PDB Short entry for 4KCF HEADER OXIDOREDUCTASE 24-APR-13 4KCF TITLE X-RAY STRUCTURE OF A KIJD3 IN COMPLEX WITH FMN AND DTDP-3-AMINO-2,3,6- TITLE 2 TRIDEOXY-4-KETO-3-METHYL-D-GLUCOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FAD-DEPENDENT OXIDOREDUCTASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACTINOMADURA KIJANIATA; SOURCE 3 ORGANISM_TAXID: 46161; SOURCE 4 GENE: KIJD3; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA2 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS KIJD3, FATTY ACYL-COA DEHYDROGENASE FAMILY, KIJANOSE, KIJANIMICIN, KEYWDS 2 FAD, FLAVOPROTEIN, OXIDOREDUCTASE, CLASS D FLAVIN CONTAINING KEYWDS 3 MONOOXYGENASES, N-OXYGENASE, NUCLEOTIDE LINKED SUGAR, DTDP-3-AMINO- KEYWDS 4 2, 3, 6-TRIDEOXY-4-KETO-3-METHYL-D-GLUCOSE, FMN EXPDTA X-RAY DIFFRACTION AUTHOR H.M.HOLDEN,J.B.THODEN,M.C.BRANCH,A.L.ZIMMER,N.A.BRUENDER REVDAT 4 20-SEP-23 4KCF 1 REMARK SEQADV REVDAT 3 18-DEC-13 4KCF 1 JRNL REVDAT 2 29-MAY-13 4KCF 1 HETATM HETNAM REVDAT 1 22-MAY-13 4KCF 0 JRNL AUTH J.B.THODEN,M.C.BRANCH,A.L.ZIMMER,N.A.BRUENDER,H.M.HOLDEN JRNL TITL ACTIVE SITE ARCHITECTURE OF A SUGAR N-OXYGENASE. JRNL REF BIOCHEMISTRY V. 52 3191 2013 JRNL REFN ISSN 0006-2960 JRNL PMID 23621882 JRNL DOI 10.1021/BI400407X REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 76.31 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 89.9 REMARK 3 NUMBER OF REFLECTIONS : 23596 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1193 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1465 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.58 REMARK 3 BIN R VALUE (WORKING SET) : 0.1800 REMARK 3 BIN FREE R VALUE SET COUNT : 67 REMARK 3 BIN FREE R VALUE : 0.2070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3025 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 61 REMARK 3 SOLVENT ATOMS : 102 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.68000 REMARK 3 B22 (A**2) : -0.93000 REMARK 3 B33 (A**2) : -1.75000 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): 0.223 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.188 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.117 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.307 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3157 ; 0.012 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4315 ; 2.269 ; 1.990 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 408 ; 6.238 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 129 ;29.001 ;22.093 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 472 ;15.195 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;18.978 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 500 ; 0.131 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2400 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2023 ; 1.218 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3226 ; 2.078 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1134 ; 3.124 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1089 ; 4.839 ; 4.500 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 REMARK 4 REMARK 4 4KCF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000079162. