HEADER IMMUNE SYSTEM PROTEIN, RECEPTOR 23-MAY-95 1CDC TITLE CD2, N-TERMINAL DOMAIN (1-99), TRUNCATED FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: CD2; COMPND 3 CHAIN: B, A; COMPND 4 SYNONYM: LFA-2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: PET; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PET; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: GST-FUSION; SOURCE 10 OTHER_DETAILS: PET KEYWDS MISFOLDED, METASTABLE, IMMUNE SYSTEM PROTEIN, RECEPTOR EXPDTA X-RAY DIFFRACTION AUTHOR A.J.MURRAY,A.N.BARCLAY,R.L.BRADY REVDAT 5 07-FEB-24 1CDC 1 REMARK REVDAT 4 14-AUG-19 1CDC 1 REMARK REVDAT 3 17-JUL-19 1CDC 1 REMARK REVDAT 2 24-FEB-09 1CDC 1 VERSN REVDAT 1 15-SEP-95 1CDC 0 JRNL AUTH A.J.MURRAY,S.J.LEWIS,A.N.BARCLAY,R.L.BRADY JRNL TITL ONE SEQUENCE, TWO FOLDS: A METASTABLE STRUCTURE OF CD2. JRNL REF PROC.NATL.ACAD.SCI.USA V. 92 7337 1995 JRNL REFN ISSN 0027-8424 JRNL PMID 7638192 JRNL DOI 10.1073/PNAS.92.16.7337 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.3 REMARK 3 NUMBER OF REFLECTIONS : 12944 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1518 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.00 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 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.338 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.109 ; 2.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.829 ; 2.500 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.483 ; 3.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1CDC 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_1000172248. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAY-94 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.88 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 : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13465 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 6.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.06500 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 27.95000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.28000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.52500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.28000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.95000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.52500 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: 7680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A 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 450 REMARK 450 SOURCE REMARK 450 MOLECULE_NAME: CD2 (N-TERMINAL DOMAIN). EXPRESSED AS A REMARK 450 GST-FUSION PROTEIN. 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 ARG B 1 REMARK 465 ASP B 2 REMARK 465 SER B 3 REMARK 465 ARG A 1 REMARK 465 ASP A 2 REMARK 465 SER A 3 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 CD LYS B 43 O HOH B 131 1.61 REMARK 500 CG LYS B 43 O HOH B 131 2.04 REMARK 500 CB LYS B 43 O HOH B 131 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 ASP B 28 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 GLU B 29 OE1 - CD - OE2 ANGL. DEV. = -7.2 DEGREES REMARK 500 ARG B 31 NE - CZ - NH1 ANGL. DEV. = 7.6 DEGREES REMARK 500 ARG B 34 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG B 34 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG B 70 NE - CZ - NH1 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG B 70 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG B 87 NE - CZ - NH2 ANGL. DEV. = -6.3 DEGREES