HEADER SIGNALING PROTEIN 18-DEC-17 5Z05 TITLE CRYSTAL STRUCTURE OF SIGNALLING PROTEIN FROM BUFFALO (SPB-40) WITH AN TITLE 2 ACETONE INDUCED CONFORMATION OF TRP78 AT 1.49 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHITINASE-3-LIKE PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 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 5 22-NOV-23 5Z05 1 HETSYN REVDAT 4 29-JUL-20 5Z05 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 11-APR-18 5Z05 1 JRNL REVDAT 2 21-MAR-18 5Z05 1 SPRSDE JRNL REVDAT 1 31-JAN-18 5Z05 0 SPRSDE 21-MAR-18 5Z05 5WSI JRNL AUTH A.CHAUDHARY,V.KUMAR,P.K.SINGH,P.SHARMA,H.R.BAIRAGYA,P.KAUR, JRNL AUTH 2 S.SHARMA,S.S.CHAUHAN,T.P.SINGH JRNL TITL A GLYCOPROTEIN FROM MAMMARY GLAND SECRETED DURING INVOLUTION JRNL TITL 2 PROMOTES APOPTOSIS: STRUCTURAL AND BIOLOGICAL STUDIES JRNL REF ARCH. BIOCHEM. BIOPHYS. V. 644 72 2018 JRNL REFN ESSN 1096-0384 JRNL PMID 29524427 JRNL DOI 10.1016/J.ABB.2018.03.006 REMARK 2 REMARK 2 RESOLUTION. 1.49 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 : 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) : 0.147 REMARK 3 FREE R VALUE : 0.176 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) : 0.2150 REMARK 3 BIN FREE R VALUE SET COUNT : 244 REMARK 3 BIN FREE R VALUE : 0.1980 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 : 40 REMARK 3 SOLVENT ATOMS : 413 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.29000 REMARK 3 B22 (A**2) : -0.75000 REMARK 3 B33 (A**2) : -0.54000 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): 0.061 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.041 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.435 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): 3003 ; 0.038 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2723 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4078 ; 3.117 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6300 ; 1.840 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 359 ; 7.178 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 141 ;33.158 ;23.262 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 479 ;13.297 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;24.269 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 438 ; 0.191 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3339 ; 0.017 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 668 ; 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): 1444 ; 1.672 ; 1.389 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1442 ; 1.667 ; 1.385 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1801 ; 2.307 ; 2.076 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1802 ; 2.309 ; 2.078 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1559 ; 2.536 ; 1.676 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1560 ; 2.535 ; 1.677 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2278 ; 3.723 ; 2.422 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3572 ; 4.811 ;17.709 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3572 ; 4.811 ;17.710 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 912 REMARK 3 ORIGIN FOR THE GROUP (A): 8.6865 2.4425 46.1225 REMARK 3 T TENSOR REMARK 3 T11: 0.0062 T22: 0.0306 REMARK 3 T33: 0.0412 T12: 0.0021 REMARK 3 T13: 0.0030 T23: -0.0256 REMARK 3 L TENSOR REMARK 3 L11: 1.1054 L22: 1.4136 REMARK 3 L33: 1.6532 L12: -0.1033 REMARK 3 L13: 0.1866 L23: -0.8330 REMARK 3 S TENSOR REMARK 3 S11: 0.0051 S12: 0.0717 S13: -0.0586 REMARK 3 S21: 0.0199 S22: 0.0079 S23: 0.0313 REMARK 3 S31: -0.0891 S32: -0.0702 S33: -0.0130 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 5Z05 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1300006208. 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 : 5-8 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 : 11.4000 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 : 2.200 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: 5WSI 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): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35MM TRIS -HCL PH- 8.0, 25MM NACL, 20% REMARK 280 ACETONE., 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, 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: 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 504 O HOH A 804 2.07 REMARK 500 O HOH A 701 O HOH A 781 2.14 REMARK 500 OE2 GLU A 269 O HOH A 501 2.14 REMARK 500 O3 NAG B 1 O HOH A 502 2.19 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 0.100 REMARK 500 CYS A 5 CA CYS A 5 CB -0.080 REMARK 500 TYR A 6 CZ TYR A 6 CE2 -0.098 REMARK 500 TYR A 7 CZ TYR A 7 OH 0.180 REMARK 500 SER A 9 CA SER A 9 CB -0.128 REMARK 500 CYS A 20 CB CYS A 20 SG -0.113 REMARK 500 CYS A 20 C CYS A 20 O 0.139 REMARK 500 TYR A 35 CE1 TYR A 35 CZ -0.093 REMARK 500 