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23596 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.098 REMARK 200 RESOLUTION RANGE LOW (A) : 76.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.4 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.11000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 17.50 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3M9V REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PENTAERYTHRITOL PROPOXYLATE 5/4 REMARK 280 100 MM MOPS, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 35.41400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.64850 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 76.31400 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 35.41400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.64850 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 76.31400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 35.41400 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 40.64850 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 76.31400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 35.41400 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 40.64850 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 76.31400 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 15460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 53290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -99.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 SER A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 GLU A -7 REMARK 465 ASN A -6 REMARK 465 LEU A -5 REMARK 465 TYR A -4 REMARK 465 GLU A -3 REMARK 465 GLN A -2 REMARK 465 GLY A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 PRO A 2 REMARK 465 PRO A 3 REMARK 465 TRP A 4 REMARK 465 THR A 5 REMARK 465 ALA A 6 REMARK 465 ARG A 7 REMARK 465 GLN A 8 REMARK 465 ARG A 416 REMARK 465 SER A 417 REMARK 465 GLY A 418 REMARK 465 GLY A 419 REMARK 465 ASN A 420 REMARK 465 GLY A 421 REMARK 465 LYS A 422 REMARK 465 SER A 423 REMARK 465 ALA A 424 REMARK 465 ASP A 425 REMARK 465 ALA A 426 REMARK 465 ALA A 427 REMARK 465 GLY A 428 REMARK 465 PRO A 429 REMARK 465 ARG A 430 REMARK 465 ARG A 431 REMARK 465 PRO A 432 REMARK 465 THR A 433 REMARK 465 PRO A 434 REMARK 465 THR A 435 REMARK 465 SER A 436 REMARK 465 ARG A 437 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 ASP A 156 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 166 NE - CZ - NH1 ANGL. DEV. = 8.1 DEGREES REMARK 500 ARG A 166 NE - CZ - NH2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG A 282 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 306 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 306 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ASP A 326 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 MET A 384 CG - SD - CE ANGL. DEV. = -12.6 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 ASP A 118 178.01 -57.31 REMARK 500 ALA A 158 26.66 -157.51 REMARK 500 LEU A 169 70.39 66.13 REMARK 500 THR A 188 -132.59 -100.53 REMARK 500 ASP A 189 -23.98 -142.28 REMARK 500 SER A 196 79.37 -118.90 REMARK 500 THR A 222 59.88 -92.43 REMARK 500 ARG A 240 -151.62 -104.