HEADER TRANSFERASE 02-JUL-13 3WE9 TITLE THE CRYSTAL STRUCTURE OF YISP FROM BACILLUS SUBTILIS SUBSP. SUBTILIS TITLE 2 STRAIN 168 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE PHYTOENE/SQUALENE SYNTHASE YISP; COMPND 3 CHAIN: A; COMPND 4 EC: 2.5.1.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS SUBSP. SUBTILIS; SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: YISP, YUCD, BSU10810; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21TRXB (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET32 XA/LIC KEYWDS BACILLUS SUBTILIS YISP, ISOPRENOID, BIOFILM, DXXXD MOTIF, SQUALENE KEYWDS 2 SYNTHASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.HU,C.H.HUANG,H.C.CHAN,T.P.KO,X.FENG,E.OLDFIELD,R.T.GUO REVDAT 2 20-MAR-24 3WE9 1 REMARK REVDAT 1 02-JUL-14 3WE9 0 JRNL AUTH Y.HU,C.H.HUANG,H.C.CHAN,T.P.KO,X.FENG,E.OLDFIELD,R.T.GUO JRNL TITL CRYSTAL STRUCTURE OF BACILLUS SUBTILIS YISP IN COMPLEX WITH JRNL TITL 2 A PEG FRAGMENT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 23740 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1156 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.92 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.99 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2620 REMARK 3 BIN FREE R VALUE : 0.3100 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 113 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2006 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 219 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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: NULL REMARK 4 REMARK 4 3WE9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-JUL-13. REMARK 100 THE DEPOSITION ID IS D_1000096225. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13C1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97622 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24603 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.48200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: SOLVE, RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 M LICL, 0.1 M BICINE PH 9.0, 18 REMARK 280 -20%(W/V) POLYETHYLENE GLYCOL 6000, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298K 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 21.98300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.68900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.78800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.68900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.98300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.78800 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 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 1 REMARK 465 ALA A 57 REMARK 465 ASP A 58 REMARK 465 GLU A 59 REMARK 465 LYS A 60 REMARK 465 VAL A 61 REMARK 465 LEU A 62 REMARK 465 PRO A 63 REMARK 465 ALA A 64 REMARK 465 PHE A 65 REMARK 465 GLU A 66 REMARK 465 ALA A 67 REMARK 465 LYS A 68 REMARK 465 ALA A 69 REMARK 465 ASP A 70 REMARK 465 HIS A 71 REMARK 465 VAL A 72 REMARK 465 TYR A 73 REMARK 465 GLN A 74 REMARK 465 ARG A 75 REMARK 465 THR A 76 REMARK 465 ASN A 77 REMARK 465 ASN A 78 REMARK 465 GLY A 79 REMARK 465 LYS A 80 