HEADER SIGNALING PROTEIN 15-JAN-18 5Z4V TITLE CRYSTAL STRUCTURE OF THE SHEEP SIGNALLING GLYCOPROTEIN (SPS-40) TITLE 2 COMPLEX WITH 2-METHYL-2-4-PENTANEDIOL AT 1.65A RESOLUTION REVEALS TITLE 3 SPECIFIC BINDING CHARACTERISTICS OF SPS-40 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHITINASE-3-LIKE PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SECRETORY GLYCOPROTEIN OF 40 KDA,SIGNAL-PROCESSING PROTEIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: OVIS ARIES; SOURCE 3 ORGANISM_COMMON: SHEEP; SOURCE 4 ORGANISM_TAXID: 9940 KEYWDS SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.SHARMA,P.K.SINGH,N.SINGH,S.SHARMA,P.KAUR,C.BETZEL,T.P.SINGH REVDAT 3 22-NOV-23 5Z4V 1 HETSYN REVDAT 2 29-JUL-20 5Z4V 1 COMPND REMARK HETNAM LINK REVDAT 2 2 1 SITE REVDAT 1 14-FEB-18 5Z4V 0 JRNL AUTH P.SHARMA,P.K.SINGH,N.SINGH,S.SHARMA,P.KAUR,C.BETZEL, JRNL AUTH 2 T.P.SINGH JRNL TITL CRYSTAL STRUCTURE OF THE SHEEP SIGNALLING GLYCOPROTEIN JRNL TITL 2 (SPS-40) COMPLEX WITH 2-METHYL-2-4-PENTANEDIOL AT 1.65A JRNL TITL 3 RESOLUTION REVEALS SPECIFIC BINDING CHARACTERISTICS OF JRNL TITL 4 SPS-40 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 50989 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) : 0.139 REMARK 3 R VALUE (WORKING SET) : 0.138 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1075 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.70 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3688 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.1780 REMARK 3 BIN FREE R VALUE SET COUNT : 96 REMARK 3 BIN FREE R VALUE : 0.2090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2876 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 599 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.13000 REMARK 3 B22 (A**2) : -0.41000 REMARK 3 B33 (A**2) : 0.28000 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): 0.071 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.082 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.053 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.490 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3025 ; 0.035 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2761 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4113 ; 2.892 ; 1.951 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6379 ; 1.763 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 367 ; 6.637 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 144 ;33.048 ;22.917 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 485 ;12.785 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;21.857 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 443 ; 0.204 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3380 ; 0.018 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 684 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1458 ; 1.556 ; 1.266 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1457 ; 1.541 ; 1.265 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1824 ; 2.399 ; 1.893 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1825 ; 2.401 ; 1.894 