PDB Short entry for 2DKB HEADER LYASE(DECARBOXYLASE) 12-JUL-94 2DKB TITLE DIALKYLGLYCINE DECARBOXYLASE STRUCTURE: BIFUNCTIONAL ACTIVE SITE AND TITLE 2 ALKALI METAL BINDING SITES COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE); COMPND 3 CHAIN: A; COMPND 4 EC: 4.1.1.64; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BURKHOLDERIA CEPACIA; SOURCE 3 ORGANISM_TAXID: 292; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LYASE(DECARBOXYLASE) EXPDTA X-RAY DIFFRACTION AUTHOR M.D.TONEY,E.HOHENESTER,J.N.JANSONIUS REVDAT 5 29-NOV-17 2DKB 1 REMARK HELIX REVDAT 4 13-JUL-11 2DKB 1 VERSN REVDAT 3 24-FEB-09 2DKB 1 VERSN REVDAT 2 01-APR-03 2DKB 1 JRNL REVDAT 1 15-OCT-94 2DKB 0 JRNL AUTH M.D.TONEY,E.HOHENESTER,S.W.COWAN,J.N.JANSONIUS JRNL TITL DIALKYLGLYCINE DECARBOXYLASE STRUCTURE: BIFUNCTIONAL ACTIVE JRNL TITL 2 SITE AND ALKALI METAL SITES. JRNL REF SCIENCE V. 261 756 1993 JRNL REFN ISSN 0036-8075 JRNL PMID 8342040 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.D.TONEY,J.W.KELLER,R.A.PAUPTIT,J.JAEGER,M.K.WISE,U.SAUDER, REMARK 1 AUTH 2 J.N.JANSONIUS REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION STUDIES OF REMARK 1 TITL 2 DIALKYLGLYCINE DECARBOXYLASE, A DECARBOXYLATING TRANSAMINASE REMARK 1 REF J.MOL.BIOL. V. 222 873 1991 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.W.KELLER,K.B.BAURICK,G.C.RUTT,M.V.O'MALLEY,N.L.SONAFRANK, REMARK 1 AUTH 2 R.A.REYNOLDS,L.O.EBBESSON,F.F.VAJDOS REMARK 1 TITL PSEUDOMONAS CEPACIA 2.2-DIALKYLGLYCINE DECARBOXYLASE. REMARK 1 TITL 2 SEQUENCE AND EXPRESSION IN ESCHERICHIA COLI OF STRUCTURAL REMARK 1 TITL 3 AND REPRESSOR GENES REMARK 1 REF J.BIOL.CHEM. V. 265 5531 1990 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3252 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 229 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.011 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 2.200 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : 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 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 ATOMS THAT ARE NOT WELL DEFINED DUE TO POOR ELECTRON REMARK 3 DENSITY OR REFINE TO B-FACTORS (GREATER THAN) 100 REMARK 3 ANGSTROMS**2 HAVE A WEIGHT OF ZERO. REMARK 4 REMARK 4 2DKB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000178002. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL 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 <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) : 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+1/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.86667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 57.73333 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 28.86667 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 57.73333 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 28.86667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 57.73333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 28.86667 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 57.73333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: DGD IS A TETRAMER OF IDENTICAL SUBUNITS. THE FOLLOWING REMARK 300 TRANSFORMATIONS WILL GENERATE THE OTHER THREE SUBUNITS OF REMARK 300 THE TETRAMER: REMARK 300 REMARK 300 MTRIX1 1 -0.500000 0.866010 