10 20 30 40 50 60 70 80 1D7V - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER LYASE 19-OCT-99 1D7V
TITLE CRYSTAL STRUCTURE OF THE COMPLEX OF 2,2-DIALKYLGLYCINE DECARBOXYLASE TITLE 2 WITH NMA
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE)); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DGD; COMPND 5 EC: 4.1.1.64; COMPND 6 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; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: TY103; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PKDHE19
KEYWDS ENZYME COMPLEXES, CATALYTIC MECHANISM, DECARBOXYLATION INHIBITOR, KEYWDS 2 LYASE
EXPDTA X-RAY DIFFRACTION
AUTHOR V.N.MALASHKEVICH,M.D.TONEY,P.STROP,J.KELLER,J.N.JANSONIUS
REVDAT 5 13-JUL-11 1D7V 1 VERSN REVDAT 4 22-DEC-10 1D7V 1 REMARK REVDAT 3 24-FEB-09 1D7V 1 VERSN REVDAT 2 01-APR-03 1D7V 1 JRNL REVDAT 1 19-NOV-99 1D7V 0
JRNL AUTH V.N.MALASHKEVICH,P.STROP,J.W.KELLER,J.N.JANSONIUS,M.D.TONEY JRNL TITL CRYSTAL STRUCTURES OF DIALKYLGLYCINE DECARBOXYLASE INHIBITOR JRNL TITL 2 COMPLEXES. JRNL REF J.MOL.BIOL. V. 294 193 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10556038 JRNL DOI 10.1006/JMBI.1999.3254
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. 2.80 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 14654 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : 96.000 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 : 3246 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 36 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : 37.240 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.012 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 1.620 ; 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 : FLAT MODEL REMARK 3 KSOL : 0.67 REMARK 3 BSOL : 164.50 REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : RESTRAINED REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1D7V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-NOV-99. REMARK 100 THE RCSB ID CODE IS RCSB009873.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAY-94 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : ELLIOTT GX-20 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.542 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (AGROVATA, ROTAVATA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14654 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 2DKB REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.50, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K
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 28.96667 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 57.93333 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 28.96667 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 57.93333 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 28.96667 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 57.93333 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 28.96667 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 57.93333 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA.
REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 28560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 51560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -166.0 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 76.60000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 132.67509 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 28.96667 REMARK 350 BIOMT1 4 0.500000 -0.866025 0.000000 76.60000 REMARK 350 BIOMT2 4 -0.866025 -0.500000 0.000000 132.67509 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 28.96667
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: 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 PRO A 62 C - N - CD ANGL. DEV. = -22.6 DEGREES REMARK 500 PRO A 409 C - N - CD ANGL. DEV. = -18.6 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 6 100.69 -35.02 REMARK 500 PHE A 9 -72.49 -53.22 REMARK 500 PRO A 26 40.51 -68.71 REMARK 500 GLN A 52 53.75 -99.75 REMARK 500 ALA A 55 68.77 -55.78 REMARK 500 CYS A 60 61.00 65.62 REMARK 500 PRO A 62 -44.34 -18.23 REMARK 500 LYS A 74 -51.78 -120.28 REMARK 500 ASP A 76 -80.62 -110.48 REMARK 500 SER A 80 -7.39 -53.47 REMARK 500 PRO A 99 172.10 -52.59 REMARK 500 LEU A 108 -150.44 -117.05 REMARK 500 TYR A 129 -6.11 -144.08 REMARK 500 ASP A 184 78.60 -112.86 REMARK 500 LEU A 213 91.56 -65.88 REMARK 500 GLU A 244 40.48 -103.44 REMARK 500 SER A 271 -103.84 -168.69 REMARK 500 LYS A 272 -71.28 -17.75 REMARK 500 ALA A 408 92.64 -162.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 TRP A 10 23.9 L L OUTSIDE RANGE REMARK 500 HIS A 16 24.6 L L OUTSIDE RANGE REMARK 500 SER A 80 24.1 L L OUTSIDE RANGE REMARK 500 ARG A 85 24.6 L L OUTSIDE RANGE REMARK 500 GLU A 178 22.7 L L OUTSIDE RANGE REMARK 500 VAL A 249 20.8 L L OUTSIDE RANGE REMARK 500 ARG A 251 24.0 L L OUTSIDE RANGE REMARK 500 HIS A 304 22.9 L L OUTSIDE RANGE REMARK 500 SER A 306 24.8 L L OUTSIDE RANGE REMARK 500 VAL A 320 22.2 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 565 DISTANCE = 16.82 ANGSTROMS
