PDB Short entry for 5AJP HEADER TRANSFERASE 26-FEB-15 5AJP TITLE CRYSTAL STRUCTURE OF THE ACTIVE FORM OF GALNAC-T2 IN COMPLEX WITH UDP TITLE 2 AND THE GLYCOPEPTIDE MUC5AC-13 COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POLYPEPTIDE GALNAC TRANSFERASE 2, GALNAC-T2, PP-GANTASE 2, COMPND 5 PROTEIN-UDP ACETYLGALACTOSAMINYLTRANSFERASE 2, UDP- COMPND 6 GALNAC\:POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2, POLYPEPTIDE COMPND 7 N-ACETYLGALACTOSAMINYLTRANSFERASE 2 SOLUBLE FORM; COMPND 8 EC: 2.4.1.41; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: MUCIN; COMPND 13 CHAIN: B; COMPND 14 FRAGMENT: RESIDUES 65-79; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: SMD1168; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PPICZALPHAA; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: SMD1168; SOURCE 15 EXPRESSION_SYSTEM_VECTOR: PPICZALPHAA KEYWDS TRANSFERASE, GALNAC-T2, AFM, SAXS, LECTIN DOMAIN, COARSE-GRAINED KEYWDS 2 MODEL, GLYCOPEPTIDES, INACTIVE FORM, ACTIVE FORM, COMPACT FORM, KEYWDS 3 EXTENDED FORM EXPDTA X-RAY DIFFRACTION AUTHOR E.LIRA-NAVARRETE,M.DELASRIVAS,I.COMPANON,M.C.PALLARES,Y.KONG, AUTHOR 2 J.IGLESIAS-FERNANDEZ,G.J.L.BERNARDES,J.M.PEREGRINA,C.ROVIRA, AUTHOR 3 P.BERNADO,P.BRUSCOLINI,H.CLAUSEN,A.LOSTAO,F.CORZANA,R.HURTADO- AUTHOR 4 GUERRERO REVDAT 4 10-JAN-24 5AJP 1 HETSYN REVDAT 3 29-JUL-20 5AJP 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 20-MAY-15 5AJP 1 JRNL REVDAT 1 11-MAR-15 5AJP 0 JRNL AUTH E.LIRA-NAVARRETE,M.DE LAS RIVAS,I.COMPANON,M.C.PALLARES, JRNL AUTH 2 Y.KONG,J.IGLESIAS-FERNANDEZ,G.J.L.BERNARDES,J.M.PEREGRINA, JRNL AUTH 3 C.ROVIRA,P.BERNADO,P.BRUSCOLINI,H.CLAUSEN,A.LOSTAO, JRNL AUTH 4 F.CORZANA,R.HURTADO-GUERRERO JRNL TITL DYNAMIC INTERPLAY BETWEEN CATALYTIC AND LECTIN DOMAINS OF JRNL TITL 2 GALNAC-TRANSFERASES MODULATES PROTEIN O-GLYCOSYLATION. JRNL REF NAT.COMMUN. V. 6 6937 2015 JRNL REFN ESSN 2041-1723 JRNL PMID 25939779 JRNL DOI 10.1038/NCOMMS7937 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 89.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 77496 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) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.700 REMARK 3 FREE R VALUE TEST SET COUNT : 2187 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) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5645 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.41 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE SET COUNT : 161 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4061 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 145 REMARK 3 SOLVENT ATOMS : 611 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.75000 REMARK 3 B22 (A**2) : -0.75000 REMARK 3 B33 (A**2) : 1.51000 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): 0.075 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.077 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.056 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.196 