HEADER TRANSFERASE 05-DEC-05 2F9F TITLE CRYSTAL STRUCTURE OF THE PUTATIVE MANNOSYL TRANSFERASE (WBAZ-1)FROM TITLE 2 ARCHAEOGLOBUS FULGIDUS, NORTHEAST STRUCTURAL GENOMICS TARGET GR29A. COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIRST MANNOSYL TRANSFERASE (WBAZ-1); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARCHAEOGLOBUS FULGIDUS; SOURCE 3 ORGANISM_TAXID: 224325; SOURCE 4 STRAIN: DSM 4304; SOURCE 5 GENE: WBAZ-1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)+MAGIC; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PET21; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: JM109 KEYWDS ALPHA-BETA PROTEIN, STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, KEYWDS 3 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR W.ZHOU,F.FOROUHAR,K.CONOVER,R.XIAO,T.B.ACTON,G.T.MONTELIONE,L.TONG, AUTHOR 2 J.F.HUNT,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 4 18-OCT-17 2F9F 1 REMARK REVDAT 3 13-JUL-11 2F9F 1 VERSN REVDAT 2 24-FEB-09 2F9F 1 VERSN REVDAT 1 06-JUN-06 2F9F 0 JRNL AUTH W.ZHOU,F.FOROUHAR,K.CONOVER,R.XIAO,T.B.ACTON,G.T.MONTELIONE, JRNL AUTH 2 L.TONG,J.F.HUNT JRNL TITL CRYSTAL STRUCTURE OF THE PUTATIVE MANNOSYL TRANSFERASE JRNL TITL 2 (WBAZ-1)FROM ARCHAEOGLOBUS FULGIDUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 326462.040 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 13431 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) : 0.186 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.400 REMARK 3 FREE R VALUE TEST SET COUNT : 2197 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2959 REMARK 3 BIN R VALUE (WORKING SET) : 0.1830 REMARK 3 BIN FREE R VALUE : 0.2210 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 285 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.013 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1345 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 118 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.77000 REMARK 3 B22 (A**2) : -1.80000 REMARK 3 B33 (A**2) : -1.97000 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) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.04 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) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.10 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) : 22.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.740 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : OVERALL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 45.86 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: XTALVIEW WAS ALSO USED FOR REFINEMENT. REMARK 4 REMARK 4 2F9F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1000035616. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-NOV-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13624 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.60 REMARK 200 R MERGE (I) : 0.11800 REMARK 200 R SYM (I) : 0.09400 REMARK 200 FOR THE DATA SET : 26.8600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.80 REMARK 200 R MERGE FOR SHELL (I) : 0.43200 REMARK 200 R SYM FOR SHELL (I) : 0.41200 REMARK 200 FOR SHELL : 7.040 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SNB, SOLVE, RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM ACETATE, 25% PEG 4K, 200 REMARK 280 MM AMMONIUM SULFATE, AND 5 MM DTT, PH 4.6, MICROBATCH, REMARK 280 TEMPERATURE 293K 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 20.53600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.29450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.56200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.29450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.53600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.56200 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 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 MSE A -9 REMARK 465 GLY A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 PRO A 1 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 10 -55.48 -123.63 REMARK 500 ASP A 14 32.77 -96.78 REMARK 500 ASN A 20 134.35 -172.14 REMARK 500 TRP A 48 -150.57 -133.89 REMARK 500 ALA A 137 81.81 -69.