HEADER IMMUNE SYSTEM 09-FEB-07 2OTT TITLE CRYSTAL STRUCTURE OF CD5_DIII COMPND MOL_ID: 1; COMPND 2 MOLECULE: T-CELL SURFACE GLYCOPROTEIN CD5; COMPND 3 CHAIN: X, Y; COMPND 4 FRAGMENT: CD5_DIII; COMPND 5 SYNONYM: LYMPHOCYTE ANTIGEN T1/LEU- 1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL: B-LYMPHOCYTE; SOURCE 6 GENE: CD5, LEU1; SOURCE 7 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 8 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 10 EXPRESSION_SYSTEM_CELL_LINE: HEK-293EBNA; SOURCE 11 EXPRESSION_SYSTEM_TISSUE: KIDNEY CELLS; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PCEP-PU KEYWDS SRCR GROUP B DOMAIN, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR B.RODAMILANS REVDAT 6 31-MAR-21 2OTT 1 SOURCE SEQADV REVDAT 5 18-OCT-17 2OTT 1 REMARK REVDAT 4 13-JUL-11 2OTT 1 VERSN REVDAT 3 24-FEB-09 2OTT 1 VERSN REVDAT 2 29-MAY-07 2OTT 1 JRNL REVDAT 1 13-MAR-07 2OTT 0 JRNL AUTH B.RODAMILANS,I.G.MUNOZ,E.BRAGADO-NILSSON,M.R.SARRIAS, JRNL AUTH 2 O.PADILLA,F.J.BLANCO,F.LOZANO,G.MONTOYA JRNL TITL CRYSTAL STRUCTURE OF THE THIRD EXTRACELLULAR DOMAIN OF CD5 JRNL TITL 2 REVEALS THE FOLD OF A GROUP B SCAVENGER CYSTEINE-RICH JRNL TITL 3 RECEPTOR DOMAIN. JRNL REF J.BIOL.CHEM. V. 282 12669 2007 JRNL REFN ISSN 0021-9258 JRNL PMID 17322294 JRNL DOI 10.1074/JBC.M611699200 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 12350 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 + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 631 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 868 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.98 REMARK 3 BIN R VALUE (WORKING SET) : 0.2900 REMARK 3 BIN FREE R VALUE SET COUNT : 53 REMARK 3 BIN FREE R VALUE : 0.3270 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1452 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 77 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : 0.04000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.273 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.232 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.141 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.690 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.925 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.894 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1486 ; 0.025 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2010 ; 2.409 ; 1.929 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 182 ; 9.829 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 74 ;40.536 ;23.784 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 248 ;20.622 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;24.979 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 212 ; 0.187 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1134 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 551 ; 0.251 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 989 ; 0.318 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 73 ; 0.167 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 37 ; 0.224 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.127 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 946 ; 1.447 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1470 ; 2.385 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 627 ; 3.719 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 540 ; 5.694 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : X 7 X 104 REMARK 3 ORIGIN FOR THE GROUP (A): 19.7903 53.0589 -0.7280 REMARK 3 T TENSOR REMARK 3 T11: 0.1163 T22: 0.2732 