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1567 ; 2.432 ; 1.543 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1568 ; 2.431 ; 1.544 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2287 ; 3.633 ; 2.220 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 17498 ; 7.299 ;29.095 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 17493 ; 7.301 ;29.086 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 : 1 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 : A 1 A 1098 REMARK 3 ORIGIN FOR THE GROUP (A): -21.7984 -2.5073 6.8018 REMARK 3 T TENSOR REMARK 3 T11: 0.0011 T22: 0.0241 REMARK 3 T33: 0.0161 T12: 0.0012 REMARK 3 T13: -0.0005 T23: -0.0166 REMARK 3 L TENSOR REMARK 3 L11: 1.0927 L22: 1.1468 REMARK 3 L33: 1.4191 L12: 0.2163 REMARK 3 L13: -0.0802 L23: -0.4553 REMARK 3 S TENSOR REMARK 3 S11: 0.0132 S12: -0.0587 S13: 0.0441 REMARK 3 S21: 0.0235 S22: -0.0059 S23: 0.0619 REMARK 3 S31: 0.0024 S32: -0.0802 S33: -0.0073 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 5Z4V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1300006484. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5-8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.81 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52135 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 55.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 20.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03500 REMARK 200 FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 2PI6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRI-HCL, 20% ETHANOL, PH 7.8, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K, TEMPERATURE 298.0K 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 30.43650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.84600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.20750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.84600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.43650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.20750 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 THR A 131 OG1 CG2 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 A 521 O HOH A 884 1.89 REMARK 500 O HOH A 1013 O HOH A 1049 1.99 REMARK 500 O HOH A 502 O HOH A 926 2.00 REMARK 500 O HOH A 657 O HOH A 899 2.01 REMARK 500 O HOH A 508 O HOH A 590 2.01 REMARK 500 OE2 GLU A 269 O HOH A 501 2.13 REMARK 500 OH TYR A 1 O HOH A 502 2.14 REMARK 500 O HOH A 736 O HOH A 948 2.15 REMARK 500 O HOH A 1093 O HOH A 1094 2.15 REMARK 500 NH1 ARG A 242 O HOH A 503 2.17 REMARK 500 O HOH A 755 O HOH A 912 2.18 REMARK 500 O2 MPD A 403 O HOH A 504 2.18 REMARK 500 O HOH A 592 O HOH A 848 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 857 O HOH A 880 4545 1.89 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 SER A 9 CB SER A 9 OG -0.097 REMARK 500 TRP A 10 CB TRP A 10 CG -0.122 REMARK 500 THR A 36 CB THR A 36 CG2 -0.216 REMARK 500 TRP A 48 CE3 TRP A 48 CZ3 0.103 REMARK 500 GLU A 49 CD GLU A 49 OE1 -0.068 REMARK 500 GLU A 49 CD GLU A 49 OE2 -0.110 REMARK 500 ASN A 60 CG ASN A 60 ND2 0.214 REMARK 500 GLY A 81 N GLY A 81 