HEADER SIGNALING PROTEIN 07-DEC-16 5WSI OBSLTE 21-MAR-18 5WSI 5Z05 TITLE CRYSTAL STRUCTURE OF ETHANOL MODIFIED SIGNALLING PROTEIN FROM BUFFALO TITLE 2 (SPB-40) AT 1.49 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHITINASE-3-LIKE PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 22-383; COMPND 5 SYNONYM: MAMMARY GLAND PROTEIN 40,SPB-40 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BUBALUS BUBALIS; SOURCE 3 ORGANISM_COMMON: DOMESTIC WATER BUFFALO; SOURCE 4 ORGANISM_TAXID: 89462 KEYWDS SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.K.SINGH,A.CHAUDHARY,T.K.TYAGI,P.KAUR,S.SHARMA,T.P.SINGH REVDAT 4 21-MAR-18 5WSI 1 OBSLTE REVDAT 3 31-JAN-18 5WSI 1 REMARK REVDAT 2 28-DEC-16 5WSI 1 SPRSDE REVDAT 1 21-DEC-16 5WSI 0 SPRSDE 28-DEC-16 5WSI 4S06 JRNL AUTH P.K.SINGH,A.CHAUDHARY,T.K.TYAGI,P.KAUR,S.SHARMA,T.P.SINGH JRNL TITL CRYSTAL STRUCTURE OF ETHANOL MODIFIED SIGNALLING PROTEIN JRNL TITL 2 FROM BUFFALO (SPB-40) AT 1.49 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 65450 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) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.175 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3479 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) : 1.49 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.53 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4608 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.31 REMARK 3 BIN R VALUE (WORKING SET) : 0.2170 REMARK 3 BIN FREE R VALUE SET COUNT : 244 REMARK 3 BIN FREE R VALUE : 0.2040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2877 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 412 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.95000 REMARK 3 B22 (A**2) : -0.77000 REMARK 3 B33 (A**2) : -0.19000 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): 0.057 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.060 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.041 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.393 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.967 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3002 ; 0.036 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2722 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4076 ; 2.968 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6298 ; 1.819 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 359 ; 7.171 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 141 ;33.072 ;23.262 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 479 ;12.447 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;22.897 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 438 ; 0.182 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3335 ; 0.016 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 667 ; 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): 1443 ; 1.875 ; 1.560 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1442 ; 1.869 ; 1.557 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1801 ; 2.809 ; 2.334 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1802 ; 2.811 ; 2.337 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1559 ; 2.831 ; 1.880 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1560 ; 2.831 ; 1.882 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2276 ; 4.208 ; 2.718 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 15033 ; 6.183 ;32.278 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 15034 ; 6.184 ;32.278 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 690 REMARK 3 ORIGIN FOR THE GROUP (A): 8.6453 2.6868 46.0024 REMARK 3 T TENSOR REMARK 3 T11: 0.0110 T22: 0.0195 REMARK 3 T33: 0.0094 T12: 0.0059 REMARK 3 T13: 0.0007 T23: -0.0117 REMARK 3 L TENSOR REMARK 3 L11: 1.1023 L22: 1.4172 REMARK 3 L33: 1.6034 L12: -0.1054 REMARK 3 L13: 0.2368 L23: -0.8641 REMARK 3 S TENSOR REMARK 3 S11: 0.0069 S12: 0.0860 S13: -0.0648 REMARK 3 S21: 0.0230 S22: 0.0067 S23: 0.0294 REMARK 3 S31: -0.1133 S32: -0.0688 S33: -0.0136 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 5WSI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-DEC-16. REMARK 100 THE DEPOSITION ID IS D_1300002316. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5-9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 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 : GRAPHITE REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65450 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.490 REMARK 200 RESOLUTION RANGE LOW (A) : 56.