HEADER TRANSFERASE 18-AUG-11 3VGP TITLE CRYSTAL STRUCTURE OF THE C-TERMINAL GLOBULAR DOMAIN OF TITLE 2 OLIGOSACCHARYLTRANSFERASE (AF_0329) FROM ARCHAEOGLOBUS FULGIDUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSMEMBRANE OLIGOSACCHARYL TRANSFERASE, PUTATIVE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL GLOBULAR DOMAIN; COMPND 5 EC: 2.4.1.119; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARCHAEOGLOBUS FULGIDUS; SOURCE 3 ORGANISM_TAXID: 224325; SOURCE 4 STRAIN: DSM 4304; SOURCE 5 GENE: AF_0329; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 GOLD (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-47B KEYWDS GLYCOSYLTRANSFERASE, CELL MEMBRANE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.MATSUMOTO,M.IGURA,J.NYIRENDA,S.YUZAWA,N.N.NODA,F.INAGAKI,D.KOHDA REVDAT 2 30-OCT-24 3VGP 1 SEQADV LINK REVDAT 1 04-JUL-12 3VGP 0 JRNL AUTH S.MATSUMOTO,M.IGURA,J.NYIRENDA,M.MATSUMOTO,S.YUZAWA, JRNL AUTH 2 N.N.NODA,F.INAGAKI,D.KOHDA JRNL TITL CRYSTAL STRUCTURE OF THE C-TERMINAL GLOBULAR DOMAIN OF JRNL TITL 2 OLIGOSACCHARYLTRANSFERASE FROM ARCHAEOGLOBUS FULGIDUS AT JRNL TITL 3 1.75 A RESOLUTION JRNL REF BIOCHEMISTRY V. 51 4157 2012 JRNL REFN ISSN 0006-2960 JRNL PMID 22559858 JRNL DOI 10.1021/BI300076U REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 234062.630 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 18598 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 SET) : 0.223 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1838 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2654 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 268 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1301 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 154 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.54000 REMARK 3 B22 (A**2) : 1.54000 REMARK 3 B33 (A**2) : -3.08000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.07 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.13 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.670 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.210 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.750 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.610 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.500 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.45 REMARK 3 BSOL : 55.72 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3VGP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1000095022. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-10 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9798 REMARK 200 MONOCHROMATOR : A DOUBLE-CRYSTAL MONOCHROMATOR REMARK 200 AND A HORIZONTAL FOCUSING MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER SMART 6500 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18986 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 27.00 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 98.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.9 REMARK 200 DATA REDUNDANCY IN SHELL : 24.80 REMARK 200 R MERGE FOR SHELL (I) : 0.39900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 13.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12.5% PEG 3350, 0.1M BIS-TRIS, PH 6.