REMARK 3 T33: 0.1835 T12: 0.0294 REMARK 3 T13: 0.0170 T23: 0.0293 REMARK 3 L TENSOR REMARK 3 L11: 7.6415 L22: 1.3863 REMARK 3 L33: 1.8939 L12: 0.9449 REMARK 3 L13: 0.5072 L23: 0.2946 REMARK 3 S TENSOR REMARK 3 S11: -0.0823 S12: 0.8015 S13: 0.1066 REMARK 3 S21: -0.2313 S22: 0.0785 S23: 0.0094 REMARK 3 S31: -0.0696 S32: 0.0615 S33: 0.0038 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : Y 7 Y 104 REMARK 3 ORIGIN FOR THE GROUP (A): 28.7053 72.9264 15.3588 REMARK 3 T TENSOR REMARK 3 T11: 0.3891 T22: 0.1051 REMARK 3 T33: 0.1857 T12: -0.0596 REMARK 3 T13: 0.1188 T23: 0.0562 REMARK 3 L TENSOR REMARK 3 L11: 3.2003 L22: 7.4032 REMARK 3 L33: 4.3299 L12: 1.9873 REMARK 3 L13: 1.0100 L23: 2.7133 REMARK 3 S TENSOR REMARK 3 S11: -0.2821 S12: 0.6243 S13: 0.4015 REMARK 3 S21: -1.1375 S22: 0.3089 S23: -0.3461 REMARK 3 S31: -1.0391 S32: 0.3531 S33: -0.0268 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2OTT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-FEB-07. REMARK 100 THE DEPOSITION ID IS D_1000041576. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-AUG-06 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : LN2 COOLED FIXED-EXIT SI(11) REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : DINAMICALLY BENDABLE MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12350 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 8.900 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 9.10 REMARK 200 R MERGE FOR SHELL (I) : 0.34000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SNB REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10MM HEPES, 300MM NA,CL PH7.4, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 2 2 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+1/4 REMARK 290 4555 Y,-X,Z+3/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+3/4 REMARK 290 8555 -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 64.49500 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 32.24750 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 96.74250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 64.49500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 96.74250 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 32.24750 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: X 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: Y 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH X 109 LIES ON A SPECIAL POSITION. 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 SER X 39 REMARK 465 SER X 40 REMARK 465 ALA X 41 REMARK 465 ARG X 42 REMARK 465 SER Y 38 REMARK 465 SER Y 39 REMARK 465 SER Y 40 REMARK 465 ALA Y 41 REMARK 465 ARG Y 42 REMARK 465 SER Y 43 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 O HOH X 110 O HOH X 127 2.09 REMARK 500 REMARK 500 REMARK: NULL 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 ALA X 30 CA ALA X 30 CB 0.129 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 ARG X 63 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 ARG X 63 NE - CZ - NH2 ANGL. DEV. = -7.0 DEGREES REMARK 500 ARG X 91 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG X 91 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ALA Y 30 N - CA - C ANGL. DEV. = -19.0 DEGREES REMARK 500 ASP Y 66 CB - CG - OD1 ANGL. DEV. = 7.1 DEGREES REMARK 500 ARG Y 91 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG Y 91 NE - CZ - NH2 ANGL. DEV. = -5.4 DEGREES 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 GLN X 28 -94.06 -109.46 REMARK 500 HIS X 79 138.51 -170.51 REMARK 500 SER X 83 -4.19 -58.48 REMARK 500 ALA Y 30 -162.18 -117.