HEADER LYASE(DECARBOXYLASE) 18-JUN-93 1DKA
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 1DKA 1 HELIX
REVDAT 4 13-JUL-11 1DKA 1 VERSN
REVDAT 3 24-FEB-09 1DKA 1 VERSN
REVDAT 2 01-APR-03 1DKA 1 JRNL
REVDAT 1 15-OCT-94 1DKA 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.E.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. 2.60 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) : 2.60
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) : 0.176
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 : 145
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) : 0.013 ; NULL ; NULL
REMARK 3 BOND ANGLES (DEGREES) : 2.500 ; 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: NULL
REMARK 4
REMARK 4 1DKA 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_1000172820.
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
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: DIALKYLGLYCINE DECARBOXYLASE IS A TETRAMER OF IDENTICAL
REMARK 300 SUBUNITS. THE FOLLOWING TRANSFORMATIONS WILL GENERATE THE
REMARK 300 OTHER THREE SUBUNITS OF THE TETRAMER WHEN APPLIED TO THE
REMARK 300 COORDINATES PRESENTED IN THIS ENTRY:
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: TETRAMERIC
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 BIOMT1 3 0.500000 -0.866025 0.000000 76.35000
REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 132.24208
REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 28.86667
REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 76.35000
REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 132.24208
REMARK 350 BIOMT3 4 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 SER A 2
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 NH2 ARG A 176 O HOH A 594 2.19
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 GLY A 51 C GLN A 52 N 0.220
REMARK 500 GLN A 52 C MET A 53 N 0.177
REMARK 500 GLU A 70 CD GLU A 70 OE2 0.069
REMARK 500 GLU A 178 CD GLU A 178 OE2 0.070
REMARK 500 GLU A 220 CD GLU A 220 OE1 0.081
REMARK 500 GLU A 234 CD GLU A 234 OE1 0.068
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. = -6.6 DEGREES
REMARK 500 ASP A 6 CB - CG - OD1 ANGL. DEV. = 7.8 DEGREES
REMARK 500 ASP A 6 CB - CG - OD2 ANGL. DEV. = -7.4 DEGREES
REMARK 500 ARG A 11 CD - NE - CZ ANGL. DEV. = 8.9 DEGREES
REMARK 500 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 GLY A 101 C - N - CA ANGL. DEV. = -15.6 DEGREES
REMARK 500 ASP A 190 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES
REMARK 500 ASP A 190 CB - CG - OD2 ANGL. DEV. = -7.6 DEGREES
REMARK 500 ASP A 197 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES
REMARK 500 ASP A 197 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES
REMARK 500 ASP A 223 CB - CG - OD1 ANGL. DEV. = -5.6 DEGREES
REMARK 500 ASP A 261 CB - CG - OD1 ANGL. DEV. = -5.6 DEGREES
REMARK 500 ASP A 266 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES
REMARK 500 ASP A 266 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES
REMARK 500 SER A 271 N - CA - CB ANGL. DEV. = -10.6 DEGREES
REMARK 500 ASP A 307 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES
REMARK 500 ASP A 307 CB - CG - OD2 ANGL. DEV. = -7.8 DEGREES
REMARK 500 ASP A 319 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES
REMARK 500 ARG A 323 N - CA - CB ANGL. DEV. = 11.8 DEGREES
REMARK 500 ASP A 343 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES
REMARK 500 ASP A 343 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES
REMARK 500 ASP A 349 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES
REMARK 500 ASP A 349 CB - CG - OD2 ANGL. DEV. = -6.5 DEGREES
REMARK 500 ASP A 353 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES
REMARK 500 ASP A 368 CB - CG - OD1 ANGL. DEV. = -5.7 DEGREES
REMARK 500 ASP A 368 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES
REMARK 500 VAL A 413 CB - CA - C ANGL. DEV. = -11.6 DEGREES
REMARK 500 ASP A 416 CB - CG - OD1 ANGL. DEV. = -5.7 DEGREES
REMARK 500 ASP A 416 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES
REMARK 500 ASP A 419 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES
