HEADER TRANSFERASE 25-APR-13 4KDR TITLE CRYSTAL STRUCTURE OF UBIG/SAH COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-DEMETHYLUBIQUINONE-9 3-METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 2-POLYPRENYL-6-HYDROXYPHENYL METHYLASE, 3,4-DIHYDROXY-5- COMPND 5 HEXAPRENYLBENZOATE METHYLTRANSFERASE, DHHB METHYLTRANSFERASE; COMPND 6 EC: 2.1.1.64, 2.1.1.222; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: UBIG, PUFX, YFAB, B2232, JW2226; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ROSSMANN FOLD, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHU,M.TENG,X.LI REVDAT 3 17-JUL-19 4KDR 1 REMARK REVDAT 2 16-AUG-17 4KDR 1 SOURCE REMARK REVDAT 1 30-APR-14 4KDR 0 JRNL AUTH Y.ZHU,M.TENG,X.LI JRNL TITL CRYSTAL STRUCTURE OF THE UBIG/SAH COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 15024 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 752 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 38.0369 - 3.4243 0.98 2896 153 0.1902 0.2175 REMARK 3 2 3.4243 - 2.7182 0.99 2850 151 0.1932 0.2376 REMARK 3 3 2.7182 - 2.3747 0.99 2860 145 0.1948 0.2403 REMARK 3 4 2.3747 - 2.1576 0.99 2837 155 0.1770 0.2497 REMARK 3 5 2.1576 - 2.0030 0.99 2829 148 0.1841 0.2497 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.840 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.56000 REMARK 3 B22 (A**2) : -0.67000 REMARK 3 B33 (A**2) : -0.80000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.56000 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 : 0.007 1626 REMARK 3 ANGLE : 1.096 2213 REMARK 3 CHIRALITY : 0.074 248 REMARK 3 PLANARITY : 0.006 287 REMARK 3 DIHEDRAL : 13.677 574 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: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4KDR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000079210. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 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 : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NI FILTER 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.003 REMARK 200 RESOLUTION RANGE LOW (A) : 38.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CITRIC ACID PH 5.0 AND 20% V/V 2 REMARK 280 -METHYL-2,4-PENTANEDIOL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 287K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 70.56650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.75000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 70.56650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.75000 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 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 ALA A 3 REMARK 465 GLU A 4 REMARK 465 LYS A 5 REMARK 465 SER A 6 REMARK 465 PRO A 7 REMARK 465 VAL A 8 REMARK 465 ASN A 9 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 HIS A 10 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 26 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 39 NH1 NH2 REMARK 470 ILE A 40 CD1 REMARK 470 GLU A 89 CG CD OE1 OE2 REMARK 470 GLN A 104 OE1 NE2 REMARK 470 GLU A 114 CG CD OE1 OE2 REMARK 470 LYS A 118 CG CD CE NZ REMARK 470 VAL A 188 C O CG1 CG2 REMARK 470 LYS A 189 CG CD CE NZ REMARK 470 LYS A 190 CE NZ REMARK 470 LYS A 193 CG CD CE NZ REMARK 470 GLN A 203 OE1 NE2 REMARK 470 LYS A 207 CG CD CE NZ REMARK 470 LYS A 224 CG CD CE NZ REMARK 470 ASP A 