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 FMN A 502 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AKM A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN A 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3M9V RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF A KIJD3 IN COMPLEX WITH DTDP DBREF 4KCF A 1 437 UNP B3TMR1 B3TMR1_9ACTO 1 437 SEQADV 4KCF HIS A -16 UNP B3TMR1 EXPRESSION TAG SEQADV 4KCF HIS A -15 UNP B3TMR1 EXPRESSION TAG SEQADV 4KCF HIS A -14 UNP B3TMR1 EXPRESSION TAG SEQADV 4KCF HIS A -13 UNP B3TMR1 EXPRESSION TAG SEQADV 4KCF HIS A -12 UNP B3TMR1 EXPRESSION TAG SEQADV 4KCF HIS A -11 UNP B3TMR1 EXPRESSION TAG SEQADV 4KCF SER A -10 UNP B3TMR1 EXPRESSION TAG SEQADV 4KCF SER A -9 UNP B3TMR1 EXPRESSION TAG SEQADV 4KCF GLY A -8 UNP B3TMR1 EXPRESSION TAG SEQADV 4KCF GLU A -7 UNP B3TMR1 EXPRESSION TAG SEQADV 4KCF ASN A -6 UNP B3TMR1 EXPRESSION TAG SEQADV 4KCF LEU A -5 UNP B3TMR1 EXPRESSION TAG SEQADV 4KCF TYR A -4 UNP B3TMR1 EXPRESSION TAG SEQADV 4KCF GLU A -3 UNP B3TMR1 EXPRESSION TAG SEQADV 4KCF GLN A -2 UNP B3TMR1 EXPRESSION TAG SEQADV 4KCF GLY A -1 UNP B3TMR1 EXPRESSION TAG SEQADV 4KCF HIS A 0 UNP B3TMR1 EXPRESSION TAG SEQRES 1 A 454 HIS HIS HIS HIS HIS HIS SER SER GLY GLU ASN LEU TYR SEQRES 2 A 454 GLU GLN GLY HIS MET PRO PRO TRP THR ALA ARG GLN ASP SEQRES 3 A 454 SER THR THR GLY LEU TYR ALA PRO VAL THR PRO ALA GLY SEQRES 4 A 454 ARG VAL LEU LEU ASP ARG LEU ALA ALA HIS LEU PRO ARG SEQRES 5 A 454 ILE ARG SER THR ALA ALA GLU HIS ASP ARG ASP GLY THR SEQRES 6 A 454 PHE PRO THR ASP THR PHE ASP ALA LEU ARG LYS ASP GLY SEQRES 7 A 454 LEU MET GLY ALA THR VAL PRO ALA GLU LEU GLY GLY LEU SEQRES 8 A 454 GLY VAL ASP ARG LEU TYR ASP VAL ALA VAL ALA LEU LEU SEQRES 9 A 454 ALA VAL ALA ARG ALA ASP ALA SER THR ALA LEU ALA LEU SEQRES 10 A 454 HIS MET GLN LEU SER ARG GLY LEU THR LEU GLY TYR GLU SEQRES 11 A 454 TRP ARG HIS GLY ASP GLU ARG ALA ARG THR LEU ALA GLU SEQRES 12 A 454 ARG ILE LEU ARG GLY MET VAL ALA GLY ASP ALA VAL VAL SEQRES 13 A 454 CYS SER GLY ILE LYS ASP HIS HIS THR ALA VAL THR THR SEQRES 14 A 454 LEU ARG PRO ASP GLY ALA GLY GLY TRP LEU LEU SER GLY SEQRES 15 A 454 ARG LYS THR LEU VAL SER MET ALA PRO VAL GLY THR HIS SEQRES 16 A 454 PHE VAL ILE ASN ALA ARG THR ASP GLY THR ASP GLY PRO SEQRES 17 A 454 PRO ARG LEU ALA SER PRO VAL VAL THR ARG ASP THR PRO SEQRES 18 A 454 GLY PHE THR VAL LEU ASP ASN TRP ASP GLY LEU GLY MET SEQRES 19 A 454 ARG ALA SER GLY THR VAL ASP ILE VAL PHE ASP ASP CYS SEQRES 20 A 454 PRO ILE PRO ALA ASP HIS VAL LEU MET ARG ASP PRO VAL SEQRES 21 A 454 GLY ALA ARG ASN ASP ALA VAL LEU ALA GLY GLN THR VAL SEQRES 22 A 454 SER SER VAL SER VAL LEU GLY VAL TYR VAL GLY VAL ALA SEQRES 23 A 454 GLN ALA ALA TYR ASP THR ALA VAL ALA ALA LEU GLU ARG SEQRES 24 A 454 ARG PRO GLU PRO PRO GLN ALA ALA ALA LEU THR LEU VAL SEQRES 25 A 454 ALA GLU ILE ASP SER ARG LEU TYR ALA LEU ARG ALA THR SEQRES 26 A 454 ALA GLY SER ALA LEU THR ALA ALA ASP ALA LEU SER ALA SEQRES 27 A 454 ASP LEU SER GLY ASP MET ASP GLU ARG GLY ARG GLN MET SEQRES 28 A 454 MET ARG HIS PHE GLN CYS ALA LYS LEU ALA VAL ASN ARG SEQRES 29 A 454 LEU ALA PRO GLU ILE VAL SER ASP CYS LEU SER LEU VAL SEQRES 30 A 454 GLY GLY ALA SER TYR THR ALA GLY HIS PRO LEU ALA ARG SEQRES 31 A 