223 PHE B 233 -1 O THR B 227 N ILE B 212 SHEET 3 C1 4 TYR B 265 GLN B 274 -1 N TYR B 265 O PHE B 233 SHEET 4 C1 4 ILE B 258 MET B 259 -1 N ILE B 258 O PHE B 266 SHEET 1 D 4 GLN B 247 PRO B 248 0 SHEET 2 D 4 THR B 239 TRP B 244 -1 N TRP B 244 O GLN B 247 SHEET 3 D 4 THR B 283 LEU B 289 -1 N THR B 285 O GLN B 243 SHEET 4 D 4 HIS B 297 SER B 303 -1 O THR B 298 N VAL B 288 SSBOND 1 CYS A 28 CYS A 86 1555 1555 2.31 SSBOND 2 CYS B 228 CYS B 286 1555 1555 2.39 CISPEP 1 PHE A 34 PRO A 35 0 -0.59 CISPEP 2 PHE B 234 PRO B 235 0 -0.10 CRYST1 48.700 42.800 50.400 90.00 105.93 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 0.020534 0.000000 0.005861 0.00000 SCALE2 0.000000 0.023364 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020634 0.00000