HEADER TRANSFERASE 07-MAR-18 6FWT TITLE CRYSTAL STRUCTURE OF HUMAN WILD TYPE BETA-1,4-GALACTOSYLTRANSFERASE-1 TITLE 2 (B4GALT1) IN APO-OPEN MONOMERIC FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-1,4-GALACTOSYLTRANSFERASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: B4GAL-T1,UDP-GAL:BETA-GLCNAC BETA-1,4-GALACTOSYLTRANSFERASE COMPND 5 1,UDP-GALACTOSE:BETA-N-ACETYLGLUCOSAMINE BETA-1; COMPND 6 EC: 2.4.1.-,2.4.1.22,2.4.1.90,2.4.1.38; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: B4GALT1, GGTB2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS GALACTOSYLTRANSFERASE, BETA-1, 4-GALACTOSYLTRANSFERASE I, B4GALT1, KEYWDS 2 GALT1, GLYCOSYLTRANSFERASE, N-LINKED GLYCOSYLATION, APO, MONOMER, KEYWDS 3 MONOMERIC, OPEN CONFORMATION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.HARRUS,S.KELLOKUMPU,T.GLUMOFF REVDAT 3 17-JAN-24 6FWT 1 REMARK REVDAT 2 07-NOV-18 6FWT 1 COMPND JRNL REVDAT 1 10-OCT-18 6FWT 0 JRNL AUTH D.HARRUS,F.KHODER-AGHA,M.PELTONIEMI,A.HASSINEN,L.RUDDOCK, JRNL AUTH 2 S.KELLOKUMPU,T.GLUMOFF JRNL TITL THE DIMERIC STRUCTURE OF WILD-TYPE HUMAN GLYCOSYLTRANSFERASE JRNL TITL 2 B4GALT1. JRNL REF PLOS ONE V. 13 05571 2018 JRNL REFN ESSN 1932-6203 JRNL PMID 30352055 JRNL DOI 10.1371/JOURNAL.PONE.0205571 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 23814 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1191 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 42.2891 - 3.8374 1.00 2685 142 0.1623 0.1792 REMARK 3 2 3.8374 - 3.0461 1.00 2557 134 0.1378 0.2024 REMARK 3 3 3.0461 - 2.6611 1.00 2529 133 0.1646 0.2164 REMARK 3 4 2.6611 - 2.4178 1.00 2499 132 0.1601 0.2291 REMARK 3 5 2.4178 - 2.2446 1.00 2491 131 0.1586 0.2183 REMARK 3 6 2.2446 - 2.1122 1.00 2465 130 0.1764 0.2677 REMARK 3 7 2.1122 - 2.0064 1.00 2474 130 0.1938 0.2828 REMARK 3 8 2.0064 - 1.9191 1.00 2477 131 0.2250 0.3011 REMARK 3 9 1.9191 - 1.8452 0.99 2446 128 0.2658 0.3283 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.550 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 2354 REMARK 3 ANGLE : 1.012 3206 REMARK 3 CHIRALITY : 0.058 339 REMARK 3 PLANARITY : 0.008 423 REMARK 3 DIHEDRAL : 16.439 1431 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6FWT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1200009062. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-FEB-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97950 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23816 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.845 REMARK 200 RESOLUTION RANGE LOW (A) : 42.280 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.11010 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.4700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.96670 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: PHASER REMARK 200 STARTING MODEL: 4EE3 REMARK 200 REMARK 200 REMARK: 50-200 UM STICKS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM NITRATE, 20% (W/V) PEG REMARK 280 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.85800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.17400 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.85800 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 72.17400 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: 280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 SER A 373 O