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03000 REMARK 200 FOR THE DATA SET : 0.0120 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 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 : 20.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35MM TRIS -HCL PH- 8.0, 25MM NACL, 20% REMARK 280 ETHANOL., PH 6.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 30.22850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.92350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.25850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.92350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.22850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.25850 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: 850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 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 627 O HOH A 774 2.16 REMARK 500 OE2 GLU A 269 O HOH A 501 2.17 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 509 O HOH A 675 4546 2.03 REMARK 500 O HOH A 675 O HOH A 831 4446 2.11 REMARK 500 O HOH A 703 O HOH A 785 4456 2.12 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 TYR A 1 CB TYR A 1 CG 0.115 REMARK 500 CYS A 5 CA CYS A 5 CB -0.079 REMARK 500 TYR A 6 CZ TYR A 6 CE2 -0.088 REMARK 500 TYR A 7 CZ TYR A 7 OH 0.189 REMARK 500 SER A 9 CA SER A 9 CB -0.127 REMARK 500 CYS A 20 C CYS A 20 O 0.128 REMARK 500 TYR A 35 CE1 TYR A 35 CZ -0.094 REMARK 500 TYR A 35 CZ TYR A 35 CE2 -0.080 REMARK 500 SER A 36 CB SER A 36 OG -0.162 REMARK 500 GLU A 44 CG GLU A 44 CD -0.103 REMARK 500 GLU A 49 CD GLU A 49 OE1 -0.073 REMARK 500 TYR A 56 CZ TYR A 56 CE2 -0.113 REMARK 500 LYS A 63 CD LYS A 63 CE -0.163 REMARK 500 TRP A 78 CB TRP A 78 CG -0.123 REMARK 500 GLY A 81 N GLY A 81 CA 0.119 REMARK 500 SER A 82 CB SER A 82 OG 0.086 REMARK 500 ARG A 84 CZ ARG A 84 NH2 -0.081 REMARK 500 PHE A 85 CD1 PHE A 85 CE1 -0.139 REMARK 500 LYS A 91 CE LYS A 91 NZ -0.211 REMARK 500 SER A 174 CB SER A 174 OG -0.093 REMARK 500 TRP A 191 CE2 TRP A 191 CZ2 0.129 REMARK 500 TRP A 191 CE3 TRP A 191 CZ3 0.147 REMARK 500 HIS A 198 NE2 HIS A 198 CD2 -0.068 REMARK 500 ARG A 225 CG ARG A 225 CD 0.172 REMARK 500 GLY A 227 CA GLY A 227 C -0.123 REMARK 500 TYR A 244 CE1 TYR A 244 CZ -0.078 REMARK 500 GLN A 265 CD GLN A 265 OE1 0.136 REMARK 500 GLN A 303 CD GLN A 303 OE1 0.161 REMARK 500 GLU A 311 CG GLU A 311 CD 0.140 REMARK 500 GLU A 311 CD GLU A 311 OE1 0.067 REMARK 500 TRP A 331 CE3 TRP A 331 CZ3 0.108 REMARK 500 ASP A 357 CB ASP A 357 CG 0.162 REMARK 500 GLY A 361 CA GLY A 361 C 0.111 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 CYS A 20 CB - CA - C ANGL. DEV. = 7.6 DEGREES REMARK 500 ASP A 26 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP A 26 CB - CG - OD2 ANGL. DEV. = -7.1 DEGREES REMARK 500 TYR A 56 CB - CG - CD2 ANGL. DEV. = -4.5 DEGREES REMARK 500 TYR A 56 CB - CG - CD1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 84 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 84 NE - CZ - NH2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ARG A 84 O - C - N ANGL. DEV. = -12.1 DEGREES REMARK 500 LYS A 91 CD - CE - NZ ANGL. DEV. = 19.7 DEGREES REMARK 500 ARG A 95 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 107 NE - CZ - NH1 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG A 124 CD - NE - CZ ANGL. DEV. = 9.0 DEGREES REMARK 500 ARG A 124 NE - CZ - NH1 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG A 124 NE - CZ - NH2 ANGL. DEV. = 8.2 DEGREES REMARK 500 ARG A 127 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 142 CD - NE - CZ ANGL. DEV. = 10.2 DEGREES REMARK 500 ARG A 142 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 GLU A 143 OE1 - CD - OE2 ANGL. DEV. = -7.7 DEGREES REMARK 500 TYR A 168 CB - CG - CD2 ANGL. DEV. = 4.8 DEGREES REMARK 500 TYR A 168 CB - CG - CD1 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 175 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ASP A 178 CB - CG - OD2 ANGL. DEV. = 12.2 DEGREES REMARK 500 GLN A 193 C - N - CA ANGL. DEV. = -18.8 DEGREES REMARK 500 ASP A 207 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ARG A 225 NE - CZ - NH2 ANGL. DEV. = 6.9 DEGREES REMARK 500 ASP A 