REMARK 500 LEU B 89 CA - CB - CG ANGL. DEV. = 32.3 DEGREES REMARK 500 ARG B 96 CD - NE - CZ ANGL. DEV. = 8.6 DEGREES REMARK 500 ARG A 34 CD - NE - CZ ANGL. DEV. = 9.4 DEGREES REMARK 500 ARG A 34 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 34 NE - CZ - NH2 ANGL. DEV. = -6.9 DEGREES REMARK 500 ARG A 44 CD - NE - CZ ANGL. DEV. = 17.9 DEGREES REMARK 500 ARG A 44 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 MET A 46 CA - CB - CG ANGL. DEV. = 11.1 DEGREES REMARK 500 ARG A 70 CD - NE - CZ ANGL. DEV. = 29.7 DEGREES REMARK 500 ARG A 70 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 96 CD - NE - CZ ANGL. DEV. = 43.8 DEGREES REMARK 500 ARG A 96 NE - CZ - NH1 ANGL. DEV. = -5.1 DEGREES REMARK 500 LEU A 98 O - C - N ANGL. DEV. = -14.4 DEGREES REMARK 500 GLU A 99 C - N - CA ANGL. DEV. = 20.6 DEGREES REMARK 500 GLU A 99 CB - CA - C ANGL. DEV. = -35.5 DEGREES REMARK 500 GLU A 99 N - CA - CB ANGL. DEV. = 43.1 DEGREES REMARK 500 GLU A 99 OE1 - CD - OE2 ANGL. DEV. = 9.1 DEGREES REMARK 500 GLU A 99 CG - CD - OE1 ANGL. DEV. = -12.0 DEGREES REMARK 500 GLU A 99 N - CA - C ANGL. DEV. = -31.4 DEGREES REMARK 500 GLU A 99 CA - C - O ANGL. DEV. = -20.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 1CDC B 1 99 UNP P08921 CD2_RAT 23 121 DBREF 1CDC A 1 99 UNP P08921 CD2_RAT 23 121 SEQRES 1 B 99 ARG ASP SER GLY THR VAL TRP GLY ALA LEU GLY HIS GLY SEQRES 2 B 99 ILE ASN LEU ASN ILE PRO ASN PHE GLN MET THR ASP ASP SEQRES 3 B 99 ILE ASP GLU VAL ARG TRP GLU ARG GLY SER THR LEU VAL SEQRES 4 B 99 ALA GLU PHE LYS ARG LYS MET LYS PRO PHE LEU LYS SER SEQRES 5 B 99 GLY ALA PHE GLU ILE LEU ALA ASN GLY ASP LEU LYS ILE SEQRES 6 B 99 LYS ASN LEU THR ARG ASP ASP SER GLY THR TYR ASN VAL SEQRES 7 B 99 THR VAL TYR SER THR ASN GLY THR ARG ILE LEU ASP LYS SEQRES 8 B 99 ALA LEU ASP LEU ARG ILE LEU GLU SEQRES 1 A 99 ARG ASP SER GLY THR VAL TRP GLY ALA LEU GLY HIS GLY SEQRES 2 A 99 ILE ASN LEU ASN ILE PRO ASN PHE GLN MET THR ASP ASP SEQRES 3 A 99 ILE ASP GLU VAL ARG TRP GLU ARG GLY SER THR LEU VAL SEQRES 4 A 99 ALA GLU PHE LYS ARG LYS MET LYS PRO PHE LEU LYS SER SEQRES 5 A 99 GLY ALA PHE GLU ILE LEU ALA ASN GLY ASP LEU LYS ILE SEQRES 6 A 99 LYS ASN LEU THR ARG ASP ASP SER GLY THR TYR ASN VAL SEQRES 7 A 99 THR VAL TYR SER THR ASN GLY THR ARG ILE LEU ASP LYS SEQRES 8 A 99 ALA LEU ASP LEU ARG ILE LEU GLU FORMUL 3 HOH *110(H2 O) HELIX 1 1 ARG B 70 ASP B 72 5 3 HELIX 2 2 ARG A 70 ASP A 72 5 3 SHEET 1 A 5 THR B 5 GLY B 8 0 SHEET 2 A 5 ARG A 87 ILE A 97 1 N ASP A 94 O VAL B 6 SHEET 3 A 5 GLY A 74 SER A 82 -1 N VAL A 80 O ILE A 88 SHEET 4 A 5 ILE B 27 ARG B 34 -1 N GLU B 33 O ASN A 77 SHEET 5 A 5 THR B 37 LYS B 43 -1 N PHE B 42 O VAL B 30 SHEET 1 B 3 ILE B 14 LEU B 16 0 SHEET 2 B 3 LEU A 63 ILE A 65 -1 N ILE A 65 O ILE B 14 SHEET 3 B 3 PHE A 55 ILE A 57 -1 N GLU A 56 O LYS A 64 SHEET 1 C 3 PHE B 55 ILE B 57 0 SHEET 2 C 3 LEU B 63 ILE B 65 -1 N LYS B 64 O GLU B 56 SHEET 3 C 3 ILE A 14 LEU A 16 -1 N LEU A 16 O LEU B 63 SHEET 1 D 5 THR A 5 ALA A 9 0 SHEET 2 D 5 ARG B 87 LEU B 98 1 N ASP B 94 O VAL A 6 SHEET 3 D 5 GLY B 74 SER B 82 -1 N VAL B 80 O ILE B 88 SHEET 4 D 5 ILE A 27 ARG A 34 -1 N GLU A 33 O ASN B 77 SHEET 5 D 5 THR A 37 LYS A 43 -1 N PHE A 42 O VAL A 30 CRYST1 55.900 57.050 60.560 90.00 90.00 90.00 P 21 21 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 0.017889 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017528 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016513 0.00000