0.000000 0.00000 REMARK 300 MTRIX2 1 0.866041 0.500000 0.000000 0.00000 REMARK 300 MTRIX3 1 0.000000 0.000000 -1.000000 28.86753 REMARK 300 REMARK 300 MTRIX1 2 0.500000 -0.866010 0.000000 76.34753 REMARK 300 MTRIX2 2 -0.866041 -0.500000 0.000000 132.24016 REMARK 300 MTRIX3 2 0.000000 0.000000 -1.000000 28.86753 REMARK 300 REMARK 300 MTRIX1 3 -1.000000 0.000000 0.000000 76.34753 REMARK 300 MTRIX2 3 0.000000 -1.000000 0.000000 132.24016 REMARK 300 MTRIX3 3 0.000000 0.000000 1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -97.0 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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 28.86667 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 29650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 51250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -201.0 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 76.35000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 132.24208 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 28.86667 REMARK 350 BIOMT1 4 0.500000 -0.866025 0.000000 76.35000 REMARK 350 BIOMT2 4 -0.866025 -0.500000 0.000000 132.24208 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 28.86667 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 SER A 2 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 GLY A 143 REMARK 475 ARG A 370 REMARK 475 ASP A 376 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASP A 5 C O CB CG OD1 OD2 REMARK 480 ALA A 7 CB REMARK 480 ARG A 11 CD NE CZ NH1 NH2 REMARK 480 ARG A 14 CG CD NE CZ NH1 NH2 REMARK 480 HIS A 15 CD2 CE1 REMARK 480 GLU A 25 CG CD OE1 OE2 REMARK 480 ARG A 31 CD NE CZ NH1 NH2 REMARK 480 LYS A 33 CE REMARK 480 ARG A 43 NE CZ NH1 NH2 REMARK 480 SER A 66 OG REMARK 480 GLU A 70 CG CD OE1 OE2 REMARK 480 LYS A 74 CG CD CE NZ REMARK 480 GLU A 81 CD OE1 OE2 REMARK 480 GLU A 116 CG CD OE1 OE2 REMARK 480 ARG A 120 CZ NH1 NH2 REMARK 480 GLN A 136 CD OE1 NE2 REMARK 480 MET A 141 CE REMARK 480 THR A 142 CA C OG1 CG2 REMARK 480 ARG A 176 CD NE CZ REMARK 480 GLU A 178 CG CD OE1 OE2 REMARK 480 ARG A 179 NE CZ NH1 NH2 REMARK 480 ASN A 180 CG OD1 ND2 REMARK 480 ALA A 182 CB REMARK 480 ASP A 190 OD2 REMARK 480 ASP A 194 CG OD1 OD2 REMARK 480 ARG A 198 NE CZ NH1 NH2 REMARK 480 SER A 215 OG REMARK 480 GLU A 220 CD REMARK 480 ASP A 223 CB CG OD1 OD2 REMARK 480 ARG A 231 NE CZ NH1 NH2 REMARK 480 ARG A 260 CD NE CZ NH1 NH2 REMARK 480 VAL A 263 CG1 CG2 REMARK 480 ARG A 292 NE CZ NH1 NH2 REMARK 480 GLU A 295 CG CD OE1 OE2 REMARK 480 LEU A 299 CG CD1 CD2 REMARK 480 TYR A 301 CG CD1 CD2 CE1 CE2 CZ OH REMARK 480 ARG A 329 CZ NH1 NH2 REMARK 480 MET A 333 CE REMARK 480 ARG A 336 NH1 REMARK 480 ARG A 338 NE CZ NH1 NH2 REMARK 480 ARG A 339 NE CZ NH1 NH2 REMARK 480 ASP A 343 CG OD1 OD2 REMARK 480 MET A 345 CE REMARK 480 GLU A 346 CB CG CD OE1 OE2 REMARK 480 ARG A 347 CG CD NE CZ NH1 NH2 REMARK 480 ASP A 349 CG OD1 OD2 REMARK 480 LYS A 367 CB CG CD CE NZ REMARK 480 ASP A 368 N CB CG OD1 OD2 REMARK 480 ARG A 369 CD NE CZ NH1 NH2 REMARK 480 THR A 371 C O CB OG1 CG2 REMARK 480 GLU A 373 CB CG CD OE1 OE2 REMARK 480 PRO A 374 CB REMARK 480 ALA A 375 C O CB REMARK 480 ARG A 384 NE CZ NH1 NH2 REMARK 480 ASN A 388 CG OD1 ND2 REMARK 480 GLN A 397 CD OE1 NE2 REMARK 480 MET A 401 CE REMARK 480 GLU A 415 