REMARK 500 ASP A 419 CB - CG - OD2 ANGL. DEV. = -5.5 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 6 101.80 -45.56
REMARK 500 PRO A 26 46.16 -88.61
REMARK 500 ALA A 55 64.12 -62.16
REMARK 500 ASP A 76 -72.77 -109.92
REMARK 500 LEU A 108 -156.69 -128.00
REMARK 500 ASN A 180 78.62 38.72
REMARK 500 GLU A 244 40.60 -93.63
REMARK 500 SER A 271 -100.57 -157.05
REMARK 500 PHE A 300 70.50 -154.78
REMARK 500 ASP A 324 0.63 -66.36
REMARK 500 LEU A 359 34.54 -94.03
REMARK 500 ASP A 376 92.04 -51.74
REMARK 500 ALA A 408 80.35 -150.16
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 NA A 435 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ALA A 95 O
REMARK 620 2 HOH A 573 O 97.1
REMARK 620 3 PRO A 99 O 164.9 95.7
REMARK 620 4 THR A 98 O 89.5 125.0 76.6
REMARK 620 5 THR A 98 OG1 74.9 160.8 95.1 73.1
REMARK 620 6 LEU A 102 O 94.1 83.7 95.2 150.5 79.6
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 K A 436 K
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A 530 O
REMARK 620 2 LEU A 78 O 72.1
REMARK 620 3 SER A 80 OG 106.4 101.7
REMARK 620 4 THR A 303 O 178.1 106.6 75.1
REMARK 620 5 ASP A 307 OD1 83.3 82.0 170.3 95.3
REMARK 620 6 VAL A 305 O 78.1 150.2 87.1 103.2 94.1
REMARK 620 N 1 2 3 4 5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: ME1
REMARK 800 EVIDENCE_CODE: AUTHOR
REMARK 800 SITE_DESCRIPTION: METAL BINDING SITE 1. LIGANDS TO THE SODIUM ION
REMARK 800 NA+ 435 ARE INDICATED
REMARK 800
REMARK 800 SITE_IDENTIFIER: ME2
REMARK 800 EVIDENCE_CODE: AUTHOR
REMARK 800 SITE_DESCRIPTION: METAL BINDING SITE 2. LIGANDS TO THE POTASSIUM
REMARK 800 ION 436 ARE INDICATED
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 K 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 NUMBER IS THAT FROM SWISS-PROT ENTRY
REMARK 999 CYS 308
REMARK 999
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 (REFERENCE 1) HAS BEEN
REMARK 999 CORRECTED (J.W. KELLER, PRIVATE COMMUNICATION). THE
REMARK 999 SEQUENCE PRESENTED IN THIS ENTRY IS THE CORRECTED SEQUENCE.
REMARK 999
REMARK 999 THE FIRST TWO RESIDUES ARE NOT INCLUDED IN THE MODEL SINCE
REMARK 999 THEY ARE DISORDERED.
DBREF 1DKA A 2 433 UNP P16932 DGDA_BURCE 1 432
SEQADV 1DKA HIS A 15 UNP P16932 GLN 14 CONFLICT
SEQADV 1DKA 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 K A 436 1
HET PLP A 437 15
HET MES A 434 12
HETNAM NA SODIUM ION
HETNAM K POTASSIUM ION
HETNAM PLP PYRIDOXAL-5'-PHOSPHATE
HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
HETSYN PLP VITAMIN B6 PHOSPHATE
FORMUL 2 NA NA 1+
FORMUL 3 K K 1+
FORMUL 4 PLP C8 H10 N O6 P
FORMUL 5 MES C6 H13 N O4 S
FORMUL 6 HOH *145(H2 O)
HELIX 1 H1 ALA A 7 HIS A 16 1 10
HELIX 2 H2 PRO A 62 ALA A 72 1 11
HELIX 3 H3 ARG A 85 ILE A 97 1 13
HELIX 4 H4 GLY A 111 THR A 126 1 16
HELIX 5 H5 GLY A 143 SER A 147 1 5
HELIX 6 H6 TYR A 185 GLN A 199 1 15
HELIX 7 H7 TYR A 225 ALA A 235 1 11
HELIX 8 H8 ALA A 257 ASP A 261 1 5
HELIX 9 H9 ALA A 287 LEU A 296 1 10
HELIX 10 H10 PRO A 308 ARG A 323 1 16
HELIX 11 H11 LEU A 326 ARG A 347 1 22
HELIX 12 H12 LEU A 378 LEU A 389 1 12
HELIX 13 H13 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 1.33
LINK NA NA A 435 O ALA A 95 1555 1555 2.33
LINK NA NA A 435 O HOH A 573 1555 1555 2.20
LINK NA NA A 435 O PRO A 99 1555 1555 2.10
LINK NA NA A 435 O THR A 98 1555 1555 2.42
LINK K K A 436 O HOH A 530 1555 1555 2.74
LINK K K A 436 O LEU A 78 1555 1555 2.70
LINK K K A 436 OG SER A 80 1555 1555 2.84
LINK K K A 436 O THR A 303 1555 1555 2.75
LINK K K A 436 OD1 ASP A 307 1555 1555 2.47
LINK K K A 436 O VAL A 305 1555 1555 2.87
LINK OG1 THR A 98 NA NA A 435 1555 1555 2.65
LINK O LEU A 102 NA NA A 435 1555 1555 2.62
SITE 1 ME1 4 ALA A 95 THR A 98 PRO A 99 LEU A 102
SITE 1 ME2 5 LEU A 78 SER A 80 THR A 303 VAL A 305
SITE 2 ME2 5 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 573
SITE 1 AC2 6 LEU A 78 SER A 80 THR A 303 VAL A 305
SITE 2 AC2 6 ASP A 307 HOH A 530
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 502 HOH A 512
SITE 5 AC3 19 HOH A 518 HOH A 540 HOH A 550
SITE 1 AC4 8 GLN A 52 TRP A 138 SER A 215 GLN A 246
SITE 2 AC4 8 LYS A 272 TYR A 301 ARG A 406 PLP A 437
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
(ATOM LINES ARE NOT SHOWN.)
END