HOH A 501 2.12 REMARK 500 OD1 ASP A 357 O HOH A 502 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 166 NE - CZ - NH1 ANGL. DEV. = 3.0 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 308 -117.97 49.05 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 GOL A 401 DBREF 6FWT A 122 398 UNP P15291 B4GT1_HUMAN 122 398 SEQRES 1 A 277 THR THR ALA LEU SER LEU PRO ALA CYS PRO GLU GLU SER SEQRES 2 A 277 PRO LEU LEU VAL GLY PRO MET LEU ILE GLU PHE ASN MET SEQRES 3 A 277 PRO VAL ASP LEU GLU LEU VAL ALA LYS GLN ASN PRO ASN SEQRES 4 A 277 VAL LYS MET GLY GLY ARG TYR ALA PRO ARG ASP CYS VAL SEQRES 5 A 277 SER PRO HIS LYS VAL ALA ILE ILE ILE PRO PHE ARG ASN SEQRES 6 A 277 ARG GLN GLU HIS LEU LYS TYR TRP LEU TYR TYR LEU HIS SEQRES 7 A 277 PRO VAL LEU GLN ARG GLN GLN LEU ASP TYR GLY ILE TYR SEQRES 8 A 277 VAL ILE ASN GLN ALA GLY ASP THR ILE PHE ASN ARG ALA SEQRES 9 A 277 LYS LEU LEU ASN VAL GLY PHE GLN GLU ALA LEU LYS ASP SEQRES 10 A 277 TYR ASP TYR THR CYS PHE VAL PHE SER ASP VAL ASP LEU SEQRES 11 A 277 ILE PRO MET ASN ASP HIS ASN ALA TYR ARG CYS PHE SER SEQRES 12 A 277 GLN PRO ARG HIS ILE SER VAL ALA MET ASP LYS PHE GLY SEQRES 13 A 277 PHE SER LEU PRO TYR VAL GLN TYR PHE GLY GLY VAL SER SEQRES 14 A 277 ALA LEU SER LYS GLN GLN PHE LEU THR ILE ASN GLY PHE SEQRES 15 A 277 PRO ASN ASN TYR TRP GLY TRP GLY GLY GLU ASP ASP ASP SEQRES 16 A 277 ILE PHE ASN ARG LEU VAL PHE ARG GLY MET SER ILE SER SEQRES 17 A 277 ARG PRO ASN ALA VAL VAL GLY ARG CYS ARG MET ILE ARG SEQRES 18 A 277 HIS SER ARG ASP LYS LYS ASN GLU PRO ASN PRO GLN ARG SEQRES 19 A 277 PHE ASP ARG ILE ALA HIS THR LYS GLU THR MET LEU SER SEQRES 20 A 277 ASP GLY LEU ASN SER LEU THR TYR GLN VAL LEU ASP VAL SEQRES 21 A 277 GLN ARG TYR PRO LEU TYR THR GLN ILE THR VAL ASP ILE SEQRES 22 A 277 GLY THR PRO SER HET GOL A 401 14 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *191(H2 O) HELIX 1 AA1 ASP A 150 ASN A 158 1 9 HELIX 2 AA2 ARG A 187 GLN A 205 1 19 HELIX 3 AA3 ASN A 223 TYR A 239 1 17 HELIX 4 AA4 LYS A 275 GLY A 277 5 3 HELIX 5 AA5 LYS A 294 ILE A 300 1 7 HELIX 6 AA6 GLY A 312 ARG A 324 1 13 HELIX 7 AA7 HIS A 343 LYS A 347 5 5 HELIX 8 AA8 ARG A 358 MET A 366 1 9 HELIX 9 AA9 GLY A 370 LEU A 374 5 5 SHEET 1 AA1 6 ARG A 166 TYR A 167 0 SHEET 2 AA1 6 ASP A 208 GLN A 216 -1 O TYR A 209 N TYR A 167 SHEET 3 AA1 6 LYS A 177 PHE A 184 1 N ILE A 180 O TYR A 212 SHEET 4 AA1 6 CYS A 243 SER A 247 1 O VAL A 245 N ILE A 181 SHEET 5 AA1 6 VAL A 289 SER A 293 -1 O LEU A 292 N PHE A 244 SHEET 6 AA1 6 ARG A 267 HIS A 268 -1 N ARG A 267 O ALA A 291 SHEET 1 AA2 4 ARG A 166 TYR A 167 0 SHEET 2 AA2 4 ASP A 208 GLN A 216 -1 O TYR A 209 N TYR A 167 SHEET 3 AA2 4 THR A 388 ASP A 393 1 O THR A 388 N VAL A 213 SHEET 4 AA2 4 GLN A 377 ARG A 383 -1 N LEU A 379 O THR A 391 SHEET 1 AA3 3 LEU A 251 PRO A 253 0 SHEET 2 AA3 3 ARG A 337 MET A 340 -1 O ARG A 339 N ILE A 252 SHEET 3 AA3 3 ALA A 272 MET A 273 1 N ALA A 272 O CYS A 338 SSBOND 1 CYS A 130 CYS A 172 1555 1555 2.03 SSBOND 2 CYS A 243 CYS A 262 1555 1555 2.01 SITE 1 AC1 6 ARG A 224 PHE A 246 PHE A 286 GLY A 288 SITE 2 AC1 6 SER A 290 ASP A 314 CRYST1 42.278 43.716 144.348 90.00 90.00 90.00 P 2 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 0.023653 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022875 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006928 0.00000