CD OE1 OE2 REMARK 480 ASP A 416 CG OD1 OD2 REMARK 480 GLN A 427 CD OE1 NE2 REMARK 480 GLU A 430 CG CD OE1 OE2 REMARK 480 ARG A 431 CZ NH1 NH2 REMARK 480 LEU A 433 C O OXT 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 GLY A 51 C GLN A 52 N -0.177 REMARK 500 GLN A 52 C MET A 53 N -0.166 REMARK 500 GLU A 210 CD GLU A 210 OE2 0.073 REMARK 500 GLU A 220 CD GLU A 220 OE1 0.073 REMARK 500 GLU A 234 CD GLU A 234 OE1 0.069 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 ASP A 5 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP A 41 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ASP A 47 CB - CG - OD1 ANGL. DEV. = -6.4 DEGREES REMARK 500 ASP A 47 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 GLY A 51 O - C - N ANGL. DEV. = -12.7 DEGREES REMARK 500 ASP A 89 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 89 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG A 93 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 93 NE - CZ - NH2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ARG A 174 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP A 184 CB - CG - OD2 ANGL. DEV. = -7.1 DEGREES REMARK 500 ASP A 194 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ASP A 197 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 197 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ASP A 223 CB - CG - OD1 ANGL. DEV. = -5.5 DEGREES REMARK 500 MET A 226 CG - SD - CE ANGL. DEV. = -9.8 DEGREES REMARK 500 ARG A 323 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ASP A 335 CB - CG - OD1 ANGL. DEV. = -6.2 DEGREES REMARK 500 ASP A 335 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 343 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP A 349 CB - CG - OD1 ANGL. DEV. = -5.5 DEGREES REMARK 500 ASP A 368 CB - CG - OD1 ANGL. DEV. = -6.5 DEGREES REMARK 500 ASP A 368 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 376 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP A 419 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ASP A 419 CB - CG - OD2 ANGL. DEV. = -5.6 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 PRO A 26 47.47 -88.22 REMARK 500 GLN A 52 53.55 -117.60 REMARK 500 ALA A 55 66.70 -67.53 REMARK 500 ASP A 76 -69.31 -108.78 REMARK 500 LEU A 108 -156.45 -124.54 REMARK 500 VAL A 249 43.31 70.05 REMARK 500 SER A 271 -83.45 -161.16 REMARK 500 ALA A 408 81.88 -155.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 PLP A 437 REMARK 615 MES A 434 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 NA A 435 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 95 O REMARK 620 2 PRO A 99 O 162.1 REMARK 620 3 LEU A 102 O 97.0 100.8 REMARK 620 4 HOH A 526 O 83.2 96.6 83.9 REMARK 620 5 THR A 98 OG1 83.1 99.7 87.1 162.5 REMARK 620 6 THR A 98 O 90.8 73.2 158.9 116.6 74.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 436 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 78 O REMARK 620 2 HOH A 519 O 85.8 REMARK 620 3 HOH A 509 O 82.4 124.3 REMARK 620 4 ASP A 307 OD1 91.6 123.2 111.4 REMARK 620 5 VAL A 305 O 164.4 92.9 85.6 102.0 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: PLP REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: RESIDUE LYS 272 HAS THE COFACTOR PYRIDOXAL-5' REMARK 800 -PHOSPHATE COVALENTLY ATTACHED TO IT REMARK 