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.963 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4313 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3980 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5867 ; 1.627 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9153 ; 0.831 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 517 ; 6.360 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 206 ;33.460 ;23.398 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 722 ;13.110 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;18.211 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 634 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4792 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1013 ; 0.001 ; 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): 2044 ; 1.632 ; 2.166 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2043 ; 1.631 ; 2.165 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2554 ; 2.393 ; 3.244 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2269 ; 2.820 ; 2.640 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : A 75 A 569 REMARK 3 ORIGIN FOR THE GROUP (A): 9.7578 13.5425 0.2182 REMARK 3 T TENSOR REMARK 3 T11: 0.0310 T22: 0.0063 REMARK 3 T33: 0.0156 T12: -0.0051 REMARK 3 T13: -0.0199 T23: 0.0034 REMARK 3 L TENSOR REMARK 3 L11: 0.0127 L22: 0.4326 REMARK 3 L33: 0.1423 L12: -0.0065 REMARK 3 L13: 0.0113 L23: -0.0782 REMARK 3 S TENSOR REMARK 3 S11: 0.0142 S12: 0.0017 S13: -0.0103 REMARK 3 S21: 0.0197 S22: -0.0262 S23: -0.0404 REMARK 3 S31: -0.0242 S32: 0.0070 S33: 0.0120 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 : B 2 B 16 REMARK 3 ORIGIN FOR THE GROUP (A): 3.9872 8.7275 8.7583 REMARK 3 T TENSOR REMARK 3 T11: 0.0405 T22: 0.0274 REMARK 3 T33: 0.0136 T12: 0.0062 REMARK 3 T13: -0.0175 T23: 0.0086 REMARK 3 L TENSOR REMARK 3 L11: 0.0051 L22: 0.8997 REMARK 3 L33: 3.2653 L12: -0.0628 REMARK 3 L13: -0.0084 L23: -0.3511 REMARK 3 S TENSOR REMARK 3 S11: 0.0035 S12: 0.0012 S13: -0.0020 REMARK 3 S21: 0.0625 S22: 0.0198 S23: 0.0075 REMARK 3 S31: -0.1069 S32: -0.2010 S33: -0.0234 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 5AJP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1290063150. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 79709 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.1000 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) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.60000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.900 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: PDB ENTRY 4D0T REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,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 43.63300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 43.63300 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 89.29500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 43.63300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 44.64750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 