CA 0.159 REMARK 500 ARG A 95 CD ARG A 95 NE -0.111 REMARK 500 ARG A 166 CZ ARG A 166 NH1 0.087 REMARK 500 SER A 174 CA SER A 174 CB 0.116 REMARK 500 SER A 174 CB SER A 174 OG -0.090 REMARK 500 ALA A 208 C ALA A 208 O 0.133 REMARK 500 SER A 210 CB SER A 210 OG 0.089 REMARK 500 SER A 210 C ARG A 212 N 0.183 REMARK 500 TYR A 218 CG TYR A 218 CD1 -0.079 REMARK 500 ARG A 225 CZ ARG A 225 NH1 0.080 REMARK 500 GLY A 227 CA GLY A 227 C -0.105 REMARK 500 VAL A 234 CB VAL A 234 CG1 -0.163 REMARK 500 GLY A 259 N GLY A 259 CA -0.114 REMARK 500 GLU A 311 CD GLU A 311 OE1 0.072 REMARK 500 ALA A 362 N ALA A 362 CA 0.134 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 A 26 CB - CG - OD1 ANGL. DEV. = 9.4 DEGREES REMARK 500 ASP A 26 CB - CG - OD2 ANGL. DEV. = -8.6 DEGREES REMARK 500 THR A 36 OG1 - CB - CG2 ANGL. DEV. = -15.0 DEGREES REMARK 500 GLU A 44 OE1 - CD - OE2 ANGL. DEV. = 7.2 DEGREES REMARK 500 ASP A 46 CB - CG - OD1 ANGL. DEV. = 6.9 DEGREES REMARK 500 ASP A 46 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP A 52 CB - CG - OD2 ANGL. DEV. = -7.4 DEGREES REMARK 500 LEU A 55 CB - CG - CD1 ANGL. DEV. = 16.1 DEGREES REMARK 500 TYR A 56 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 TYR A 56 CB - CG - CD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 LEU A 62 CB - CG - CD1 ANGL. DEV. = -10.7 DEGREES REMARK 500 ARG A 84 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 84 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 PHE A 85 CB - CG - CD2 ANGL. DEV. = -6.6 DEGREES REMARK 500 PHE A 85 CB - CG - CD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 96 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG A 124 NE - CZ - NH1 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG A 124 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 VAL A 157 CA - CB - CG1 ANGL. DEV. = 9.1 DEGREES REMARK 500 ARG A 166 NE - CZ - NH1 ANGL. DEV. = -9.0 DEGREES REMARK 500 ARG A 166 NE - CZ - NH2 ANGL. DEV. = 5.0 DEGREES REMARK 500 SER A 174 CA - CB - OG ANGL. DEV. = -20.6 DEGREES REMARK 500 ASP A 178 CB - CG - OD2 ANGL. DEV. = 12.9 DEGREES REMARK 500 TYR A 185 CB - CG - CD1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ASP A 207 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 SER A 210 O - C - N ANGL. DEV. = -24.5 DEGREES REMARK 500 ARG A 212 CG - CD - NE ANGL. DEV. = -13.6 DEGREES REMARK 500 ARG A 212 NE - CZ - NH1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 212 NE - CZ - NH2 ANGL. DEV. = -10.8 DEGREES REMARK 500 ARG A 225 CD - NE - CZ ANGL. DEV. = 16.1 DEGREES REMARK 500 ARG A 225 NE - CZ - NH1 ANGL. DEV. = 16.3 DEGREES REMARK 500 ARG A 225 NE - CZ - NH2 ANGL. DEV. = -12.8 DEGREES REMARK 500 LYS A 232 CD - CE - NZ ANGL. DEV. = 15.6 DEGREES REMARK 500 LEU A 233 CB - CG - CD1 ANGL. DEV. = 10.5 DEGREES REMARK 500 ARG A 242 NH1 - CZ - NH2 ANGL. DEV. = 9.8 DEGREES REMARK 500 ARG A 242 NE - CZ - NH1 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG A 242 NE - CZ - NH2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ASP A 252 CB - CG - OD1 ANGL. DEV. = 7.9 DEGREES REMARK 500 ARG A 265 