800 REMARK 800 SITE_IDENTIFIER: ME1 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: METAL BINDING SITE 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: ME2 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: METAL BINDING SITE 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 435 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 436 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP A 437 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 434 REMARK 999 REMARK 999 SEQUENCE REMARK 999 SEQUENCE ADVISORY NOTICE REMARK 999 DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. REMARK 999 REMARK 999 SWISS-PROT ENTRY NAME: DGDA_BURCE REMARK 999 REMARK 999 SWISS-PROT RESIDUE PDB SEQRES REMARK 999 REMARK 999 NAME NUMBER NAME CHAIN SEQ/INSERT CODE REMARK 999 GLN 14 HIS 15 REMARK 999 GLU 51 GLN 52 REMARK 999 GLY 80 GLU 81 REMARK 999 ILE 81 MET 82 REMARK 999 VAL 82 LEU 83 REMARK 999 ARG 307 PRO 308 REMARK 999 PRO 309 LEU 309 REMARK 999 GLY 312 ALA 312 REMARK 999 REMARK 999 THE PUBLISHED AMINO ACID SEQUENCE (REF. 1) WAS CORRECTED REMARK 999 AT TWO POSITIONS (J.W. KELLER, PRIVATE COMMUNICATION): REMARK 999 RESIDUES 81 - 83: GLY-ILE-VAL TO GLU-MET-LEU. REMARK 999 RESIDUES 308 - 313: ARG-CYS-PRO-PRO-ALA-GLY TO REMARK 999 -PRO-LEU-PRO-ALA-ALA (INCLUDES A DELETION!). REMARK 999 RESIDUE 15 IS HIS AS IN REFERENCE 1. REMARK 999 RESIDUE 52 IS GLN (J.W. KELLER, PRIVATE COMMUNICATION). REMARK 999 THE FIRST TWO RESIDUES ARE NOT INCLUDED IN THE MODEL SINCE REMARK 999 THEY ARE DISORDERED. DBREF 2DKB A 2 433 UNP P16932 DGDA_BURCE 1 432 SEQADV 2DKB HIS A 15 UNP P16932 GLN 14 CONFLICT SEQADV 2DKB GLU A 81 UNP P16932 GLY 80 CONFLICT SEQRES 1 A 433 MET SER LEU ASN ASP ASP ALA THR PHE TRP ARG ASN ALA SEQRES 2 A 433 ARG HIS HIS LEU VAL ARG TYR GLY GLY THR PHE GLU PRO SEQRES 3 A 433 MET ILE ILE GLU ARG ALA LYS GLY SER PHE VAL TYR ASP SEQRES 4 A 433 ALA ASP GLY ARG ALA ILE LEU ASP PHE THR SER GLY GLN SEQRES 5 A 433 MET SER ALA VAL LEU GLY HIS CYS HIS PRO GLU ILE VAL SEQRES 6 A 433 SER VAL ILE GLY GLU TYR ALA GLY LYS LEU ASP HIS LEU SEQRES 7 A 433 PHE SER GLU MET LEU SER ARG PRO VAL VAL ASP LEU ALA SEQRES 8 A 433 THR ARG LEU ALA ASN ILE THR PRO PRO GLY LEU ASP ARG SEQRES 9 A 433 ALA LEU LEU LEU SER THR GLY ALA GLU SER ASN GLU ALA SEQRES 10 A 433 ALA ILE ARG MET ALA LYS LEU VAL THR GLY LYS TYR GLU SEQRES 11 A 433 ILE VAL GLY PHE ALA GLN SER TRP HIS GLY MET THR GLY SEQRES 12 A 433 ALA ALA ALA SER ALA THR TYR SER ALA GLY ARG LYS GLY SEQRES 13 A 433 VAL GLY PRO ALA ALA VAL GLY SER PHE ALA ILE PRO ALA SEQRES 14 A 433 PRO PHE THR TYR ARG PRO ARG PHE GLU ARG ASN GLY ALA SEQRES 15 A 433 TYR ASP TYR LEU ALA GLU LEU ASP TYR ALA PHE ASP LEU SEQRES 16 A 433 ILE ASP ARG GLN SER SER GLY ASN LEU ALA ALA PHE ILE SEQRES 17 A 433 ALA GLU PRO ILE LEU SER SER GLY GLY ILE ILE GLU LEU SEQRES 18 A 433 PRO ASP GLY TYR MET ALA ALA LEU LYS ARG LYS CYS GLU SEQRES 19 A 433 ALA ARG GLY MET LEU LEU ILE LEU ASP GLU ALA GLN THR SEQRES 20 A 433 GLY VAL GLY ARG THR GLY THR MET PHE ALA CYS GLN ARG SEQRES 21 A 433 ASP GLY VAL THR PRO ASP ILE LEU THR LEU SER LYS THR SEQRES 22 A 433 LEU GLY ALA GLY LEU PRO LEU ALA ALA ILE VAL THR SER SEQRES 23 A 433 ALA ALA ILE GLU GLU ARG ALA HIS GLU LEU GLY TYR LEU SEQRES 24 A 433 PHE TYR THR THR HIS VAL