REMARK 465 GLN A 81 REMARK 465 ILE A 274 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 ALA A 26 60.59 -159.58 REMARK 500 GLU A 110 -151.77 -100.01 REMARK 500 THR A 128 -74.34 -109.90 REMARK 500 ARG A 143 -86.15 -102.79 REMARK 500 LYS A 144 52.42 -62.26 REMARK 500 ASP A 167 111.43 -162.82 REMARK 500 ASP A 254 47.82 -77.37 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 PGE A 900 REMARK 999 REMARK 999 SEQUENCE REMARK 999 AUTHORS SAY THIS SEQUENCE INCLUDES MATURE PROTEIN OF YISP. DBREF 3WE9 A 8 274 UNP O06728 YISP_BACSU 1 267 SEQADV 3WE9 MET A 1 UNP O06728 SEE REMARK 999 SEQADV 3WE9 ILE A 2 UNP O06728 SEE REMARK 999 SEQADV 3WE9 HIS A 3 UNP O06728 SEE REMARK 999 SEQADV 3WE9 ARG A 4 UNP O06728 SEE REMARK 999 SEQADV 3WE9 SER A 5 UNP O06728 SEE REMARK 999 SEQADV 3WE9 GLU A 6 UNP O06728 SEE REMARK 999 SEQADV 3WE9 LYS A 7 UNP O06728 SEE REMARK 999 SEQRES 1 A 274 MET ILE HIS ARG SER GLU LYS MET LYS GLU ILE LYS GLU SEQRES 2 A 274 ALA TYR GLN GLN CYS GLY GLN ILE VAL GLY GLU TYR ALA SEQRES 3 A 274 PRO ALA CYS PHE LYS ALA LEU SER TYR LEU PRO LEU LYS SEQRES 4 A 274 GLN ARG GLN ALA SER TRP ALA VAL LEU SER PHE CYS HIS SEQRES 5 A 274 THR ALA ALA SER ALA ASP GLU LYS VAL LEU PRO ALA PHE SEQRES 6 A 274 GLU ALA LYS ALA ASP HIS VAL TYR GLN ARG THR ASN ASN SEQRES 7 A 274 GLY LYS GLN HIS LEU TRP LYS ALA PHE ASP HIS ALA TYR SEQRES 8 A 274 ARG THR PHE THR LEU GLU SER GLU PRO PHE ARG GLU PHE SEQRES 9 A 274 ILE ALA ALA GLN LYS GLU ASP ALA LYS PRO TYR ASP ASP SEQRES 10 A 274 LEU ASP GLU LEU LEU MET TYR ALA TYR ARG THR GLY GLY SEQRES 11 A 274 ALA ALA GLY LEU MET LEU LEU PRO ILE LEU THR ARG ARG SEQRES 12 A 274 LYS GLN ASP GLN LEU LYS GLN ALA ALA VAL SER LEU GLY SEQRES 13 A 274 LEU ALA ILE GLN LEU VAL ARG PHE LEU SER ASP LEU GLY SEQRES 14 A 274 THR ASP GLN GLN LYS ASN ARG ILE PRO ARG GLN VAL MET SEQRES 15 A 274 GLN GLN PHE GLY TYR THR GLU ALA ASP LEU GLN LYS GLY SEQRES 16 A 274 THR VAL ASN LYS ALA PHE THR MET THR TRP GLU TYR ILE SEQRES 17 A 274 ALA PHE GLU ALA GLU ALA TYR LEU GLU GLU CYS GLN ASP SEQRES 18 A 274 ALA LEU PRO LEU PHE PRO GLN TYR SER GLN LYS THR VAL SEQRES 19 A 274 LYS ALA ALA LEU HIS LEU HIS ARG ALA VAL LEU GLU LYS SEQRES 20 A 274 ILE ARG ALA LYS GLN HIS ASP VAL PHE GLN TYR HIS PHE SEQRES 21 A 274 ALA LEU THR GLU THR GLU VAL LYS GLN ILE LEU SER ASP SEQRES 22 A 274 ILE HET PGE A 900 10 HETNAM PGE TRIETHYLENE GLYCOL FORMUL 2 PGE C6 H14 O4 FORMUL 3 HOH *219(H2 O) HELIX 1 1 SER A 5 ALA A 26 1 22 HELIX 2 2 ALA A 26 SER A 34 1 9 HELIX 3 3 PRO A 37 ALA A 55 1 19 HELIX 4 4 LEU A 83 THR A 95 1 13 HELIX 5 5 GLU A 97 GLN A 108 1 12 HELIX 6 6 ASP A 117 THR A 141 1 25 HELIX 7 7 LYS A 144 SER A 166 1 23 HELIX 8 8 THR A 170 ASN A 175 1 6 HELIX 9 9 PRO A 178 GLY A 186 1 9 HELIX 10 10 THR A 188 GLY A 195 1 8 HELIX 11 11 ASN A 198 ALA A 222 1 25 HELIX 12 12 LEU A 223 PHE A 226 5 4 HELIX 13 13 PRO A 227 LYS A 251 1 25 HELIX 14 14 THR A 263 SER A 272 1 10 SITE 1 AC1 1 ILE A 159 CRYST1 43.966 77.576 91.378 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 0.022745 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012891 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010944 0.00000