NE - CZ - NH1 ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG A 265 NE - CZ - NH2 ANGL. DEV. = 7.7 DEGREES REMARK 500 ARG A 289 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 291 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ASP A 292 CB - CG - OD1 ANGL. DEV. = 10.9 DEGREES REMARK 500 ASP A 292 CB - CG - OD2 ANGL. DEV. = -11.2 DEGREES REMARK 500 ARG A 318 NE - CZ - NH1 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG A 323 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 323 NE - CZ - NH2 ANGL. DEV. = -5.7 DEGREES REMARK 500 LEU A 347 CB - CG - CD1 ANGL. DEV. = -11.0 DEGREES REMARK 500 ASP A 357 CB - CG - OD2 ANGL. DEV. = -8.3 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 TRP A 48 -64.60 -128.92 REMARK 500 TYR A 185 25.35 -157.20 REMARK 500 ALA A 190 -34.81 -36.31 REMARK 500 VAL A 253 125.66 -38.92 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 SER A 210 ARG A 212 120.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 212 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 SER A 210 -31.69 REMARK 500 THR A 239 11.25 REMARK 500 REMARK 500 REMARK: NULL 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 A1095 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH A1096 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A1097 DISTANCE = 6.11 ANGSTROMS REMARK 525 HOH A1098 DISTANCE = 6.45 ANGSTROMS REMARK 525 HOH A1099 DISTANCE = 6.75 ANGSTROMS REMARK 999 REMARK 999 SEQUENCE REMARK 999 CONFLICTS ARE OBSERVED BETWEEN THE SEQUENCE IN THIS STRUCTURE AND REMARK 999 DATABASE UNIPROTKB Q6TMG6 (CH3L1_SHEEP) THE AUTHOR EXPECTS SEQUENCE REMARK 999 IN THIS STRUCTURE TO BE AN ISOFORM. RESIDUE NUMBER 211 IS SIMPLY REMARK 999 SKIPPED. DBREF 5Z4V A 1 362 UNP Q6TMG6 CH3L1_SHEEP 1 361 SEQADV 5Z4V THR A 36 UNP Q6TMG6 SER 36 CONFLICT SEQADV 5Z4V LYS A 87 UNP Q6TMG6 ALA 87 CONFLICT SEQADV 5Z4V ARG A 203 UNP Q6TMG6 ALA 203 CONFLICT SEQADV 5Z4V ILE A 262 UNP Q6TMG6 VAL 261 CONFLICT SEQADV 5Z4V ALA A 362 UNP Q6TMG6 VAL 361 CONFLICT SEQRES 1 A 361 TYR LYS LEU ILE CYS TYR TYR THR SER TRP SER GLN TYR SEQRES 2 A 361 ARG GLU GLY ASP GLY SER CYS PHE PRO ASP ALA ILE ASP SEQRES 3 A 361 PRO PHE LEU CYS THR HIS VAL ILE TYR THR PHE ALA ASN SEQRES 4 A 361 ILE SER ASN ASN GLU ILE ASP THR TRP GLU TRP ASN ASP SEQRES 5 A 361 VAL THR LEU TYR ASP THR LEU ASN THR LEU LYS ASN ARG SEQRES 6 A 361 ASN PRO LYS LEU LYS THR LEU LEU SER VAL GLY GLY TRP SEQRES 7 A 361 ASN PHE GLY PRO GLU ARG PHE SER LYS ILE ALA SER LYS SEQRES 8 A 361 THR GLN SER ARG ARG THR PHE ILE LYS SER VAL PRO PRO SEQRES 9 A 361 PHE LEU ARG THR HIS GLY PHE ASP GLY LEU ASP LEU ALA SEQRES 10 A 361 TRP LEU TYR PRO GLY ARG ARG ASP LYS ARG HIS LEU THR SEQRES 11 A 361 THR LEU VAL LYS GLU MET LYS ALA GLU PHE ILE ARG GLU SEQRES 12 A 361 ALA GLN ALA GLY THR GLU GLN LEU LEU LEU SER ALA ALA SEQRES 13 A 361 VAL SER ALA GLY LYS ILE ALA ILE ASP ARG GLY TYR ASP SEQRES 14 A 361 ILE ALA GLN ILE SER ARG HIS LEU ASP PHE ILE SER LEU SEQRES 15 A 361 LEU THR TYR ASP PHE HIS GLY ALA TRP ARG GLN THR VAL SEQRES 16 A 361 GLY HIS HIS SER PRO LEU PHE ARG GLY ASN GLU ASP