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA X 30 GLN X 31 148.77 REMARK 500 ASP X 37 SER X 38 135.26 REMARK 500 GLN Y 28 GLY Y 29 -149.25 REMARK 500 GLY Y 29 ALA Y 30 -34.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JA4 RELATED DB: PDB DBREF 2OTT X 11 103 UNP P06127 CD5_HUMAN 276 368 DBREF 2OTT Y 11 103 UNP P06127 CD5_HUMAN 276 368 SEQADV 2OTT PRO X 7 UNP P06127 CLONING ARTIFACT SEQADV 2OTT ALA X 8 UNP P06127 CLONING ARTIFACT SEQADV 2OTT VAL X 9 UNP P06127 CLONING ARTIFACT SEQADV 2OTT GLU X 10 UNP P06127 CLONING ARTIFACT SEQADV 2OTT ASP X 104 UNP P06127 CLONING ARTIFACT SEQADV 2OTT PRO Y 7 UNP P06127 CLONING ARTIFACT SEQADV 2OTT ALA Y 8 UNP P06127 CLONING ARTIFACT SEQADV 2OTT VAL Y 9 UNP P06127 CLONING ARTIFACT SEQADV 2OTT GLU Y 10 UNP P06127 CLONING ARTIFACT SEQADV 2OTT ASP Y 104 UNP P06127 CLONING ARTIFACT SEQRES 1 X 98 PRO ALA VAL GLU SER ARG LEU VAL GLY GLY SER SER ILE SEQRES 2 X 98 CYS GLU GLY THR VAL GLU VAL ARG GLN GLY ALA GLN TRP SEQRES 3 X 98 ALA ALA LEU CYS ASP SER SER SER ALA ARG SER SER LEU SEQRES 4 X 98 ARG TRP GLU GLU VAL CYS ARG GLU GLN GLN CYS GLY SER SEQRES 5 X 98 VAL ASN SER TYR ARG VAL LEU ASP ALA GLY ASP PRO THR SEQRES 6 X 98 SER ARG GLY LEU PHE CYS PRO HIS GLN LYS LEU SER GLN SEQRES 7 X 98 CYS HIS GLU LEU TRP GLU ARG ASN SER TYR CYS LYS LYS SEQRES 8 X 98 VAL PHE VAL THR CYS GLN ASP SEQRES 1 Y 98 PRO ALA VAL GLU SER ARG LEU VAL GLY GLY SER SER ILE SEQRES 2 Y 98 CYS GLU GLY THR VAL GLU VAL ARG GLN GLY ALA GLN TRP SEQRES 3 Y 98 ALA ALA LEU CYS ASP SER SER SER ALA ARG SER SER LEU SEQRES 4 Y 98 ARG TRP GLU GLU VAL CYS ARG GLU GLN GLN CYS GLY SER SEQRES 5 Y 98 VAL ASN SER TYR ARG VAL LEU ASP ALA GLY ASP PRO THR SEQRES 6 Y 98 SER ARG GLY LEU PHE CYS PRO HIS GLN LYS LEU SER GLN SEQRES 7 Y 98 CYS HIS GLU LEU TRP GLU ARG ASN SER TYR CYS LYS LYS SEQRES 8 Y 98 VAL PHE VAL THR CYS GLN ASP FORMUL 3 HOH *77(H2 O) HELIX 1 1 SER X 43 GLN X 54 1 12 HELIX 2 2 LYS X 81 CYS X 85 5 5 HELIX 3 3 SER Y 44 GLN Y 55 1 12 HELIX 4 4 LYS Y 81 CYS Y 85 5 5 SHEET 1 A 3 GLU X 10 GLY X 15 0 SHEET 2 A 3 GLU X 21 ARG X 27 -1 O ARG X 27 N GLU X 10 SHEET 3 A 3 ALA X 33 ALA X 34 -1 O ALA X 33 N VAL X 26 SHEET 1 B 4 GLU X 10 GLY X 15 0 SHEET 2 B 4 GLU X 21 ARG X 27 -1 O ARG X 27 N GLU X 10 SHEET 3 B 4 LYS X 97 CYS X 102 -1 O VAL X 100 N GLY X 22 SHEET 4 B 4 VAL X 59 LEU X 65 -1 N ASN X 60 O THR X 101 SHEET 1 C 2 GLY X 74 PHE X 76 0 SHEET 2 C 2 TRP X 89 ARG X 91 -1 O TRP X 89 N PHE X 76 SHEET 1 D 3 GLU Y 10 GLY Y 15 0 SHEET 2 D 3 GLU Y 21 ARG Y 27 -1 O GLU Y 25 N ARG Y 12 SHEET 3 D 3 ALA Y 33 ALA Y 34 -1 O ALA Y 33 N VAL Y 26 SHEET 1 E 4 GLU Y 10 GLY Y 15 0 SHEET 2 E 4 GLU Y 21 ARG Y 27 -1 O GLU Y 25 N ARG Y 12 SHEET 3 E 4 LYS Y 97 CYS Y 102 -1 O VAL Y 100 N GLY Y 22 SHEET 4 E 4 VAL Y 59 LEU Y 65 -1 N ARG Y 63 O PHE Y 99 SHEET 1 F 2 GLY Y 74 PHE Y 76 0 SHEET 2 F 2 TRP Y 89 ARG Y 91 -1 O ARG Y 91 N GLY Y 74 SSBOND 1 CYS X 20 CYS X 56 1555 1555 2.15 SSBOND 2 CYS X 36 CYS X 95 1555 1555 2.12 SSBOND 3 CYS X 51 CYS X 102 1555 1555 2.06 SSBOND 4 CYS X 77 CYS X 85 1555 1555 2.04 SSBOND 5 CYS Y 20 CYS Y 56 1555 1555 2.10 SSBOND 6 CYS Y 36 CYS Y 95 1555 1555 2.07 SSBOND 7 CYS Y 51 CYS Y 102 1555 1555 2.06 SSBOND 8 CYS Y 77 CYS Y 85 1555 1555 2.08 CISPEP 1 ALA Y 30 GLN Y 31 0 19.44 CRYST1 74.161 74.161 128.990 90.00 90.00 90.00 P 41 2 2 16 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 0.013484 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013484 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007753 0.00000