HEADER TRANSFERASE 26-JUN-12 4AZW TITLE CRYSTAL STRUCTURE OF MONOMERIC WBDD. COMPND MOL_ID: 1; COMPND 2 MOLECULE: WBDD; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 2-458; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: ORF708; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSFERASE, METHYLTRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.HAGELUEKEN,H.HUANG,J.H.NAISMITH REVDAT 3 08-MAY-24 4AZW 1 REMARK LINK REVDAT 2 14-NOV-12 4AZW 1 JRNL REVDAT 1 26-SEP-12 4AZW 0 JRNL AUTH G.HAGELUEKEN,H.HUANG,B.R.CLARKE,T.LEBL,C.WHITFIELD, JRNL AUTH 2 J.H.NAISMITH JRNL TITL STRUCTURE OF WBDD; A BIFUNCTIONAL KINASE AND JRNL TITL 2 METHYLTRANSFERASE THAT REGULATES THE CHAIN LENGTH OF THE O JRNL TITL 3 ANTIGEN IN ESCHERICHIA COLI O9A. JRNL REF MOL.MICROBIOL. V. 86 730 2012 JRNL REFN ISSN 0950-382X JRNL PMID 22970759 JRNL DOI 10.1111/MMI.12014 REMARK 2 REMARK 2 RESOLUTION. 2.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 67.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 17212 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 + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 927 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.47 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.53 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1105 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.33 REMARK 3 BIN R VALUE (WORKING SET) : 0.2580 REMARK 3 BIN FREE R VALUE SET COUNT : 70 REMARK 3 BIN FREE R VALUE : 0.3830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3346 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 77 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.63000 REMARK 3 B22 (A**2) : -0.29000 REMARK 3 B33 (A**2) : -0.33000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.499 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.270 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.200 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.916 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3503 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2359 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4765 ; 1.673 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5706 ; 0.956 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 411 ; 6.356 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 185 ;35.808 ;24.054 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 556 ;17.336 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;18.912 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 506 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3896 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 766 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 5 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 5 A 39 REMARK 3 RESIDUE RANGE : A 40 A 192 REMARK 3 RESIDUE RANGE : A 193 A 269 REMARK 3 RESIDUE RANGE : A 270 A 419 REMARK 