ALA SEQRES 17 A 361 SER SER ARG PHE SER ASN ALA ASP TYR ALA VAL SER TYR SEQRES 18 A 361 MET LEU ARG LEU GLY ALA PRO ALA ASN LYS LEU VAL MET SEQRES 19 A 361 GLY ILE PRO THR PHE GLY ARG SER PHE THR LEU ALA SER SEQRES 20 A 361 SER LYS THR ASP VAL GLY ALA PRO VAL SER GLY PRO GLY SEQRES 21 A 361 ILE PRO GLY ARG PHE THR LYS GLU LYS GLY ILE LEU ALA SEQRES 22 A 361 TYR TYR GLU ILE CYS ASP PHE LEU HIS GLY ALA THR THR SEQRES 23 A 361 HIS ARG PHE ARG ASP GLN GLN VAL PRO TYR ALA THR LYS SEQRES 24 A 361 GLY ASN GLN TRP VAL ALA TYR ASP ASP GLN GLU SER VAL SEQRES 25 A 361 LYS ASN LYS ALA ARG TYR LEU LYS ASN ARG GLN LEU ALA SEQRES 26 A 361 GLY ALA MET VAL TRP ALA LEU ASP LEU ASP ASP PHE ARG SEQRES 27 A 361 GLY THR PHE CYS GLY GLN ASN LEU THR PHE PRO LEU THR SEQRES 28 A 361 SER ALA VAL LYS ASP VAL LEU ALA GLU ALA HET NAG A 401 14 HET MPD A 402 8 HET MPD A 403 16 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 NAG C8 H15 N O6 FORMUL 3 MPD 2(C6 H14 O2) FORMUL 5 HOH *599(H2 O) HELIX 1 AA1 TRP A 10 ARG A 14 5 5 HELIX 2 AA2 GLU A 15 SER A 19 5 5 HELIX 3 AA3 PHE A 21 ILE A 25 5 5 HELIX 4 AA4 ASN A 51 THR A 61 1 11 HELIX 5 AA5 THR A 61 ASN A 66 1 6 HELIX 6 AA6 GLY A 81 SER A 90 1 10 HELIX 7 AA7 LYS A 91 GLY A 110 1 20 HELIX 8 AA8 GLY A 122 ARG A 124 5 3 HELIX 9 AA9 ASP A 125 GLN A 145 1 21 HELIX 10 AB1 GLY A 160 TYR A 168 1 9 HELIX 11 AB2 ASP A 169 LEU A 177 1 9 HELIX 12 AB3 ASN A 215 LEU A 226 1 12 HELIX 13 AB4 PRO A 229 ASN A 231 5 3 HELIX 14 AB5 TYR A 275 LEU A 282 1 8 HELIX 15 AB6 ASP A 309 ARG A 323 1 15 HELIX 16 AB7 ALA A 332 ASP A 336 5 5 HELIX 17 AB8 PHE A 349 GLU A 361 1 13 SHEET 1 AA110 GLU A 44 ASP A 46 0 SHEET 2 AA110 HIS A 32 SER A 41 -1 N SER A 41 O GLU A 44 SHEET 3 AA110 LYS A 70 GLY A 76 1 O SER A 74 N ALA A 38 SHEET 4 AA110 GLY A 113 ALA A 117 1 O ALA A 117 N VAL A 75 SHEET 5 AA110 LEU A 152 VAL A 157 1 O SER A 154 N LEU A 114 SHEET 6 AA110 PHE A 179 LEU A 182 1 O SER A 181 N ALA A 155 SHEET 7 AA110 LEU A 233 PRO A 238 1 O VAL A 234 N LEU A 182 SHEET 8 AA110 GLY A 327 TRP A 331 1 O MET A 329 N MET A 235 SHEET 9 AA110 LYS A 2 THR A 8 1 N ILE A 4 O ALA A 328 SHEET 10 AA110 HIS A 32 SER A 41 1 O ILE A 34 N CYS A 5 SHEET 1 AA2 3 VAL A 257 PRO A 260 0 SHEET 2 AA2 3 PHE A 240 LEU A 246 -1 N THR A 245 O GLY A 259 SHEET 3 AA2 3 ILE A 272 ALA A 274 -1 O LEU A 273 N GLY A 241 SHEET 1 AA3 5 VAL A 257 PRO A 260 0 SHEET 2 AA3 5 PHE A 240 LEU A 246 -1 N THR A 245 O GLY A 259 SHEET 3 AA3 5 GLN A 303 ALA A 306 -1 O ALA A 306 N ARG A 242 SHEET 4 AA3 5 VAL A 295 LYS A 300 -1 N ALA A 298 O VAL A 305 SHEET 5 AA3 5 THR A 286 PHE A 290 -1 N THR A 286 O THR A 299 SSBOND 1 CYS A 5 CYS A 30 1555 1555 2.05 SSBOND 2 CYS A 279 CYS A 343 1555 1555 2.08 LINK ND2 ASN A 39 C1 NAG A 401 1555 1555 1.55 CISPEP 1 THR A 36 PHE A 37 0 -1.75 CISPEP 2 LEU A 119 TYR A 120 0 2.40 CISPEP 3 TRP A 331 ALA A 332 0 7.80 CRYST1 60.873 66.415 105.692 90.00 90.00 90.00 P 21 21 21 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 0.016428 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015057 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009461 0.00000