43.63300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 133.94250 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 43.63300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.63300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 89.29500 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 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 43.63300 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 133.94250 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 43.63300 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 44.64750 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -238.2 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 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 A2112 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2165 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2166 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 MET A 1 REMARK 465 ARG A 2 REMARK 465 ARG A 3 REMARK 465 ARG A 4 REMARK 465 SER A 5 REMARK 465 ARG A 6 REMARK 465 MET A 7 REMARK 465 LEU A 8 REMARK 465 LEU A 9 REMARK 465 CYS A 10 REMARK 465 PHE A 11 REMARK 465 ALA A 12 REMARK 465 PHE A 13 REMARK 465 LEU A 14 REMARK 465 TRP A 15 REMARK 465 VAL A 16 REMARK 465 LEU A 17 REMARK 465 GLY A 18 REMARK 465 ILE A 19 REMARK 465 ALA A 20 REMARK 465 TYR A 21 REMARK 465 TYR A 22 REMARK 465 MET A 23 REMARK 465 TYR A 24 REMARK 465 SER A 25 REMARK 465 GLY A 26 REMARK 465 GLY A 27 REMARK 465 GLY A 28 REMARK 465 SER A 29 REMARK 465 ALA A 30 REMARK 465 LEU A 31 REMARK 465 ALA A 32 REMARK 465 GLY A 33 REMARK 465 GLY A 34 REMARK 465 ALA A 35 REMARK 465 GLY A 36 REMARK 465 GLY A 37 REMARK 465 GLY A 38 REMARK 465 ALA A 39 REMARK 465 GLY A 40 REMARK 465 ARG A 41 REMARK 465 LYS A 42 REMARK 465 GLU A 43 REMARK 465 ASP A 44 REMARK 465 TRP A 45 REMARK 465 ASN A 46 REMARK 465 GLU A 47 REMARK 465 ILE A 48 REMARK 465 ASP A 49 REMARK 465 PRO A 50 REMARK 465 ILE A 51 REMARK 465 LYS A 52 REMARK 465 LYS A 53 REMARK 465 LYS A 54 REMARK 465 ASP A 55 REMARK 465 LEU A 56 REMARK 465 HIS A 57 REMARK 465 HIS A 58 REMARK 465 SER A 59 REMARK 465 ASN A 60 REMARK 465 GLY A 61 REMARK 465 GLU A 62 REMARK 465 GLU A 63 REMARK 465 LYS A 64 REMARK 465 ALA A 65 REMARK 465 GLN A 66 REMARK 465 SER A 67 REMARK 465 MET A 68 REMARK 465 GLU A 69 REMARK 465 THR A 70 REMARK 465 LEU A 71 REMARK 465 PRO A 72 REMARK 465 PRO A 73 REMARK 465 GLY A 74 REMARK 465 GLN A 570 REMARK 465 GLN A 571 REMARK 465 ALA B 0 REMARK 465 GLY B 1 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 ALA B 16 CA C O CB 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 A 116 CB - CG - CD ANGL. DEV. = 19.6 DEGREES REMARK 500 ARG A 116 CD - NE - CZ ANGL. DEV. = 14.9 DEGREES REMARK 500 ARG A 116 NE - CZ - NH1 ANGL. DEV. = 12.7 DEGREES REMARK 500 ARG A 116 NE - CZ - NH2 ANGL. DEV. = -11.2 DEGREES REMARK 500 ARG A 154 NE - CZ - NH2 ANGL. DEV. = -3.1 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 LYS A 192 -17.13 82.49 REMARK 500 LYS A 323 -119.83 56.08 REMARK 500 VAL A 330 -77.90 58.41 REMARK 500 ASP A 390 -136.10 57.20 REMARK 500 PHE A 463 -167.52 -124.40 REMARK 500 ASP A 465 -2.24 78.51 REMARK 500 MET A 493 -120.71 54.97 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 A2118 DISTANCE = 6.46 ANGSTROMS REMARK 525 HOH A2119 DISTANCE = 6.61 ANGSTROMS REMARK 525 HOH A2132 DISTANCE = 5.98 ANGSTROMS REMARK 525 HOH A3013 DISTANCE = 6.65 ANGSTROMS REMARK 525 HOH A3014 DISTANCE = 6.54 ANGSTROMS REMARK 525 HOH A3015 DISTANCE = 9.54 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A1572 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 224 OD2 REMARK 620 2 HIS A 226 NE2 101.7 REMARK 620 3 HIS A 359 NE2 87.9 95.5 REMARK 620 4 UDP A1570 O2A 95.1 85.5 176.5 REMARK 620 5 UDP A1570 O1B 86.2 169.5 91.6 87.0 REMARK 620 6 HOH A2257 O 173.6 84.3 89.2 87.7 88.1 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5AJN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE INACTIVE FORM OF GALNAC-T2 IN COMPLEX WITH REMARK 900 THE GLYCOPEPTIDE MUC5AC-CYS13 REMARK 900 RELATED ID: 5AJO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE INACTIVE FORM OF GALNAC-T2 IN COMPLEX WITH REMARK 900 THE GLYCOPEPTIDE MUC5AC-3,13 DBREF 5AJP A 1 571 UNP Q10471 GALT2_HUMAN 1 571 DBREF 5AJP B 1 15 UNP Q14886 Q14886_HUMAN 65 79 SEQADV 5AJP ASP A 516 UNP Q10471 ASN 516 ENGINEERED MUTATION SEQADV 5AJP ALA B 0 UNP Q14886 EXPRESSION TAG SEQADV 5AJP ALA B 16 UNP Q14886 EXPRESSION TAG SEQRES 1 A 571 MET ARG ARG ARG SER ARG MET LEU LEU CYS PHE ALA PHE SEQRES 2 A 571 LEU TRP VAL LEU GLY ILE ALA TYR TYR MET TYR SER GLY SEQRES 3 A 571 GLY GLY SER ALA LEU ALA GLY GLY ALA GLY GLY GLY ALA SEQRES 4 A 571 GLY ARG LYS GLU ASP TRP ASN GLU ILE ASP PRO ILE LYS SEQRES 5 A 571 LYS LYS ASP LEU HIS HIS SER ASN GLY GLU GLU LYS ALA SEQRES 6 A 571 GLN SER MET GLU THR LEU PRO PRO GLY LYS VAL ARG TRP SEQRES 7 A 571 PRO ASP PHE ASN GLN GLU ALA TYR VAL GLY GLY THR MET SEQRES 8 A 571 VAL ARG SER GLY GLN ASP PRO TYR ALA ARG ASN LYS PHE SEQRES 9 A 571 ASN GLN VAL GLU SER ASP LYS LEU ARG MET ASP ARG ALA SEQRES 10 A 571 ILE PRO ASP THR ARG HIS ASP GLN CYS GLN ARG LYS GLN SEQRES 11 A 571 TRP ARG VAL ASP LEU PRO ALA THR SER VAL VAL ILE THR SEQRES 12 A 571 PHE HIS ASN GLU ALA ARG SER ALA LEU LEU ARG THR VAL SEQRES 13 A 571 VAL SER VAL LEU LYS LYS SER PRO PRO HIS LEU ILE LYS SEQRES 14 A 571 GLU ILE ILE LEU VAL ASP ASP TYR SER ASN ASP PRO GLU SEQRES 15 A 571 ASP GLY ALA LEU LEU GLY LYS ILE GLU LYS VAL ARG VAL SEQRES 16 A 571 LEU ARG ASN ASP ARG ARG GLU GLY LEU MET ARG SER ARG SEQRES 17 A 571 VAL ARG GLY ALA ASP ALA ALA GLN ALA LYS VAL LEU THR SEQRES 18 A 571 PHE LEU ASP SER HIS CYS GLU CYS ASN GLU HIS TRP LEU SEQRES 19 A 571 GLU PRO LEU LEU GLU ARG VAL ALA GLU ASP ARG THR ARG SEQRES 20 A 571 VAL VAL SER PRO ILE ILE ASP VAL ILE ASN MET ASP ASN SEQRES 21 A 571 PHE GLN TYR VAL GLY ALA SER ALA ASP LEU LYS GLY GLY SEQRES 22 A 571 PHE ASP TRP ASN LEU VAL PHE LYS TRP ASP TYR MET THR SEQRES 23 A 571 PRO GLU GLN ARG ARG SER