3 RESIDUE RANGE : A 420 A 449 REMARK 3 ORIGIN FOR THE GROUP (A): -15.8060 17.7730 -24.9900 REMARK 3 T TENSOR REMARK 3 T11: 0.1086 T22: 0.0747 REMARK 3 T33: 0.1615 T12: 0.0078 REMARK 3 T13: -0.0434 T23: -0.0184 REMARK 3 L TENSOR REMARK 3 L11: 0.7027 L22: 0.7671 REMARK 3 L33: 2.3982 L12: -0.5527 REMARK 3 L13: 1.2390 L23: -1.1096 REMARK 3 S TENSOR REMARK 3 S11: 0.0462 S12: -0.0367 S13: 0.0064 REMARK 3 S21: -0.2124 S22: 0.0506 S23: 0.0007 REMARK 3 S31: 0.2109 S32: 0.0170 S33: -0.0968 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES WITH TLS ADDED. REMARK 4 REMARK 4 4AZW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1290053080. 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 : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9173 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18171 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.470 REMARK 200 RESOLUTION RANGE LOW (A) : 67.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.100 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.3000 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: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 20.33500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.73000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.80000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 67.73000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.33500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.80000 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 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 -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 GLU A -5 REMARK 465 ASN A -4 REMARK 465 LEU A -3 REMARK 465 TYR A -2 REMARK 465 PHE A -1 REMARK 465 GLN A 0 REMARK 465 GLY A 1 REMARK 465 THR A 2 REMARK 465 LYS A 3 REMARK 465 ASP A 4 REMARK 465 THR A 196 REMARK 465 HIS A 197 REMARK 465 LEU A 198 REMARK 465 SER A 199 REMARK 465 PRO A 200 REMARK 465 VAL A 201 REMARK 465 PRO A 202 REMARK 465 PRO A 377 REMARK 465 GLN A 378 REMARK 465 ASP A 379 REMARK 465 CYS A 380 REMARK 465 SER A 381 REMARK 465 TRP A 382 REMARK 465 ALA A 399 REMARK 465 GLU A 400 REMARK 465 ASN A 401 REMARK 465 LYS A 402 REMARK 465 SER A 403 REMARK 465 TRP A 404 REMARK 465 ASN A 405 REMARK 465 GLY A 406 REMARK 465 PHE A 407 REMARK 465 TRP A 408 REMARK 465 ARG A 409 REMARK 465 SER A 410 REMARK 465 ALA A 411 REMARK 465 PRO A 412 REMARK 465 VAL A 413 REMARK 465 HIS A 414 REMARK 465 PRO A 415 REMARK 465 PHE A 416 REMARK 465 ASN A 417 REMARK 465 ALA A 450 REMARK 465 LYS A 451 REMARK 465 LEU A 452 REMARK 465 PRO A 453 REMARK 465 SER A 454 REMARK 465 ALA A 455 REMARK 465 GLU A 456 REMARK 465 GLN A 457 REMARK 465 GLN A 458 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 LEU A 418 CG CD1 CD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ASN A 6 O HOH A 2001 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS A 