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 155.5 REMARK 620 3 THR A 98 O 94.2 63.2 REMARK 620 4 LEU A 102 O 89.7 99.7 134.9 REMARK 620 5 THR A 98 OG1 76.5 83.8 61.6 75.9 REMARK 620 N 1 2 3 4 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 LEU A 78 O REMARK 620 2 ASP A 307 OD1 87.0 REMARK 620 3 SER A 80 N 57.0 142.1 REMARK 620 4 SER A 80 OG 111.6 161.3 56.0 REMARK 620 5 THR A 303 O 111.7 89.4 113.5 83.5 REMARK 620 6 VAL A 305 O 151.0 93.2 112.2 70.8 97.3 REMARK 620 N 1 2 3 4 5
REMARK 800 REMARK 800 SITE 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 NMA A 500
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1D7U RELATED DB: PDB REMARK 900 RELATED ID: 1D7R RELATED DB: PDB REMARK 900 RELATED ID: 1D7S RELATED DB: PDB
DBREF 1D7V A 1 433 UNP P16932 DGDA_BURCE 1 433
SEQRES 1 A 433 MET SER LEU ASN ASP ASP ALA THR PHE TRP ARG ASN ALA SEQRES 2 A 433 ARG GLN 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 GLY 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 NMA A 500 22
HETNAM NA SODIUM ION HETNAM K POTASSIUM ION HETNAM NMA N-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4- HETNAM 2 NMA YLMETHYL]-2-METHYLALANINE
HETSYN NMA N-PYRIDOXYL-2-METHYLALANINE-5-PHOSPHATE
FORMUL 2 NA NA 1+ FORMUL 3 K K 1+ FORMUL 4 NMA C12 H19 N2 O7 P FORMUL 5 HOH *36(H2 O)
HELIX 1 1 ASP A 6 LEU A 17 1 12 HELIX 2 2 THR A 49 SER A 54 1 6 HELIX 3 3 HIS A 61 GLY A 73 1 13 HELIX 4 4 SER A 84 THR A 98 1 15 HELIX 5 5 THR A 110 GLY A 127 1 18 HELIX 6 6 THR A 142 ALA A 148 1 7 HELIX 7 7 ASP A 184 SER A 200 1 17 HELIX 8 8 GLY A 224 ALA A 235 1 12 HELIX 9 9 PHE A 256 GLY A 262 1 7 HELIX 10 10 SER A 271 ALA A 276 1 6 HELIX 11 11 SER A 286 LEU A 296 1 11 HELIX 12 12 ASP A 307 ASP A 324 1 18 HELIX 13 13 GLY A 325 PHE A 348 1 24 HELIX 14 14 GLY A 377 GLY A 390 1 14 HELIX 15 15 SER A 414 LEU A 433 1 20
SHEET 1 A 4 ILE A 29 LYS A 33 0 SHEET 2 A 4 PHE A 36 ASP A 39 -1 O PHE A 36 N LYS A 33 SHEET 3 A 4 ALA A 44 ASP A 47 -1 N ILE A 45 O VAL A 37 SHEET 4 A 4 LEU A 391 SER A 392 1 N SER A 392 O LEU A 46 SHEET 1 B 7 ARG A 104 LEU A 108 0 SHEET 2 B 7 ALA A 281 THR A 285 -1 O ALA A 281 N LEU A 108 SHEET 3 B 7 ILE A 267 LEU A 270 -1 N LEU A 268 O VAL A 284 SHEET 4 B 7 LEU A 239 ASP A 243 1 O LEU A 240 N ILE A 267 SHEET 5 B 7 LEU A 204 ALA A 209 1 O ALA A 205 N LEU A 239 SHEET 6 B 7 GLU A 130 PHE A 134 1 O GLU A 130 N ALA A 205 SHEET 7 B 7 SER A 164 ILE A 167 1 N PHE A 165 O ILE A 131 SHEET 1 C 2 GLU A 178 ARG A 179 0 SHEET 2 C 2 ALA A 182 TYR A 183 -1 O ALA A 182 N ARG A 179 SHEET 1 D 2 ILE A 212 LEU A 213 0 SHEET 2 D 2 ILE A 219 GLU A 220 -1 O ILE A 219 N LEU A 213 SHEET 1 E 4 ILE A 351 ARG A 357 0 SHEET 2 E 4 LEU A 360 ILE A 365 -1 O LEU A 360 N ARG A 357 SHEET 3 E 4 GLY A 403 ILE A 407 -1 O GLY A 403 N ILE A 365 SHEET 4 E 4 ILE A 395 VAL A 396 -1 O VAL A 396 N VAL A 404
LINK NA NA A 435 O ALA A 95 1555 1555 2.55 LINK NA NA A 435 O PRO A 99 1555 1555 2.30 LINK K K A 436 O LEU A 78 1555 1555 2.48 LINK K K A 436 OD1 ASP A 307 1555 1555 2.53 LINK K K A 436 N SER A 80 1555 1555 3.71 LINK K K A 436 OG SER A 80 1555 1555 2.80 LINK K K A 436 O THR A 303 1555 1555 2.76 LINK K K A 436 O VAL A 305 1555 1555 2.74 LINK O THR A 98 NA NA A 435 1555 1555 2.68 LINK O LEU A 102 NA NA A 435 1555 1555 2.69 LINK OG1 THR A 98 NA NA A 435 1555 1555 3.05
SITE 1 AC1 4 ALA A 95 THR A 98 PRO A 99 LEU A 102 SITE 1 AC2 5 LEU A 78 SER A 80 THR A 303 VAL A 305 SITE 2 AC2 5 ASP A 307 SITE 1 AC3 13 GLN A 52 GLY A 111 ALA A 112 TRP A 138 SITE 2 AC3 13 HIS A 139 GLU A 210 SER A 215 ASP A 243 SITE 3 AC3 13 GLN A 246 LYS A 272 THR A 302 THR A 303 SITE 4 AC3 13 ARG A 406
CRYST1 153.200 153.200 86.900 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 0.006527 0.003768 0.000000 0.00000
SCALE2 0.000000 0.007537 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011507 0.00000