ARG GLN GLY ASN PRO VAL ALA SEQRES 24 A 571 PRO ILE LYS THR PRO MET ILE ALA GLY GLY LEU PHE VAL SEQRES 25 A 571 MET ASP LYS PHE TYR PHE GLU GLU LEU GLY LYS TYR ASP SEQRES 26 A 571 MET MET MET ASP VAL TRP GLY GLY GLU ASN LEU GLU ILE SEQRES 27 A 571 SER PHE ARG VAL TRP GLN CYS GLY GLY SER LEU GLU ILE SEQRES 28 A 571 ILE PRO CYS SER ARG VAL GLY HIS VAL PHE ARG LYS GLN SEQRES 29 A 571 HIS PRO TYR THR PHE PRO GLY GLY SER GLY THR VAL PHE SEQRES 30 A 571 ALA ARG ASN THR ARG ARG ALA ALA GLU VAL TRP MET ASP SEQRES 31 A 571 GLU TYR LYS ASN PHE TYR TYR ALA ALA VAL PRO SER ALA SEQRES 32 A 571 ARG ASN VAL PRO TYR GLY ASN ILE GLN SER ARG LEU GLU SEQRES 33 A 571 LEU ARG LYS LYS LEU SER CYS LYS PRO PHE LYS TRP TYR SEQRES 34 A 571 LEU GLU ASN VAL TYR PRO GLU LEU ARG VAL PRO ASP HIS SEQRES 35 A 571 GLN ASP ILE ALA PHE GLY ALA LEU GLN GLN GLY THR ASN SEQRES 36 A 571 CYS LEU ASP THR LEU GLY HIS PHE ALA ASP GLY VAL VAL SEQRES 37 A 571 GLY VAL TYR GLU CYS HIS ASN ALA GLY GLY ASN GLN GLU SEQRES 38 A 571 TRP ALA LEU THR LYS GLU LYS SER VAL LYS HIS MET ASP SEQRES 39 A 571 LEU CYS LEU THR VAL VAL ASP ARG ALA PRO GLY SER LEU SEQRES 40 A 571 ILE LYS LEU GLN GLY CYS ARG GLU ASP ASP SER ARG GLN SEQRES 41 A 571 LYS TRP GLU GLN ILE GLU GLY ASN SER LYS LEU ARG HIS SEQRES 42 A 571 VAL GLY SER ASN LEU CYS LEU ASP SER ARG THR ALA LYS SEQRES 43 A 571 SER GLY GLY LEU SER VAL GLU VAL CYS GLY PRO ALA LEU SEQRES 44 A 571 SER GLN GLN TRP LYS PHE THR LEU ASN LEU GLN GLN SEQRES 1 B 17 ALA GLY THR THR PRO SER PRO VAL PRO THR THR SER THR SEQRES 2 B 17 THR SER ALA ALA MODRES 5AJP THR B 13 THR GLYCOSYLATION SITE HET UDP A1570 25 HET SO4 A1571 5 HET MN A1572 1 HET SO4 A1573 5 HET SO4 A1574 5 HET SO4 A1575 5 HET SO4 A1576 5 HET SO4 A1577 5 HET SO4 A1578 5 HET SO4 A1579 5 HET SO4 A1580 5 HET SO4 A1581 5 HET SO4 A1582 5 HET SO4 A1583 5 HET SO4 A1584 5 HET SO4 A1585 5 HET SO4 A1586 5 HET SO4 A1587 5 HET SO4 A1588 5 HET SO4 A1589 5 HET SO4 A1590 5 HET SO4 A1591 5 HET SO4 A1592 5 HET A2G B 17 14 HETNAM UDP URIDINE-5'-DIPHOSPHATE HETNAM SO4 SULFATE ION HETNAM MN MANGANESE (II) ION HETNAM A2G 2-ACETAMIDO-2-DEOXY-ALPHA-D-GALACTOPYRANOSE HETSYN A2G N-ACETYL-ALPHA-D-GALACTOSAMINE; 2-ACETAMIDO-2-DEOXY- HETSYN 2 A2G ALPHA-D-GALACTOSE; 2-ACETAMIDO-2-DEOXY-D-GALACTOSE; 2- HETSYN 3 A2G ACETAMIDO-2-DEOXY-GALACTOSE; N-ACETYL-2-DEOXY-2-AMINO- HETSYN 4 A2G GALACTOSE FORMUL 3 UDP C9 H14 N2 O12 P2 FORMUL 4 SO4 21(O4 S 2-) FORMUL 5 MN MN 2+ FORMUL 26 A2G C8 H15 N O6 FORMUL 27 HOH *611(H2 O) HELIX 1 1 ARG A 77 PHE A 81 5 5 HELIX 2 2 ASN A 82 GLY A 89 1 8 HELIX 3 3 ASN A 105 LEU A 112 1 8 HELIX 4 4 HIS A 123 LYS A 129 5 7 HELIX 5 5 ALA A 148 SER A 163 1 16 HELIX 6 6 PRO A 164 HIS A 166 5 3 HELIX 7 7 PRO A 181 LEU A 186 1 6 HELIX 8 8 LEU A 187 LYS A 189 5 3 HELIX 9 9 GLU A 202 ALA A 215 1 14 HELIX 10 10 LEU A 234 ASP A 244 1 11 HELIX 11 11 THR A 286 ASN A 296 1 11 HELIX 12 12 LYS A 315 LEU A 321 1 7 HELIX 13 13 GLY A 333 CYS A 345 1 13 HELIX 14 14 GLY A 372 MET A 389 1 18 HELIX 15 15 TYR