133 CG HIS A 133 CD2 0.055 REMARK 500 HIS A 260 CG HIS A 260 CD2 0.056 REMARK 500 HIS A 273 CG HIS A 273 CD2 0.087 REMARK 500 HIS A 276 CG HIS A 276 CD2 0.056 REMARK 500 HIS A 364 CG HIS A 364 CD2 0.060 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 212 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 PRO A 23 -16.41 -49.27 REMARK 500 CYS A 33 -19.14 74.16 REMARK 500 ALA A 63 -123.87 58.93 REMARK 500 SER A 73 2.49 -53.81 REMARK 500 ASN A 98 75.00 -111.77 REMARK 500 VAL A 130 -28.94 -141.57 REMARK 500 PRO A 167 42.95 -82.86 REMARK 500 HIS A 260 17.16 59.25 REMARK 500 ASP A 351 54.25 -149.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1453 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 274 OE2 REMARK 620 2 ASP A 369 OD1 94.7 REMARK 620 3 ASP A 369 OD2 148.9 58.1 REMARK 620 4 ATP A1450 O3G 123.4 140.4 82.2 REMARK 620 5 ATP A1450 O1B 91.8 81.2 70.9 86.7 REMARK 620 6 HOH A2055 O 105.5 84.1 87.7 94.5 158.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1452 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 356 OD1 REMARK 620 2 ASP A 369 OD2 99.2 REMARK 620 3 ATP A1450 O2G 120.8 86.4 REMARK 620 4 ATP A1450 O1A 133.9 87.0 105.1 REMARK 620 5 HOH A2069 O 85.1 172.1 97.2 85.3 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 1450 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAM A 1451 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1452 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1453 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4AX8 RELATED DB: PDB REMARK 900 MEDIUM RESOLUTION STRUCTURE OF THE BIFUNCTIONAL KINASE- REMARK 900 METHYLTRANSFERASE WBDD REMARK 900 RELATED ID: 4AZS RELATED DB: PDB REMARK 900 HIGH RESOLUTION (2.2 A) CRYSTAL STRUCTURE OF WBDD. REMARK 900 RELATED ID: 4AZT RELATED DB: PDB REMARK 900 CO-CRYSTAL STRUCTURE OF WBDD AND KINASE INHIBITOR LY294002. REMARK 900 RELATED ID: 4AZV RELATED DB: PDB REMARK 900 CO-CRYSTAL STRUCTURE OF WBDD AND KINASE INHIBITOR GW435821X. DBREF 4AZW A 2 458 UNP Q47592 Q47592_ECOLX 2 458 SEQADV 4AZW MET A -12 UNP Q47592 EXPRESSION TAG SEQADV 4AZW HIS A -11 UNP Q47592 EXPRESSION TAG SEQADV 4AZW HIS A -10 UNP Q47592 EXPRESSION TAG SEQADV 4AZW HIS A -9 UNP Q47592 EXPRESSION TAG SEQADV 4AZW HIS A -8 UNP Q47592 EXPRESSION TAG SEQADV 4AZW HIS A -7 UNP Q47592 EXPRESSION TAG SEQADV 4AZW HIS A -6 UNP Q47592 EXPRESSION TAG SEQADV 4AZW GLU A -5 UNP Q47592 EXPRESSION TAG SEQADV 4AZW ASN A -4 UNP Q47592 EXPRESSION TAG SEQADV 4AZW LEU A -3 UNP Q47592 EXPRESSION TAG SEQADV 4AZW TYR A -2 UNP Q47592 EXPRESSION TAG SEQADV 4AZW PHE A -1 UNP Q47592 EXPRESSION TAG SEQADV 4AZW GLN A 0 UNP Q47592 EXPRESSION TAG SEQADV 4AZW GLY A 1 UNP Q47592 EXPRESSION TAG SEQADV 4AZW PHE A 168 UNP Q47592 LEU 168 CONFLICT SEQADV 4AZW LYS A 345 UNP Q47592 GLN 345 CONFLICT SEQRES 1 A 471 MET HIS HIS HIS HIS HIS HIS GLU ASN LEU TYR PHE GLN SEQRES 2 A 471 