454 LEU LEU ARG ASP VAL GLN ALA GLY ARG PHE MET GLN PRO SEQRES 32 A 454 TYR ALA TYR VAL ASP ALA VAL ASP PHE LEU SER ALA GLN SEQRES 33 A 454 ALA LEU GLY ILE GLU ARG ASP ASN ASN TYR MET SER THR SEQRES 34 A 454 TRP ALA LYS ARG SER GLY GLY ASN GLY LYS SER ALA ASP SEQRES 35 A 454 ALA ALA GLY PRO ARG ARG PRO THR PRO THR SER ARG HET AKM A 501 36 HET FMN A 502 25 HETNAM AKM [(2R,4S,6R)-4-AZANYL-4,6-DIMETHYL-5,5-BIS(OXIDANYL) HETNAM 2 AKM OXAN-2-YL] [[(2R,3S,5R)-5-[5-METHYL-2,4- HETNAM 3 AKM BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-3-OXIDANYL-OXOLAN-2- HETNAM 4 AKM YL]METHOXY-OXIDANYL-PHOSPHORYL] HYDROGEN PHOSPHATE HETNAM FMN FLAVIN MONONUCLEOTIDE HETSYN AKM DTDP-3-AMINO-2,3,6-TRIDEOXY-4-KETO-3-METHYL-D-GLUCOSE HETSYN 2 AKM (HYDRATED AT C4) HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 2 AKM C17 H29 N3 O14 P2 FORMUL 3 FMN C17 H21 N4 O9 P FORMUL 4 HOH *102(H2 O) HELIX 1 1 THR A 19 ALA A 31 1 13 HELIX 2 2 HIS A 32 THR A 39 1 8 HELIX 3 3 THR A 39 GLY A 47 1 9 HELIX 4 4 PRO A 50 ASP A 60 1 11 HELIX 5 5 GLY A 61 ALA A 65 5 5 HELIX 6 6 PRO A 68 GLY A 72 5 5 HELIX 7 7 ARG A 78 ASP A 93 1 16 HELIX 8 8 ASP A 93 GLY A 117 1 25 HELIX 9 9 ASP A 118 ALA A 134 1 17 HELIX 10 10 MET A 172 GLY A 176 5 5 HELIX 11 11 PRO A 233 ASP A 235 5 3 HELIX 12 12 ALA A 249 SER A 257 1 9 HELIX 13 13 SER A 258 SER A 260 5 3 HELIX 14 14 VAL A 261 ARG A 282 1 22 HELIX 15 15 GLN A 288 ASP A 322 1 35 HELIX 16 16 ASP A 326 GLY A 361 1 36 HELIX 17 17 GLY A 362 THR A 366 5 5 HELIX 18 18 HIS A 369 VAL A 378 1 10 HELIX 19 19 GLN A 379 MET A 384 5 6 HELIX 20 20 ALA A 388 LEU A 401 1 14 HELIX 21 21 ASN A 408 LYS A 415 1 8 SHEET 1 A 8 VAL A 139 GLY A 142 0 SHEET 2 A 8 HIS A 178 ILE A 181 1 O HIS A 178 N CYS A 140 SHEET 3 A 8 ARG A 193 THR A 200 -1 O PRO A 197 N ILE A 181 SHEET 4 A 8 ALA A 183 THR A 185 -1 N ALA A 183 O ALA A 195 SHEET 5 A 8 THR A 152 PRO A 155 1 N LEU A 153 O ARG A 184 SHEET 6 A 8 TRP A 161 VAL A 170 -1 O LEU A 162 N ARG A 154 SHEET 7 A 8 VAL A 223 ILE A 232 -1 O ILE A 232 N TRP A 161 SHEET 8 A 8 PHE A 206 VAL A 208 -1 N THR A 207 O VAL A 226 SHEET 1 B 4 VAL A 139 GLY A 142 0 SHEET 2 B 4 HIS A 178 ILE A 181 1 O HIS A 178 N CYS A 140 SHEET 3 B 4 ARG A 193 THR A 200 -1 O PRO A 197 N ILE A 181 SHEET 4 B 4 VAL A 237 PRO A 242 -1 O ARG A 240 N LEU A 194 CISPEP 1 GLN A 385 PRO A 386 0 -1.66 CISPEP 2 PRO A 386 TYR A 387 0 -15.73 SITE 1 AC1 27 HIS A 101 MET A 102 SER A 105 ARG A 106 SITE 2 AC1 27 THR A 109 TYR A 112 GLU A 113 SER A 141 SITE 3 AC1 27 ILE A 143 ARG A 240 ALA A 252 GLY A 253 SITE 4 AC1 27 GLN A 254 VAL A 256 SER A 257 SER A 258 SITE 5 AC1 27 ARG A 330 MET A 410 FMN A 502 HOH A 621 SITE 6 AC1 27 HOH A 635 HOH A 646 HOH A 647 HOH A 670 SITE 7 AC1 27 HOH A 684 HOH A 687 HOH A 699 SITE 1 AC2 15 MET A 102 SER A 141 ILE A 143 LYS A 144 SITE 2 AC2 15 LEU A 169 SER A 171 THR A 222 PHE A 383 SITE 3 AC2 15 MET A 384 GLN A 385 TRP A 413 AKM A 501 SITE 4 AC2 15 HOH A 624 HOH A 666 HOH A 699 CRYST1 70.828 81.297 152.628 90.00 90.00 90.00 I 2 2 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 0.014119 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012301 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006552 0.00000