A 392 VAL A 400 1 9 HELIX 16 16 PRO A 401 VAL A 406 5 6 HELIX 17 17 ILE A 411 LEU A 421 1 11 HELIX 18 18 PRO A 425 VAL A 433 1 9 HELIX 19 19 GLY A 477 GLU A 481 5 5 HELIX 20 20 ASP A 517 GLN A 520 5 4 HELIX 21 21 THR A 544 GLY A 548 5 5 HELIX 22 22 ALA A 558 GLN A 562 5 5 SHEET 1 AA 5 VAL A 193 ARG A 197 0 SHEET 2 AA 5 ILE A 168 ASP A 175 1 O ILE A 171 N ARG A 194 SHEET 3 AA 5 THR A 138 PHE A 144 1 O THR A 138 N LYS A 169 SHEET 4 AA 5 VAL A 219 PHE A 222 1 O VAL A 219 N SER A 139 SHEET 5 AA 5 PHE A 311 ASP A 314 -1 O PHE A 311 N PHE A 222 SHEET 1 AB 2 CYS A 227 CYS A 229 0 SHEET 2 AB 2 SER A 348 HIS A 359 -1 O GLY A 358 N GLU A 228 SHEET 1 AC 4 TYR A 263 VAL A 264 0 SHEET 2 AC 4 ARG A 247 ILE A 256 -1 O VAL A 255 N VAL A 264 SHEET 3 AC 4 SER A 348 HIS A 359 1 O SER A 348 N VAL A 248 SHEET 4 AC 4 ILE A 301 LYS A 302 1 O ILE A 301 N ILE A 351 SHEET 1 AD 4 TYR A 263 VAL A 264 0 SHEET 2 AD 4 ARG A 247 ILE A 256 -1 O VAL A 255 N VAL A 264 SHEET 3 AD 4 SER A 348 HIS A 359 1 O SER A 348 N VAL A 248 SHEET 4 AD 4 CYS A 227 CYS A 229 -1 O GLU A 228 N GLY A 358 SHEET 1 AE 2 ILE A 301 LYS A 302 0 SHEET 2 AE 2 SER A 348 HIS A 359 1 O ILE A 351 N ILE A 301 SHEET 1 AF 2 LEU A 270 PHE A 274 0 SHEET 2 AF 2 PHE A 280 TYR A 284 -1 O LYS A 281 N GLY A 273 SHEET 1 AG 4 GLY A 469 GLU A 472 0 SHEET 2 AG 4 ASN A 455 ASP A 458 1 O CYS A 456 N TYR A 471 SHEET 3 AG 4 ALA A 446 GLN A 452 -1 O LEU A 450 N LEU A 457 SHEET 4 AG 4 LYS A 564 ASN A 568 -1 O LYS A 564 N GLN A 451 SHEET 1 AH 7 GLY A 469 GLU A 472 0 SHEET 2 AH 7 ASN A 455 ASP A 458 1 O CYS A 456 N TYR A 471 SHEET 3 AH 7 ALA A 446 GLN A 452 -1 O LEU A 450 N LEU A 457 SHEET 4 AH 7 TRP A 482 LEU A 484 -1 O TRP A 482 N GLY A 448 SHEET 5 AH 7 VAL A 490 HIS A 492 -1 O LYS A 491 N ALA A 483 SHEET 6 AH 7 LEU A 495 THR A 498 -1 O LEU A 495 N HIS A 492 SHEET 7 AH 7 LYS A 509 GLY A 512 -1 O LYS A 509 N THR A 498 SHEET 1 AI 2 LYS A 564 ASN A 568 0 SHEET 2 AI 2 ALA A 446 GLN A 452 -1 O PHE A 447 N LEU A 567 SHEET 1 AJ 2 TRP A 522 ILE A 525 0 SHEET 2 AJ 2 LYS A 530 HIS A 533 -1 O LYS A 530 N ILE A 525 SHEET 1 AK 2 LEU A 538 ASP A 541 0 SHEET 2 AK 2 SER A 551 VAL A 554 -1 O SER A 551 N ASP A 541 SSBOND 1 CYS A 126 CYS A 354 1555 1555 2.09 SSBOND 2 CYS A 345 CYS A 423 1555 1555 2.05 SSBOND 3 CYS A 456 CYS A 473 1555 1555 2.05 SSBOND 4 CYS A 496 CYS A 513 1555 1555 2.05 SSBOND 5 CYS A 539 CYS A 555 1555 1555 2.10 LINK OG1 THR B 13 C1 A2G B 17 1555 1555 1.41 LINK OD2 ASP A 224 MN MN A1572 1555 1555 2.28 LINK NE2 HIS A 226 MN MN A1572 1555 1555 2.23 LINK NE2 HIS A 359 MN MN A1572 1555 1555 2.22 LINK O2A UDP A1570 MN MN A1572 1555 1555 2.12 LINK O1B UDP A1570 MN MN A1572 1555 1555 2.12 LINK MN MN A1572 O HOH A2257 1555 1555 2.29 CISPEP 1 GLY A 308 GLY A 309 0 -22.82 CRYST1 87.266 87.266 178.590 90.00 90.00 90.00 I 41 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.011459 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011459 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005599 0.00000