GLY THR LYS ASP LEU ASN THR LEU VAL SER GLU LEU PRO SEQRES 3 A 471 GLU ILE TYR GLN THR ILE PHE GLY HIS PRO GLU TRP ASP SEQRES 4 A 471 GLY ASP ALA ALA ARG ASP CYS ASN GLN ARG LEU ASP LEU SEQRES 5 A 471 ILE THR GLU GLN TYR ASP ASN LEU SER ARG ALA LEU GLY SEQRES 6 A 471 ARG PRO LEU ASN VAL LEU ASP LEU GLY CYS ALA GLN GLY SEQRES 7 A 471 PHE PHE SER LEU SER LEU ALA SER LYS GLY ALA THR ILE SEQRES 8 A 471 VAL GLY ILE ASP PHE GLN GLN GLU ASN ILE ASN VAL CYS SEQRES 9 A 471 ARG ALA LEU ALA GLU GLU ASN PRO ASP PHE ALA ALA GLU SEQRES 10 A 471 PHE ARG VAL GLY ARG ILE GLU GLU VAL ILE ALA ALA LEU SEQRES 11 A 471 GLU GLU GLY GLU PHE ASP LEU ALA ILE GLY LEU SER VAL SEQRES 12 A 471 PHE HIS HIS ILE VAL HIS LEU HIS GLY ILE ASP GLU VAL SEQRES 13 A 471 LYS ARG LEU LEU SER ARG LEU ALA ASP VAL THR GLN ALA SEQRES 14 A 471 VAL ILE LEU GLU LEU ALA VAL LYS GLU GLU PRO PHE TYR SEQRES 15 A 471 TRP GLY VAL SER GLN PRO ASP ASP PRO ARG GLU LEU ILE SEQRES 16 A 471 GLU GLN CYS ALA PHE TYR ARG LEU ILE GLY GLU PHE ASP SEQRES 17 A 471 THR HIS LEU SER PRO VAL PRO ARG PRO MET TYR LEU VAL SEQRES 18 A 471 SER ASN HIS ARG VAL LEU ILE ASN ASP PHE ASN GLN PRO SEQRES 19 A 471 PHE GLN HIS TRP GLN ASN GLN PRO TYR ALA GLY ALA GLY SEQRES 20 A 471 LEU ALA HIS LYS ARG SER ARG ARG TYR PHE PHE GLY GLU SEQRES 21 A 471 ASP TYR VAL CYS LYS PHE PHE TYR TYR ASP MET PRO HIS SEQRES 22 A 471 GLY ILE LEU THR ALA GLU GLU SER GLN ARG ASN LYS HIS SEQRES 23 A 471 GLU LEU HIS ASN GLU ILE LYS PHE LEU THR GLN PRO PRO SEQRES 24 A 471 ALA GLY PHE ASP ALA PRO ALA VAL LEU ALA HIS GLY GLU SEQRES 25 A 471 ASN ALA GLN SER GLY TRP LEU VAL MET GLU LYS LEU PRO SEQRES 26 A 471 GLY ARG LEU LEU SER ASP MET LEU ALA ALA GLY GLU GLU SEQRES 27 A 471 ILE ASP ARG GLU LYS ILE LEU GLY SER LEU LEU ARG SER SEQRES 28 A 471 LEU ALA ALA LEU GLU LYS LYS GLY PHE TRP HIS ASP ASP SEQRES 29 A 471 VAL ARG PRO TRP ASN VAL MET VAL ASP ALA ARG GLN HIS SEQRES 30 A 471 ALA ARG LEU ILE ASP PHE GLY SER ILE VAL THR THR PRO SEQRES 31 A 471 GLN ASP CYS SER TRP PRO THR ASN LEU VAL GLN SER PHE SEQRES 32 A 471 PHE VAL PHE VAL ASN GLU LEU PHE ALA GLU ASN LYS SER SEQRES 33 A 471 TRP ASN GLY PHE TRP ARG SER ALA PRO VAL HIS PRO PHE SEQRES 34 A 471 ASN LEU PRO GLN PRO TRP SER ASN TRP LEU TYR ALA VAL SEQRES 35 A 471 TRP GLN GLU PRO VAL GLU ARG TRP ASN PHE ALA LEU LEU SEQRES 36 A 471 LEU ALA LEU PHE GLU LYS LYS ALA LYS LEU PRO SER ALA SEQRES 37 A 471 GLU GLN GLN HET ATP A1450 31 HET SAM A1451 27 HET MG A1452 1 HET MG A1453 1 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM SAM S-ADENOSYLMETHIONINE HETNAM MG MAGNESIUM ION FORMUL 2 ATP C10 H16 N5 O13 P3 FORMUL 3 SAM C15 H22 N6 O5 S FORMUL 4 MG 2(MG 2+) FORMUL 6 HOH *77(H2 O) HELIX 1 1 LEU A 5 LEU A 12 1 8 HELIX 2 2 HIS A 22 ASP A 26 5 5 HELIX 3 3 CYS A 33 GLY A 52 1 20 HELIX 4 4 GLY A 65 SER A 73 1 9 HELIX 5 5 GLN A 84 ASN A 98 1 15 HELIX 6 6 ARG A 109 ALA A 116 1 8 HELIX 7 7 