HEADER TRANSFERASE 11-FEB-09 3G7Y TITLE CRYSTAL STRUCTURE OF OXIDIZED OST6L COMPND MOL_ID: 1; COMPND 2 MOLECULE: DOLICHYL-DIPHOSPHOOLIGOSACCHARIDE-PROTEIN COMPND 3 GLYCOSYLTRANSFERASE SUBUNIT OST6; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: N-TERMINAL DOMAIN; COMPND 6 SYNONYM: OLIGOSACCHARYL TRANSFERASE SUBUNIT OST6, OLIGOSACCHARYL COMPND 7 TRANSFERASE 37 KDA SUBUNIT, OTASE 37 KDA SUBUNIT; COMPND 8 EC: 2.4.1.119; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BREWER'S YEAST,LAGER BEER YEAST,YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: OST6, YML019W; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: TOP 10; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PBAD-OST6L-HIS10 KEYWDS OXIDOREDUCTASE, ACTIVE SITE LOOP, REDOX STATE, MEMBRANE, TRANSFERASE, KEYWDS 2 TRANSMEMBRANE EXPDTA X-RAY DIFFRACTION AUTHOR C.U.STIRNIMANN,J.P.A.GRIMSHAW,B.L.SCHULZ,M.S.BROZZO,F.FRITSCH, AUTHOR 2 R.GLOCKSHUBER,G.CAPITANI,M.G.GRUETTER,M.AEBI REVDAT 3 03-APR-24 3G7Y 1 SEQADV REVDAT 2 21-JUL-09 3G7Y 1 JRNL REVDAT 1 16-JUN-09 3G7Y 0 JRNL AUTH B.L.SCHULZ,C.U.STIRNIMANN,J.P.GRIMSHAW,M.S.BROZZO,F.FRITSCH, JRNL AUTH 2 E.MOHORKO,G.CAPITANI,R.GLOCKSHUBER,M.G.GRUTTER,M.AEBI JRNL TITL OXIDOREDUCTASE ACTIVITY OF OLIGOSACCHARYLTRANSFERASE JRNL TITL 2 SUBUNITS OST3P AND OST6P DEFINES SITE-SPECIFIC GLYCOSYLATION JRNL TITL 3 EFFICIENCY. JRNL REF PROC.NATL.ACAD.SCI.USA V. 106 11061 2009 JRNL REFN ISSN 0027-8424 JRNL PMID 19549845 JRNL DOI 10.1073/PNAS.0812515106 REMARK 2 REMARK 2 RESOLUTION. 2.22 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.22 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 9387 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 12.360 REMARK 3 FREE R VALUE TEST SET COUNT : 1160 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 22.3169 - 4.4205 1.00 1112 144 0.2023 0.2581 REMARK 3 2 4.4205 - 3.5131 1.00 1052 138 0.1788 0.2405 REMARK 3 3 3.5131 - 3.0703 1.00 1038 133 0.2102 0.2140 REMARK 3 4 3.0703 - 2.7902 1.00 1033 133 0.2185 0.3612 REMARK 3 5 2.7902 - 2.5905 1.00 995 164 0.2203 0.2755 REMARK 3 6 2.5905 - 2.4380 1.00 1016 155 0.2262 0.2755 REMARK 3 7 2.4380 - 2.3160 1.00 991 148 0.2582 0.3328 REMARK 3 8 2.3160 - 2.2150 0.98 990 145 0.3235 0.3558 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 33.26 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.75560 REMARK 3 B22 (A**2) : 11.72880 REMARK 3 B33 (A**2) : -5.97320 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 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 : 0.005 1250 REMARK 3 ANGLE : 0.908 1706 REMARK 3 CHIRALITY : 0.059 195 REMARK 3 PLANARITY : 0.004 223 REMARK 3 DIHEDRAL : 18.382 447 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 3G7Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000051536. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : ENRAF-NONIUS FR591 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9389 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.210 REMARK 200 RESOLUTION RANGE LOW (A) : 22.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08700 REMARK 200 FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.32900 REMARK 200 FOR SHELL : 5.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: AUTOSHARP REMARK 200 STARTING MODEL: OST6L STRUCTURE SOLVED BY SAD (BROMIDE SIGNAL) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 3350, 50 MM NA-CITRATE, PH REMARK 280 3.0, PROTEIN SOLUTION BUFFER: 50 MM TRIS-HCL, PH 8.0 MIXING REMARK 280 RATIO 1.5(PROTEIN):1(PRECIPITANT), VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 29.01550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.69550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 52.93300 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 