230 CG OD1 OD2 REMARK 470 LYS A 240 CB CG CD CE NZ REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4KDC RELATED DB: PDB DBREF 4KDR A 1 159 UNP P17993 UBIG_ECOLI 1 159 DBREF 4KDR A 188 240 UNP P17993 UBIG_ECOLI 188 240 SEQADV 4KDR HIS A -5 UNP P17993 EXPRESSION TAG SEQADV 4KDR HIS A -4 UNP P17993 EXPRESSION TAG SEQADV 4KDR HIS A -3 UNP P17993 EXPRESSION TAG SEQADV 4KDR HIS A -2 UNP P17993 EXPRESSION TAG SEQADV 4KDR HIS A -1 UNP P17993 EXPRESSION TAG SEQADV 4KDR HIS A 0 UNP P17993 EXPRESSION TAG SEQADV 4KDR LEU A 160 UNP P17993 EXPRESSION TAG SEQADV 4KDR ASN A 161 UNP P17993 EXPRESSION TAG SEQADV 4KDR ARG A 162 UNP P17993 EXPRESSION TAG SEQADV 4KDR ASN A 163 UNP P17993 EXPRESSION TAG SEQADV 4KDR GLY A 187 UNP P17993 EXPRESSION TAG SEQRES 1 A 223 HIS HIS HIS HIS HIS HIS MET ASN ALA GLU LYS SER PRO SEQRES 2 A 223 VAL ASN HIS ASN VAL ASP HIS GLU GLU ILE ALA LYS PHE SEQRES 3 A 223 GLU ALA VAL ALA SER ARG TRP TRP ASP LEU GLU GLY GLU SEQRES 4 A 223 PHE LYS PRO LEU HIS ARG ILE ASN PRO LEU ARG LEU GLY SEQRES 5 A 223 TYR ILE ALA GLU ARG ALA GLY GLY LEU PHE GLY LYS LYS SEQRES 6 A 223 VAL LEU ASP VAL GLY CYS GLY GLY GLY ILE LEU ALA GLU SEQRES 7 A 223 SER MET ALA ARG GLU GLY ALA THR VAL THR GLY LEU ASP SEQRES 8 A 223 MET GLY PHE GLU PRO LEU GLN VAL ALA LYS LEU HIS ALA SEQRES 9 A 223 LEU GLU SER GLY ILE GLN VAL ASP TYR VAL GLN GLU THR SEQRES 10 A 223 VAL GLU GLU HIS ALA ALA LYS HIS ALA GLY GLN TYR ASP SEQRES 11 A 223 VAL VAL THR CYS MET GLU MET LEU GLU HIS VAL PRO ASP SEQRES 12 A 223 PRO GLN SER VAL VAL ARG ALA CYS ALA GLN LEU VAL LYS SEQRES 13 A 223 PRO GLY GLY ASP VAL PHE PHE SER THR LEU ASN ARG ASN SEQRES 14 A 223 GLY VAL LYS LYS PHE ILE LYS PRO ALA GLU LEU LEU GLY SEQRES 15 A 223 TRP VAL ASP GLN THR SER LEU LYS GLU ARG HIS ILE THR SEQRES 16 A 223 GLY LEU HIS TYR ASN PRO ILE THR ASN THR PHE LYS LEU SEQRES 17 A 223 GLY PRO GLY VAL ASP VAL ASN TYR MET LEU HIS THR GLN SEQRES 18 A 223 ASN LYS HET SAH A 301 26 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE FORMUL 2 SAH C14 H20 N6 O5 S FORMUL 3 HOH *72(H2 O) HELIX 1 1 ASP A 13 ALA A 24 1 12 HELIX 2 2 SER A 25 TRP A 27 5 3 HELIX 3 3 PHE A 34 GLY A 53 1 20 HELIX 4 4 GLY A 68 GLU A 77 1 10 HELIX 5 5 GLY A 87 GLY A 102 1 16 HELIX 6 6 THR A 111 HIS A 119 1 9 HELIX 7 7 MET A 131 VAL A 135 5 5 HELIX 8 8 ASP A 137 LEU A 148 1 12 HELIX 9 9 LYS A 193 ASP A 202 1 10 SHEET 1 A 8 ASP A 106 GLN A 109 0 SHEET 2 A 8 THR A 80 ASP A 85 1 N GLY A 83 O ASP A 106 SHEET 3 A 8 LYS A 59 VAL A 63 1 N ASP A 62 O LEU A 84 SHEET 4 A 8 TYR A 123 MET A 129 1 O THR A 127 N VAL A 63 SHEET 5 A 8 VAL A 149 THR A 159 1 O LYS A 150 N TYR A 123 SHEET 6 A 8 TYR A 233 ASN A 239 -1 O LEU A 235 N PHE A 157 SHEET 7 A 8 LEU A 206 ASN A 217 -1 N HIS A 210 O HIS A 236 SHEET 8 A 8 THR A 222 GLY A 226 -1 O GLY A 226 N GLY A 213 SITE 1 AC1 19 ASN A 11 ILE A 17 PHE A 20 TRP A 27 SITE 2 AC1 19 LEU A 37 ARG A 44 GLY A 64 CYS A 65 SITE 3 AC1 19 GLY A 66 ASP A 85 MET A 86 MET A 129 SITE 4 AC1 19 GLU A 130 HOH A 401 HOH A 402 HOH A 405 SITE 5 AC1 19 HOH A 410 HOH A 413 HOH A 467 CRYST1 141.133 39.500 40.422 90.00 94.40 90.00 C 1 2 1 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 0.007086 0.000000 0.000545 0.00000 SCALE2 0.000000 0.025316 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024812 0.00000 MASTER 248 0 1 9 8 0 5 6 0 0 0 18 END