252 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ASP A 252 CB - CG - OD2 ANGL. DEV. = -7.4 DEGREES REMARK 500 TYR A 276 CZ - CE2 - CD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP A 280 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 280 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 LYS A 300 CG - CD - CE ANGL. DEV. = 18.6 DEGREES REMARK 500 GLU A 311 OE1 - CD - OE2 ANGL. DEV. = -7.5 DEGREES REMARK 500 ARG A 318 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 323 NE - CZ - NH1 ANGL. DEV. = -8.3 DEGREES REMARK 500 ASP A 336 CB - CG - OD2 ANGL. DEV. = -5.9 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 SER A 82 -39.81 -38.51 REMARK 500 ALA A 117 60.37 -119.98 REMARK 500 TYR A 185 26.20 -158.21 REMARK 500 ASP A 207 56.99 -92.17 REMARK 500 ASP A 252 -166.06 -101.06 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 GLN A 205 GLU A 206 -130.90 REMARK 500 SER A 209 SER A 210 148.13 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 PHE A 80 0.07 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 -17.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EOH A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Poly-Saccharide residues NAG A REMARK 800 403 through NAG A 404 bound to ASN A 39 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5WSM RELATED DB: PDB REMARK 900 RELATED ID: 5WSJ RELATED DB: PDB DBREF 5WSI A 1 362 UNP Q7YS85 CH3L1_BUBBU 22 383 SEQADV 5WSI A UNP Q7YS85 ASP 232 DELETION 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 SER 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 SER GLN 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 TRP ARG ASP LYS ARG HIS LEU THR SEQRES 11 A 361 THR LEU VAL LYS GLU MET LYS ALA GLU PHE VAL ARG GLU SEQRES 12 A 361 ALA GLN ALA GLY THR GLU GLN LEU LEU LEU SER ALA ALA SEQRES 13 A 361 VAL PRO 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 GLN 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 LYS SER TYR THR LEU ALA SER SEQRES 20 A 361 SER LYS THR ASP VAL GLY ALA PRO ILE SER GLY PRO GLY SEQRES 21 A 361 ILE PRO GLY GLN 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 ALA PHE PRO LEU THR SEQRES 28 A 361 ASN ALA ILE LYS ASP VAL LEU ALA GLY VAL HET MPD A 401 8 HET EOH A 402 3 HET NAG A 403 14 HET NAG A 404 14 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM EOH ETHANOL HETNAM NAG N-ACETYL-D-GLUCOSAMINE FORMUL 2 MPD C6 H14 O2 FORMUL 3 EOH C2 H6 O FORMUL 4 NAG 2(C8 H15 N O6) FORMUL 5 HOH *412(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 LEU A 62 1 12 HELIX 5 AA5 LYS A 63 ARG A 65 5 3 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 ALA A 274 LEU A 282 1 9 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 ALA A 360 1 12 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 TYR A 35 SHEET 4 AA110 GLY A 113 ALA A 117 1 O ALA A 117 N VAL A 75 SHEET 5 AA110 LEU A 152 PRO A 158 1 O SER A 154 N LEU A 116 SHEET 6 AA110 PHE A 179 LEU A 183 1 O SER A 181 N ALA A 155 SHEET 7 AA110 LEU A 233 PRO A 238 1 O VAL A 234 N ILE A 180 SHEET 8 AA110 GLY A 327 TRP A 331 1 O MET A 329 N ILE A 237 SHEET 9 AA110 LYS A 2 THR A 8 1 N ILE A 4 O VAL A 330 SHEET 10 AA110 HIS A 32 SER A 41 1 O ILE A 34 N TYR A 7 SHEET 1 AA2 3 ILE A 257 PRO A 260 0 SHEET 2 AA2 3 GLY A 241 LEU A 246 -1 N THR A 245 O SER A 258 SHEET 3 AA2 3 ILE A 272 LEU A 273 -1 O LEU A 273 N GLY A 241 SHEET 1 AA3 5 ILE A 257 PRO A 260 0 SHEET 2 AA3 5 GLY A 241 LEU A 246 -1 N THR A 245 O SER A 258 SHEET 3 AA3 5 GLN A 303 ALA A 306 -1 O ALA A 306 N LYS 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 2.08 SSBOND 2 CYS A 279 CYS A 343 1555 1555 2.09 LINK ND2 ASN A 39 C1 NAG A 404 1555 1555 1.55 LINK C1 NAG A 403 O4 NAG A 404 1555 1555 1.42 CISPEP 1 SER A 36 PHE A 37 0 -3.54 CISPEP 2 LEU A 119 TYR A 120 0 1.88 CISPEP 3 GLU A 206 ASP A 207 0 -29.98 CISPEP 4 TRP A 331 ALA A 332 0 7.85 SITE 1 AC1 6 TRP A 10 ARG A 14 TRP A 331 LEU A 335 SITE 2 AC1 6 HOH A 543 HOH A 664 SITE 1 AC2 3 TYR A 185 TRP A 331 HOH A 561 SITE 1 AC3 10 ASN A 39 ILE A 40 SER A 41 TRP A 48 SITE 2 AC3 10 ARG A 84 HOH A 504 HOH A 509 HOH A 687 SITE 3 AC3 10 HOH A 750 HOH A 753 CRYST1 60.457 66.517 105.847 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 0.016541 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015034 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009448 0.00000