SER ASP PRO LEU PRO ALA ALA SEQRES 25 A 433 VAL GLY LEU ARG VAL LEU ASP VAL VAL GLN ARG ASP GLY SEQRES 26 A 433 LEU VAL ALA ARG ALA ASN VAL MET GLY ASP ARG LEU ARG SEQRES 27 A 433 ARG GLY LEU LEU ASP LEU MET GLU ARG PHE ASP CYS ILE SEQRES 28 A 433 GLY ASP VAL ARG GLY ARG GLY LEU LEU LEU GLY VAL GLU SEQRES 29 A 433 ILE VAL LYS ASP ARG ARG THR LYS GLU PRO ALA ASP GLY SEQRES 30 A 433 LEU GLY ALA LYS ILE THR ARG GLU CYS MET ASN LEU GLY SEQRES 31 A 433 LEU SER MET ASN ILE VAL GLN LEU PRO GLY MET GLY GLY SEQRES 32 A 433 VAL PHE ARG ILE ALA PRO PRO LEU THR VAL SER GLU ASP SEQRES 33 A 433 GLU ILE ASP LEU GLY LEU SER LEU LEU GLY GLN ALA ILE SEQRES 34 A 433 GLU ARG ALA LEU HET NA A 435 1 HET NA A 436 1 HET PLP A 437 15 HET MES A 434 12 HETNAM NA SODIUM ION HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 2 NA 2(NA 1+) FORMUL 4 PLP C8 H10 N O6 P FORMUL 5 MES C6 H13 N O4 S FORMUL 6 HOH *229(H2 O) HELIX 1 1 ALA A 7 HIS A 16 1 10 HELIX 2 2 PRO A 62 ALA A 72 1 11 HELIX 3 3 ARG A 85 ILE A 97 1 13 HELIX 4 4 GLY A 111 THR A 126 1 16 HELIX 5 5 GLY A 143 SER A 147 1 5 HELIX 6 6 TYR A 185 GLN A 199 1 15 HELIX 7 7 TYR A 225 ALA A 235 1 11 HELIX 8 8 ALA A 257 ASP A 261 1 5 HELIX 9 9 ALA A 287 LEU A 296 1 10 HELIX 10 10 PRO A 308 ARG A 323 1 16 HELIX 11 11 LEU A 326 ARG A 347 1 22 HELIX 12 12 LEU A 378 LEU A 389 1 12 HELIX 13 13 GLU A 415 ARG A 431 1 17 SHEET 1 S1 3 GLU A 30 LYS A 33 0 SHEET 2 S1 3 PHE A 36 ASP A 39 -1 SHEET 3 S1 3 ARG A 43 ASP A 47 -1 SHEET 1 S2 7 ARG A 104 SER A 109 0 SHEET 2 S2 7 LEU A 280 THR A 285 -1 SHEET 3 S2 7 ASP A 266 LEU A 270 -1 SHEET 4 S2 7 LEU A 239 GLU A 244 1 SHEET 5 S2 7 LEU A 204 ALA A 209 1 SHEET 6 S2 7 GLU A 130 PHE A 134 1 SHEET 7 S2 7 GLY A 163 ILE A 167 1 SHEET 1 S3 4 CYS A 350 ARG A 357 0 SHEET 2 S3 4 LEU A 360 VAL A 366 -1 SHEET 3 S3 4 GLY A 403 ILE A 407 -1 SHEET 4 S3 4 ASN A 394 VAL A 396 -1 LINK NZ LYS A 272 C4A PLP A 437 1555 1555 1.31 LINK NA NA A 435 O ALA A 95 1555 1555 2.39 LINK NA NA A 435 O PRO A 99 1555 1555 2.45 LINK NA NA A 435 O LEU A 102 1555 1555 2.31 LINK NA NA A 435 O HOH A 526 1555 1555 2.22 LINK NA NA A 435 OG1 THR A 98 1555 1555 2.56 LINK NA NA A 435 O THR A 98 1555 1555 2.53 LINK NA NA A 436 O LEU A 78 1555 1555 2.36 LINK NA NA A 436 O HOH A 519 1555 1555 2.19 LINK NA NA A 436 O HOH A 509 1555 1555 2.23 LINK NA NA A 436 OD1 ASP A 307 1555 1555 2.27 LINK O VAL A 305 NA NA A 436 1555 1555 2.60 SITE 1 PLP 2 LYS A 272 PLP A 437 SITE 1 ME1 4 ALA A 95 THR A 98 PRO A 99 LEU A 102 SITE 1 ME2 3 LEU A 78 VAL A 305 ASP A 307 SITE 1 AC1 5 ALA A 95 THR A 98 PRO A 99 LEU A 102 SITE 2 AC1 5 HOH A 526 SITE 1 AC2 5 LEU A 78 VAL A 305 ASP A 307 HOH A 509 SITE 2 AC2 5 HOH A 519 SITE 1 AC3 19 THR A 110 GLY A 111 ALA A 112 ASN A 115 SITE 2 AC3 19 TRP A 138 HIS A 139 GLU A 210 ASP A 243 SITE 3 AC3 19 ALA A 245 GLN A 246 LYS A 272 THR A 302 SITE 4 AC3 19 THR A 303 MES A 434 HOH A 536 HOH A 544 SITE 5 AC3 19 HOH A 552 HOH A 621 HOH A 625 SITE 1 AC4 8 GLN A 52 TRP A 138 SER A 215 GLN A 246 SITE 2 AC4 8 LYS A 272 ARG A 406 PLP A 437 HOH A 642 CRYST1 152.700 152.700 86.600 90.00 90.00 120.00 P 64 2 2 12 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 0.006549 0.003781 0.000000 0.00000 SCALE2 0.000000 0.007562 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011547 0.00000