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: GI:11497664 RELATED DB: TARGETDB REMARK 900 RELATED ID: GR29A RELATED DB: TARGETDB DBREF 2F9F A 1 167 GB 11497664 NP_068884 172 338 SEQADV 2F9F MSE A -9 GB 11497664 CLONING ARTIFACT SEQADV 2F9F GLY A -8 GB 11497664 CLONING ARTIFACT SEQADV 2F9F HIS A -7 GB 11497664 CLONING ARTIFACT SEQADV 2F9F HIS A -6 GB 11497664 CLONING ARTIFACT SEQADV 2F9F HIS A -5 GB 11497664 CLONING ARTIFACT SEQADV 2F9F HIS A -4 GB 11497664 CLONING ARTIFACT SEQADV 2F9F HIS A -3 GB 11497664 CLONING ARTIFACT SEQADV 2F9F HIS A -2 GB 11497664 CLONING ARTIFACT SEQADV 2F9F SER A -1 GB 11497664 CLONING ARTIFACT SEQADV 2F9F HIS A 0 GB 11497664 CLONING ARTIFACT SEQADV 2F9F MSE A 63 GB 11497664 MET 234 MODIFIED RESIDUE SEQADV 2F9F MSE A 108 GB 11497664 MET 279 MODIFIED RESIDUE SEQADV 2F9F MSE A 146 GB 11497664 MET 317 MODIFIED RESIDUE SEQRES 1 A 177 MSE GLY HIS HIS HIS HIS HIS HIS SER HIS PRO VAL GLU SEQRES 2 A 177 THR SER LYS PHE LYS PHE LYS CYS TYR GLY ASP PHE TRP SEQRES 3 A 177 LEU SER VAL ASN ARG ILE TYR PRO GLU LYS ARG ILE GLU SEQRES 4 A 177 LEU GLN LEU GLU VAL PHE LYS LYS LEU GLN ASP GLU LYS SEQRES 5 A 177 LEU TYR ILE VAL GLY TRP PHE SER LYS GLY ASP HIS ALA SEQRES 6 A 177 GLU ARG TYR ALA ARG LYS ILE MSE LYS ILE ALA PRO ASP SEQRES 7 A 177 ASN VAL LYS PHE LEU GLY SER VAL SER GLU GLU GLU LEU SEQRES 8 A 177 ILE ASP LEU TYR SER ARG CYS LYS GLY LEU LEU CYS THR SEQRES 9 A 177 ALA LYS ASP GLU ASP PHE GLY LEU THR PRO ILE GLU ALA SEQRES 10 A 177 MSE ALA SER GLY LYS PRO VAL ILE ALA VAL ASN GLU GLY SEQRES 11 A 177 GLY PHE LYS GLU THR VAL ILE ASN GLU LYS THR GLY TYR SEQRES 12 A 177 LEU VAL ASN ALA ASP VAL ASN GLU ILE ILE ASP ALA MSE SEQRES 13 A 177 LYS LYS VAL SER LYS ASN PRO ASP LYS PHE LYS LYS ASP SEQRES 14 A 177 CYS PHE ARG ARG ALA LYS GLU PHE MODRES 2F9F MSE A 63 MET SELENOMETHIONINE MODRES 2F9F MSE A 108 MET SELENOMETHIONINE MODRES 2F9F MSE A 146 MET SELENOMETHIONINE HET MSE A 63 8 HET MSE A 108 8 HET MSE A 146 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 HOH *118(H2 O) HELIX 1 1 TYR A 23 LYS A 26 5 4 HELIX 2 2 ARG A 27 LEU A 38 1 12 HELIX 3 3 HIS A 54 ALA A 66 1 13 HELIX 4 4 SER A 77 CYS A 88 1 12 HELIX 5 5 GLY A 101 SER A 110 1 10 HELIX 6 6 GLU A 119 VAL A 126 1 8 HELIX 7 7 ASP A 138 ASN A 152 1 15 HELIX 8 8 PHE A 156 GLU A 166 1 11 SHEET 1 A 6 VAL A 70 GLY A 74 0 SHEET 2 A 6 LEU A 43 VAL A 46 1 N ILE A 45 O LYS A 71 SHEET 3 A 6 TRP A 16 VAL A 19 1 N SER A 18 O VAL A 46 SHEET 4 A 6 GLY A 90 CYS A 93 1 O LEU A 92 N LEU A 17 SHEET 5 A 6 VAL A 114 VAL A 117 1 O ILE A 115 N LEU A 91 SHEET 6 A 6 GLY A 132 VAL A 135 1 O VAL A 135 N ALA A 116 LINK C ILE A 62 N MSE A 63 1555 1555 1.33 LINK C MSE A 63 N LYS A 64 1555 1555 1.33 LINK C ALA A 107 N MSE A 108 1555 1555 1.33 LINK C MSE A 108 N ALA A 109 1555 1555 1.33 LINK C ALA A 145 N MSE A 146 1555 1555 1.33 LINK C MSE A 146 N LYS A 147 1555 1555 1.33 CRYST1 41.072 57.124 60.589 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 0.024347 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017506 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016505 0.00000