SER A 36 CB SER A 36 OG -0.174 REMARK 500 GLU A 44 CG GLU A 44 CD -0.096 REMARK 500 GLU A 49 CD GLU A 49 OE1 -0.082 REMARK 500 TYR A 56 CZ TYR A 56 CE2 -0.115 REMARK 500 LYS A 63 CD LYS A 63 CE -0.183 REMARK 500 PHE A 80 CG PHE A 80 CD1 -0.092 REMARK 500 GLY A 81 N GLY A 81 CA 0.144 REMARK 500 SER A 82 CB SER A 82 OG 0.087 REMARK 500 ARG A 84 CZ ARG A 84 NH2 -0.091 REMARK 500 PHE A 85 CD1 PHE A 85 CE1 -0.153 REMARK 500 LYS A 91 CE LYS A 91 NZ -0.267 REMARK 500 SER A 94 CB SER A 94 OG 0.086 REMARK 500 ARG A 142 CZ ARG A 142 NH1 0.080 REMARK 500 SER A 174 CB SER A 174 OG -0.097 REMARK 500 TRP A 191 CE2 TRP A 191 CZ2 0.125 REMARK 500 TRP A 191 CE3 TRP A 191 CZ3 0.133 REMARK 500 SER A 214 CB SER A 214 OG -0.087 REMARK 500 TYR A 222 CZ TYR A 222 CE2 -0.079 REMARK 500 ARG A 225 CG ARG A 225 CD 0.188 REMARK 500 GLY A 227 CA GLY A 227 C -0.138 REMARK 500 TYR A 244 CE1 TYR A 244 CZ -0.087 REMARK 500 GLY A 261 N GLY A 261 CA 0.096 REMARK 500 GLN A 265 CD GLN A 265 OE1 0.136 REMARK 500 ASP A 280 CB ASP A 280 CG -0.158 REMARK 500 GLU A 311 CG GLU A 311 CD 0.144 REMARK 500 GLU A 311 CD GLU A 311 OE1 0.070 REMARK 500 TRP A 331 CE3 TRP A 331 CZ3 0.105 REMARK 500 ASP A 357 CB ASP A 357 CG 0.142 REMARK 500 GLY A 361 CA GLY A 361 C 0.115 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. = 8.0 DEGREES REMARK 500 ASP A 26 CB - CG - OD1 ANGL. DEV. = 8.0 DEGREES REMARK 500 ASP A 26 CB - CG - OD2 ANGL. DEV. = -8.0 DEGREES REMARK 500 GLU A 49 CG - CD - OE1 ANGL. DEV. = 12.6 DEGREES REMARK 500 ASP A 52 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 TYR A 56 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 TYR A 56 CB - CG - CD1 ANGL. DEV. = 4.2 DEGREES REMARK 500 THR A 61 OG1 - CB - CG2 ANGL. DEV. = 15.0 DEGREES REMARK 500 ARG A 84 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 84 NE - CZ - NH2 ANGL. DEV. = -6.9 DEGREES REMARK 500 ARG A 84 O - C - N ANGL. DEV. = -14.1 DEGREES REMARK 500 LYS A 91 CD - CE - NZ ANGL. DEV. = 23.6 DEGREES REMARK 500 ARG A 95 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 107 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 127 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 127 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 142 CD - NE - CZ ANGL. DEV. = 11.2 DEGREES REMARK 500 ARG A 142 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 TYR A 168 CB - CG - CD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 TYR A 168 CB - CG - CD1 ANGL. DEV. = -6.5 DEGREES REMARK 500 ARG A 175 NE - CZ - NH1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP A 178 CB - CG - OD2 ANGL. DEV. = 9.8 DEGREES REMARK 500 TYR A 185 CB - CG - CD1 ANGL. DEV. = 3.6 DEGREES REMARK 500 GLN A 193 C - N - CA ANGL. DEV. = -18.7 DEGREES REMARK 500 ASP A 207 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG A 225 NE - CZ - NH2 ANGL. DEV. = 7.8 DEGREES REMARK 500 ASP A 252 CB - CG - OD1 ANGL. DEV. = 8.1 DEGREES REMARK 500 ASP A 252 CB - CG - OD2 ANGL. DEV. = -8.7 DEGREES REMARK 500 ASP A 280 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG A 289 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 LYS A 300 CG - CD - CE ANGL. DEV. = 18.5 DEGREES REMARK 500 GLU A 311 OE1 - CD - OE2 ANGL. DEV. = -7.5 DEGREES REMARK 500 ARG A 318 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 318 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 323 NE - CZ - NH1 ANGL. DEV. = -6.8 DEGREES REMARK 500 ARG A 323 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 ASP A 334 CB - CG - OD2 ANGL. DEV. = -5.7 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 -38.28 -37.85 REMARK 500 TYR A 185 25.77 -157.43 REMARK 500 ALA A 208 105.74 -163.40 REMARK 500 SER A 209 119.50 -167.79 REMARK 500 ASN A 346 54.75 39.72 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 -129.36 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 LYS A 300 -10.09 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 A 913 DISTANCE = 5.88 ANGSTROMS DBREF 5Z05 A 1 361 UNP Q7YS85 CH3L1_BUBBU 22 383 SEQADV 5Z05 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 NAG B 1 14 HET NAG B 2 14 HET MPD A 401 8 HET ACN A 404 4 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM ACN ACETONE 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 2(C8 H15 N O6) FORMUL 3 MPD C6 H14 O2 FORMUL 4 ACN C3 H6 O FORMUL 5 HOH *413(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 PHE A 290 O VAL A 295 SSBOND 1 CYS A 5 CYS A 30 1555 1555 2.09 SSBOND 2 CYS A 279 CYS A 343 1555 1555 2.08 LINK ND2 ASN A 39 C1 NAG B 1 1555 1555 1.54 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.40 CISPEP 1 SER A 36 PHE A 37 0 -4.52 CISPEP 2 LEU A 119 TYR A 120 0 3.90 CISPEP 3 GLU A 206 ASP A 207 0 -24.33 CISPEP 4 TRP A 331 ALA A 332 0 10.54 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