HEADER CELL ADHESION 26-FEB-98 1A6P TITLE ENGINEERING OF A MISFOLDED FORM OF CD2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: T-CELL SURFACE ANTIGEN CD2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: DOMAIN 1; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 CELL: T-LYMPHOCYTES; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: MC1061; SOURCE 9 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PGEX-2T KEYWDS DOMAIN SWAPPING, HINGE LOOP, OLIGOMER EVOLUTION, T LYMPHOCYTE KEYWDS 2 ADHESION GLYCOPROTEIN, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR A.J.MURRAY,J.G.HEAD,J.J.BARKER,R.L.BRADY REVDAT 4 22-MAY-24 1A6P 1 REMARK REVDAT 3 02-AUG-23 1A6P 1 SEQADV REVDAT 2 24-FEB-09 1A6P 1 VERSN REVDAT 1 17-JUN-98 1A6P 0 JRNL AUTH A.J.MURRAY,J.G.HEAD,J.J.BARKER,R.L.BRADY JRNL TITL ENGINEERING AN INTERTWINED FORM OF CD2 FOR STABILITY AND JRNL TITL 2 ASSEMBLY. JRNL REF NAT.STRUCT.BIOL. V. 5 778 1998 JRNL REFN ISSN 1072-8368 JRNL PMID 9731771 JRNL DOI 10.1038/1816 REMARK 2 REMARK 2 RESOLUTION. 2.08 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2.080 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 10.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 10589 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 SET) : 0.219 REMARK 3 FREE R VALUE : 0.296 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 10520 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.08 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.17 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1070 REMARK 3 BIN R VALUE (WORKING SET) : 0.3005 REMARK 3 BIN FREE R VALUE : 0.3793 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 116 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.027 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1486 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 81 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.46 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) : 1.291 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 RESIDUES 20 - 29 IN BOTH CHAINS COMPRISE A FLEXIBLE LOOP REMARK 3 REGION; HENCE THE B FACTORS ARE HIGH WITH POOR PACKING, AND REMARK 3 SOME NON H-BOND DONORS IN THE AREA. REMARK 4 REMARK 4 1A6P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170460. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : AUG-97 REMARK 200 TEMPERATURE (KELVIN) : 287 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX7.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.488 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : MIRRORS 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 : 10589 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 2.890 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : 0.05900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.29500 REMARK 200 R SYM FOR SHELL (I) : 0.29500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.570 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.851 REMARK 200 STARTING MODEL: PDB ENTRY 1HNG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 4000, 5% GLYCEROL, 0.1M NACO, REMARK 280 PH 4.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 52.96000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 79.44000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.48000 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: 7390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 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: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 99 CD GLU A 99 OE2 0.074 REMARK 500 GLU B 99 CD GLU B 99 OE2 0.071 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 ASN A 20 72.64 39.43 REMARK 500 ASP A 26 30.96 -92.47 REMARK 500 ASN B 20 80.88 37.43 REMARK 500 REMARK 500 REMARK: NULL DBREF 1A6P A 4 99 UNP P08921 CD2_RAT 26 121 DBREF 1A6P B 4 99 UNP P08921 CD2_RAT 26 121 SEQADV 1A6P A UNP P08921 MET 68 DELETION SEQADV 1A6P A UNP P08921 LYS 69 DELETION SEQADV 1A6P B UNP P08921 MET 68 DELETION SEQADV 1A6P B UNP P08921 LYS 69 DELETION SEQRES 1 A 94 GLY THR VAL TRP GLY ALA LEU GLY HIS GLY ILE ASN LEU SEQRES 2 A 94 ASN ILE PRO ASN PHE GLN MET THR ASP ASP ILE ASP GLU SEQRES 3 A 94 VAL ARG TRP GLU ARG GLY SER THR LEU VAL ALA GLU PHE SEQRES 4 A 94 LYS ARG LYS PRO PHE LEU LYS SER GLY ALA PHE GLU ILE SEQRES 5 A 94 LEU ALA ASN GLY ASP LEU LYS ILE LYS ASN LEU THR ARG SEQRES 6 A 94 ASP ASP SER GLY THR TYR ASN VAL THR VAL TYR SER THR SEQRES 7 A 94 ASN GLY THR ARG ILE LEU ASP LYS ALA LEU ASP LEU ARG SEQRES 8 A 94 ILE LEU GLU SEQRES 1 B 94 GLY THR VAL TRP GLY ALA LEU GLY HIS GLY ILE ASN LEU SEQRES 2 B 94 ASN ILE PRO ASN PHE GLN MET THR ASP ASP ILE ASP GLU SEQRES 3 B 94 VAL ARG TRP GLU ARG GLY SER THR LEU VAL ALA GLU PHE SEQRES 4 B 94 LYS ARG LYS PRO PHE LEU LYS SER GLY ALA PHE GLU ILE SEQRES 5 B 94 LEU ALA ASN GLY ASP LEU LYS ILE LYS ASN LEU THR ARG SEQRES 6 B 94 ASP ASP SER GLY THR TYR ASN VAL THR VAL TYR SER THR SEQRES 7 B 94 ASN GLY THR ARG ILE LEU ASP LYS ALA LEU ASP LEU ARG SEQRES 8 B 94 ILE LEU GLU FORMUL 3 HOH *81(H2 O) HELIX 1 1 ARG A 70 ASP A 72 5 3 HELIX 2 2 ARG B 70 ASP B 72 5 3 SHEET 1 A 5 THR A 5 ALA A 9 0 SHEET 2 A 5 ARG B 87 LEU B 98 1 N ASP B 94 O VAL A 6 SHEET 3 A 5 GLY B 74 SER B 82 -1 N VAL B 80 O ILE B 88 SHEET 4 A 5 ILE A 27 ARG A 34 -1 N GLU A 33 O ASN B 77 SHEET 5 A 5 THR A 37 LYS A 43 -1 N PHE A 42 O VAL A 30 SHEET 1 B 3 ILE A 14 LEU A 16 0 SHEET 2 B 3 LEU B 63 ILE B 65 -1 N ILE B 65 O ILE A 14 SHEET 3 B 3 PHE B 55 ILE B 57 -1 N GLU B 56 O LYS B 64 SHEET 1 C 3 PHE A 55 ILE A 57 0 SHEET 2 C 3 LEU A 63 ILE A 65 -1 N LYS A 64 O GLU A 56 SHEET 3 C 3 ILE B 14 LEU B 16 -1 N LEU B 16 O LEU A 63 SHEET 1 D 5 THR B 5 ALA B 9 0 SHEET 2 D 5 ARG A 87 LEU A 98 1 N ASP A 94 O VAL B 6 SHEET 3 D 5 GLY A 74 SER A 82 -1 N VAL A 80 O ILE A 88 SHEET 4 D 5 ILE B 27 ARG B 34 -1 N GLU B 33 O ASN A 77 SHEET 5 D 5 THR B 37 LYS B 43 -1 N PHE B 42 O VAL B 30 CRYST1 41.090 41.090 105.920 90.00 90.00 90.00 P 43 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 0.024337 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024337 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009441 0.00000