29.01550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.69550 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 52.93300 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 29.01550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 29.69550 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 52.93300 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 29.01550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 29.69550 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 52.93300 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 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 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 0 REMARK 465 ALA A 1 REMARK 465 THR A 2 REMARK 465 ALA A 3 REMARK 465 SER A 4 REMARK 465 HIS A 5 REMARK 465 ASN A 6 REMARK 465 ILE A 7 REMARK 465 ASP A 8 REMARK 465 ASN A 162 REMARK 465 VAL A 163 REMARK 465 GLN A 164 REMARK 465 GLU A 165 REMARK 465 GLU A 166 REMARK 465 PHE A 167 REMARK 465 HIS A 168 REMARK 465 HIS A 169 REMARK 465 HIS A 170 REMARK 465 HIS A 171 REMARK 465 HIS A 172 REMARK 465 HIS A 173 REMARK 465 HIS A 174 REMARK 465 HIS A 175 REMARK 465 HIS A 176 REMARK 465 HIS A 177 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 GLN A 159 7.84 -152.36 REMARK 500 ALA A 160 -122.02 80.37 REMARK 500 REMARK 500 REMARK: NULL DBREF 3G7Y A 1 165 UNP Q03723 OST6_YEAST 24 188 SEQADV 3G7Y MET A 0 UNP Q03723 INITIATING METHIONINE SEQADV 3G7Y GLU A 166 UNP Q03723 EXPRESSION TAG SEQADV 3G7Y PHE A 167 UNP Q03723 EXPRESSION TAG SEQADV 3G7Y HIS A 168 UNP Q03723 EXPRESSION TAG SEQADV 3G7Y HIS A 169 UNP Q03723 EXPRESSION TAG SEQADV 3G7Y HIS A 170 UNP Q03723 EXPRESSION TAG SEQADV 3G7Y HIS A 171 UNP Q03723 EXPRESSION TAG SEQADV 3G7Y HIS A 172 UNP Q03723 EXPRESSION TAG SEQADV 3G7Y HIS A 173 UNP Q03723 EXPRESSION TAG SEQADV 3G7Y HIS A 174 UNP Q03723 EXPRESSION TAG SEQADV 3G7Y HIS A 175 UNP Q03723 EXPRESSION TAG SEQADV 3G7Y HIS A 176 UNP Q03723 EXPRESSION TAG SEQADV 3G7Y HIS A 177 UNP Q03723 EXPRESSION TAG SEQRES 1 A 178 MET ALA THR ALA SER HIS ASN ILE ASP ASP ILE LEU GLN SEQRES 2 A 178 LEU LYS ASP ASP THR GLY VAL ILE THR VAL THR ALA ASP SEQRES 3 A 178 ASN TYR PRO LEU LEU SER ARG GLY VAL PRO GLY TYR PHE SEQRES 4 A 178 ASN ILE LEU TYR ILE THR MET ARG GLY THR ASN SER ASN SEQRES 5 A 178 GLY MET SER CYS GLN LEU CYS HIS ASP PHE GLU LYS THR SEQRES 6 A 178 TYR HIS ALA VAL ALA ASP VAL ILE ARG SER GLN ALA PRO SEQRES 7 A 178 GLN SER LEU ASN LEU PHE PHE THR VAL ASP VAL ASN GLU SEQRES 8 A 178 VAL PRO GLN LEU VAL LYS ASP LEU LYS LEU GLN ASN VAL SEQRES 9 A 178 PRO HIS LEU VAL VAL TYR PRO PRO ALA GLU SER ASN LYS SEQRES 10 A 178 GLN SER GLN PHE GLU TRP LYS THR SER PRO PHE TYR GLN SEQRES 11 A 178 TYR SER LEU VAL PRO GLU ASN ALA GLU ASN THR LEU GLN SEQRES 12 A 178 PHE GLY ASP PHE LEU ALA LYS ILE LEU ASN ILE SER ILE SEQRES 13 A 178 THR VAL PRO GLN ALA PHE ASN VAL GLN GLU GLU PHE HIS SEQRES 14 A 178 HIS HIS HIS HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *77(H2 O) HELIX 1 1 ILE A 10 LYS A 14 5 5 HELIX 2 2 ASN A 26 SER A 31 1 6 HELIX 3 3 CYS A 55 ALA A 76 1 22 HELIX 4 4 VAL A 91 LEU A 98 1 8 HELIX 5 5 GLU A 113 PHE A 120 5 8 HELIX 6 6 VAL A 133 ALA A 137 5 5 HELIX 7 7 ASN A 139 ASN A 152 1 14 SHEET 1 A 5 VAL A 19 THR A 21 0 SHEET 2 A 5 ASN A 81 ASP A 87 1 O PHE A 83 N ILE A 20 SHEET 3 A 5 PHE A 38 THR A 44 1 N ILE A 40 O PHE A 84 SHEET 4 A 5 HIS A 105 TYR A 109 -1 O TYR A 109 N ASN A 39 SHEET 5 A 5 TYR A 128 TYR A 130 -1 O TYR A 128 N VAL A 108 SSBOND 1 CYS A 55 CYS A 58 1555 1555 2.05 CISPEP 1 VAL A 103 PRO A 104 0 -3.77 CRYST1 58.031 59.391 105.866 90.00 90.00 90.00 I 2 2 2 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 0.017232 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016838 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009446 0.00000