VAL A 130 GLY A 139 1 10 HELIX 8 8 GLY A 139 VAL A 153 1 15 HELIX 9 9 TRP A 170 GLN A 174 5 5 HELIX 10 10 ASP A 177 ILE A 182 5 6 HELIX 11 11 MET A 258 ILE A 262 5 5 HELIX 12 12 THR A 264 GLN A 284 1 21 HELIX 13 13 LEU A 316 ALA A 322 1 7 HELIX 14 14 ASP A 327 LYS A 345 1 19 HELIX 15 15 ARG A 353 TRP A 355 5 3 HELIX 16 16 ASP A 369 GLY A 371 5 3 HELIX 17 17 PRO A 383 PHE A 398 1 16 HELIX 18 18 PRO A 421 GLU A 432 1 12 HELIX 19 19 PRO A 433 TRP A 437 5 5 HELIX 20 20 ASN A 438 LYS A 448 1 11 SHEET 1 AA 7 ALA A 103 VAL A 107 0 SHEET 2 AA 7 THR A 77 ASP A 82 1 O ILE A 78 N GLU A 104 SHEET 3 AA 7 ASN A 56 LEU A 60 1 O VAL A 57 N VAL A 79 SHEET 4 AA 7 LEU A 124 LEU A 128 1 O LEU A 124 N LEU A 58 SHEET 5 AA 7 ALA A 156 GLU A 160 1 O ALA A 156 N ALA A 125 SHEET 6 AA 7 PRO A 204 SER A 209 -1 O TYR A 206 N LEU A 159 SHEET 7 AA 7 PHE A 187 GLU A 193 -1 O PHE A 187 N SER A 209 SHEET 1 AB 2 ARG A 212 ILE A 215 0 SHEET 2 AB 2 PHE A 218 PRO A 221 -1 O PHE A 218 N ILE A 215 SHEET 1 AC 5 HIS A 224 GLN A 226 0 SHEET 2 AC 5 ARG A 241 PHE A 245 -1 O TYR A 243 N GLN A 226 SHEET 3 AC 5 TYR A 249 TYR A 255 -1 O CYS A 251 N PHE A 244 SHEET 4 AC 5 SER A 303 GLU A 309 -1 O GLY A 304 N PHE A 254 SHEET 5 AC 5 VAL A 294 GLU A 299 -1 N LEU A 295 O VAL A 307 SHEET 1 AD 3 ARG A 314 LEU A 315 0 SHEET 2 AD 3 VAL A 357 VAL A 359 -1 O VAL A 359 N ARG A 314 SHEET 3 AD 3 ALA A 365 LEU A 367 -1 O ARG A 366 N MET A 358 SHEET 1 AE 2 TRP A 348 HIS A 349 0 SHEET 2 AE 2 ILE A 373 VAL A 374 -1 O VAL A 374 N TRP A 348 LINK OE2 GLU A 274 MG MG A1453 1555 1555 2.19 LINK OD1 ASN A 356 MG MG A1452 1555 1555 1.97 LINK OD2 ASP A 369 MG MG A1452 1555 1555 2.21 LINK OD1 ASP A 369 MG MG A1453 1555 1555 2.26 LINK OD2 ASP A 369 MG MG A1453 1555 1555 2.36 LINK O2G ATP A1450 MG MG A1452 1555 1555 2.14 LINK O1A ATP A1450 MG MG A1452 1555 1555 1.86 LINK O3G ATP A1450 MG MG A1453 1555 1555 1.98 LINK O1B ATP A1450 MG MG A1453 1555 1555 2.15 LINK MG MG A1452 O HOH A2069 1555 1555 2.03 LINK MG MG A1453 O HOH A2055 1555 1555 2.15 CISPEP 1 GLN A 420 PRO A 421 0 4.09 SITE 1 AC1 20 PRO A 229 HIS A 237 ARG A 241 TYR A 243 SITE 2 AC1 20 LYS A 252 PHE A 254 GLU A 274 MET A 308 SITE 3 AC1 20 GLU A 309 LYS A 310 LEU A 311 LEU A 315 SITE 4 AC1 20 ASN A 356 ILE A 368 ASP A 369 MG A1452 SITE 5 AC1 20 MG A1453 HOH A2041 HOH A2055 HOH A2069 SITE 1 AC2 17 TYR A 16 GLN A 17 ARG A 36 GLY A 61 SITE 2 AC2 17 ALA A 63 PHE A 67 ASP A 82 PHE A 83 SITE 3 AC2 17 GLN A 84 ASN A 87 GLY A 108 ARG A 109 SITE 4 AC2 17 ILE A 110 GLU A 111 LEU A 128 SER A 129 SITE 5 AC2 17 VAL A 130 SITE 1 AC3 4 ASN A 356 ASP A 369 ATP A1450 HOH A2069 SITE 1 AC4 4 GLU A 274 ASP A 369 ATP A1450 HOH A2055 CRYST1 40.670 89.600 135.460 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 0.024588 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011161 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007382 0.00000