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 79.91100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 23.52300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 23.52300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 39.95550 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 23.52300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 23.52300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 119.86650 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 23.52300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 23.52300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 39.95550 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 23.52300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 23.52300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 119.86650 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 79.91100 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 LEU A 452 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 ASP A 430 CG OD1 OD2 REMARK 470 ARG A 443 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 449 CG CD OE1 NE2 REMARK 470 ASN A 453 CG OD1 ND2 REMARK 470 GLU A 456 CG CD OE1 OE2 REMARK 470 LYS A 478 CG CD CE NZ REMARK 470 GLU A 503 CG CD OE1 OE2 REMARK 470 GLU A 569 CG CD OE1 OE2 DBREF 3VGP A 430 591 UNP O29918 O29918_ARCFU 430 591 SEQADV 3VGP GLY A 428 UNP O29918 EXPRESSION TAG SEQADV 3VGP PRO A 429 UNP O29918 EXPRESSION TAG SEQADV 3VGP ALA A 482 UNP O29918 CYS 482 ENGINEERED MUTATION SEQRES 1 A 164 GLY PRO ASP LEU THR GLU ASP TRP LYS GLU ALA LEU GLU SEQRES 2 A 164 TRP MSE ARG THR SER LEU GLU GLU GLN ASN TYR LEU ASN SEQRES 3 A 164 PRO TYR GLU LYS PRO GLU TYR SER VAL MSE SER TRP TRP SEQRES 4 A 164 ASP TYR GLY ASN TRP ILE LEU TYR VAL SER LYS LYS ALA SEQRES 5 A 164 VAL VAL ALA ASN ASN PHE GLN ALA GLY ALA VAL ASP ALA SEQRES 6 A 164 ALA LYS PHE PHE THR ALA LYS SER GLU ASP GLU ALA ILE SEQRES 7 A 164 LYS ILE ALA LYS LYS ARG GLY VAL ARG TYR VAL VAL THR SEQRES 8 A 164 ALA ASP GLU ILE THR MSE LYS ASP ALA ASN ASN THR LYS SEQRES 9 A 164 PHE PRO ALA ILE MSE ARG ILE ALA GLY TYR ASN VAL ASP SEQRES 10 A 164 LEU MSE THR GLU GLY GLU ILE LEU ASN PHE PHE ASN HIS SEQRES 11 A 164 THR VAL LEU TYR ARG LEU HIS MSE GLU ASN ALA GLU ASN SEQRES 12 A 164 LEU THR HIS PHE ARG LEU VAL LYS GLU PHE GLY ASP VAL SEQRES 13 A 164 LYS ILE PHE GLU VAL VAL GLY SER MODRES 3VGP MSE A 442 MET SELENOMETHIONINE MODRES 3VGP MSE A 463 MET SELENOMETHIONINE MODRES 3VGP MSE A 524 MET SELENOMETHIONINE MODRES 3VGP MSE A 536 MET SELENOMETHIONINE MODRES 3VGP MSE A 546 MET SELENOMETHIONINE MODRES 3VGP MSE A 565 MET SELENOMETHIONINE HET MSE A 442 8 HET MSE A 463 8 HET MSE A 524 8 HET MSE A 536 8 HET MSE A 546 8 HET MSE A 565 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 2 HOH *154(H2 O) HELIX 1 1 THR A 432 GLU A 448 1 17 HELIX 2 2 ASP A 467 ILE A 472 1 6 HELIX 3 3 ASN A 484 THR A 497 1 14 HELIX 4 4 SER A 500 GLY A 512 1 13 HELIX 5 5 ALA A 519 THR A 523 5 5 HELIX 6 6 LYS A 531 ALA A 539 1 9 HELIX 7 7 ASN A 542 MSE A 546 5 5 HELIX 8 8 THR A 547 HIS A 557 1 11 HELIX 9 9 THR A 558 MSE A 565 1 8 SHEET 1 A 4 VAL A 462 MSE A 463 0 SHEET 2 A 4 TYR A 515 THR A 518 1 O TYR A 515 N MSE A 463 SHEET 3 A 4 VAL A 583 VAL A 588 -1 O PHE A 586 N VAL A 516 SHEET 4 A 4 PHE A 574 PHE A 580 -1 N LYS A 578 O ILE A 585 LINK C TRP A 441 N MSE A 442 1555 1555 1.33 LINK C MSE A 442 N ARG A 443 1555 1555 1.33 LINK C VAL A 462 N MSE A 463 1555 1555 1.33 LINK C MSE A 463 N SER A 464 1555 1555 1.33 LINK C THR A 523 N MSE A 524 1555 1555 1.33 LINK C MSE A 524 N LYS A 525 1555 1555 1.33 LINK C ILE A 535 N MSE A 536 1555 1555 1.33 LINK C MSE A 536 N ARG A 537 1555 1555 1.33 LINK C LEU A 545 N MSE A 546 1555 1555 1.33 LINK C MSE A 546 N THR A 547 1555 1555 1.33 LINK C HIS A 564 N MSE A 565 1555 1555 1.33 LINK C MSE A 565 N GLU A 566 1555 1555 1.33 CRYST1 47.046 47.046 159.822 90.00 90.00 90.00 P 41 21 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 0.021256 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021256 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006257 0.00000