PDB Short entry for 2GN2 HEADER LYASE 09-APR-06 2GN2 TITLE CRYSTAL STRUCTURE OF TETRAMERIC BIODEGRADATIVE THREONINE DEAMINASE TITLE 2 (TDCB) FROM SALMONELLA TYPHIMURIUM IN COMPLEX WITH CMP AT 2.5A TITLE 3 RESOLUTION (HEXAGONAL FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: THREONINE DEHYDRATASE CATABOLIC; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: THREONINE DEAMINASE; COMPND 5 EC: 4.3.1.19; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA TYPHIMURIUM; SOURCE 3 ORGANISM_TAXID: 602; SOURCE 4 STRAIN: IFO 12529; SOURCE 5 GENE: TDCB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PRSET C KEYWDS TDCB, BIODEGRADATIVE THREONINE DEAMINASE, PLP, CMP, THREONINE KEYWDS 2 DEHYDRATASE, L-THREONINE METABOLISM, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR D.K.SIMANSHU,H.S.SAVITHRI,M.R.N.MURTHY REVDAT 6 15-NOV-23 2GN2 1 REMARK REVDAT 5 30-AUG-23 2GN2 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 2GN2 1 VERSN REVDAT 3 24-FEB-09 2GN2 1 VERSN REVDAT 2 23-JAN-07 2GN2 1 JRNL REVDAT 1 07-NOV-06 2GN2 0 JRNL AUTH D.K.SIMANSHU,H.S.SAVITHRI,M.R.MURTHY JRNL TITL CRYSTAL STRUCTURES OF SALMONELLA TYPHIMURIUM BIODEGRADATIVE JRNL TITL 2 THREONINE DEAMINASE AND ITS COMPLEX WITH CMP PROVIDE JRNL TITL 3 STRUCTURAL INSIGHTS INTO LIGAND-INDUCED OLIGOMERIZATION AND JRNL TITL 4 ENZYME ACTIVATION. JRNL REF J.BIOL.CHEM. V. 281 39630 2006 JRNL REFN ISSN 0021-9258 JRNL PMID 17046821 JRNL DOI 10.1074/JBC.M605721200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.K.SIMANSHU,S.CHITTORI,H.S.SAVITHRI,M.R.MURTHY REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY CRYSTALLOGRAPHIC REMARK 1 TITL 2 ANALYSIS OF BIODEGRADATIVE THREONINE DEAMINASE (TDCB) FROM REMARK 1 TITL 3 SALMONELLA TYPHIMURIUM REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 62 275 2006 REMARK 1 REFN ESSN 1744-3091 REMARK 1 PMID 16511321 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0009 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 17629 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 951 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1254 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE SET COUNT : 66 REMARK 3 BIN FREE R VALUE : 0.2410 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2432 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 62 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 66.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.06000 REMARK 3 B22 (A**2) : -1.06000 REMARK 3 B33 (A**2) : 1.59000 REMARK 3 B12 (A**2) : -0.53000 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): 0.289 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.218 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.150 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.455 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2484 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2325 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3362 ; 1.062 ; 1.992 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5411 ; 0.717 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 325 ; 5.360 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 93 ;38.105 ;24.839 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 436 ;14.165 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;18.223 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 398 ; 0.057 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2753 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 452 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 511 ; 0.198 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2317 ; 0.163 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1272 ; 0.168 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1465 ; 0.080 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 80 ; 0.141 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.096 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 13 ; 0.280 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 38 ; 0.126 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.106 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 1 ; 0.064 ; 0.200 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): 1606 ; 0.272 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 677 ; 0.050 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2581 ; 0.530 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 891 ; 0.883 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 781 ; 1.509 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 3 A 328 REMARK 3 ORIGIN FOR THE GROUP (A): -17.6753 -70.1772 -20.1978 REMARK 3 T TENSOR REMARK 3 T11: -0.1911 T22: -0.0229 REMARK 3 T33: -0.1280 T12: 0.1489 REMARK 3 T13: -0.0612 T23: -0.0999 REMARK 3 L TENSOR REMARK 3 L11: 2.9715 L22: 2.0612 REMARK 3 L33: 2.0035 L12: -0.0306 REMARK 3 L13: -0.2122 L23: 0.1766 REMARK 3 S TENSOR REMARK 3 S11: -0.0438 S12: -0.5148 S13: 0.3265 REMARK 3 S21: 0.2732 S22: 0.2005 S23: -0.3553 REMARK 3 S31: -0.1522 S32: 0.1058 S33: -0.1567 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2GN2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000037315. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.93 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : OSMIC MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAC SCIENCE DIP-2030 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18675 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 39.32 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 53.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.38300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.560 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: BIODEGRADATIVE THREONINE DEAMINASE FROM SALMONELLA REMARK 200 TYPHIMURIUM (PDB CODE 1GN0) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CITRATE, 25% PEG4000, 10% REMARK 280 HEXANEDIOL , PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 6 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 REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z REMARK 290 6555 X-Y,X,Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -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 0.00000 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 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 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 0.00000 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 0.00000 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 0.00000 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 0.00000 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 0.00000 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 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE MONOMERIC MOLECULE IS CENTERED AT THE POINT OF 222 REMARK 300 SYMMETRY. THE BIOLOGICAL ASSEMBLY IS A TERAMER GENERATED FROM THE REMARK 300 MONOMER IN THE ASYMMETRIC UNIT BY THE OPERATIONS: -Y,-X,-Z ; -X, -Y, REMARK 300 Z; Y, X, -Z. 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 -1.000000 0.000000 0.000000 -80.57250 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -139.55566 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 0.00000 REMARK 350 BIOMT1 4 0.500000 -0.866025 0.000000 -80.57250 REMARK 350 BIOMT2 4 -0.866025 -0.500000 0.000000 -139.55566 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 NA NA A 401 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 462 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 463 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -12 REMARK 465 ARG A -11 REMARK 465 GLY A -10 REMARK 465 SER A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 GLY A -2 REMARK 465 MET A -1 REMARK 465 ALA A 0 REMARK 465 SER A 1 REMARK 465 HIS A 2 REMARK 465 ALA A 329 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ILE A 3 CG1 CG2 CD1 REMARK 470 TYR A 5 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 111 CE NZ REMARK 470 ILE A 135 CG1 CG2 CD1 REMARK 470 VAL A 327 CG1 CG2 REMARK 470 ASP A 328 CG OD1 OD2 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 LYS A 24 -58.70 -130.36 REMARK 500 THR A 54 -8.19 76.41 REMARK 500 SER A 121 -24.21 106.88 REMARK 500 TYR A 153 -31.06 -151.62 REMARK 500 LEU A 173 84.03 -151.58 REMARK 500 HIS A 214 62.42 -156.83 REMARK 500 ARG A 229 108.57 -160.35 REMARK 500 VAL A 327 74.25 -56.05 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 401 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 171 O REMARK 620 2 GLU A 171 O 175.4 REMARK 620 N 1 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C5P A 400 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2GN0 RELATED DB: PDB REMARK 900 DIMERIC STRUCTURE OF BIODEGRADATIVE THREONINE DEAMINASE (TDCB)AT REMARK 900 1.7A RESOLUTION IN TRICLINIC FORM WITH TWO DIMERS OF TDCB IN THE REMARK 900 ASYMMETRIC UNIT REMARK 900 RELATED ID: 2GN1 RELATED DB: PDB REMARK 900 DIMERIC STRUCTURE OF BIODEGRADATIVE THREONINE DEAMINASE (TDCB) AT REMARK 900 2.2A RESOLUTION IN TRICLINIC FORM WITH ONE DIMER OF TDCB IN THE REMARK 900 ASYMMETRIC UNIT DBREF 2GN2 A 2 329 UNP P11954 THD2_SALTY 2 329 SEQADV 2GN2 MET A -12 UNP P11954 CLONING ARTIFACT SEQADV 2GN2 ARG A -11 UNP P11954 CLONING ARTIFACT SEQADV 2GN2 GLY A -10 UNP P11954 CLONING ARTIFACT SEQADV 2GN2 SER A -9 UNP P11954 CLONING ARTIFACT SEQADV 2GN2 HIS A -8 UNP P11954 EXPRESSION TAG SEQADV 2GN2 HIS A -7 UNP P11954 EXPRESSION TAG SEQADV 2GN2 HIS A -6 UNP P11954 EXPRESSION TAG SEQADV 2GN2 HIS A -5 UNP P11954 EXPRESSION TAG SEQADV 2GN2 HIS A -4 UNP P11954 EXPRESSION TAG SEQADV 2GN2 HIS A -3 UNP P11954 EXPRESSION TAG SEQADV 2GN2 GLY A -2 UNP P11954 CLONING ARTIFACT SEQADV 2GN2 MET A -1 UNP P11954 CLONING ARTIFACT SEQADV 2GN2 ALA A 0 UNP P11954 CLONING ARTIFACT SEQADV 2GN2 SER A 1 UNP P11954 CLONING ARTIFACT SEQADV 2GN2 LLP A 58 UNP P11954 LYS 58 MODIFIED RESIDUE SEQRES 1 A 342 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY MET ALA SEQRES 2 A 342 SER HIS ILE THR TYR ASP LEU PRO VAL ALA ILE GLU ASP SEQRES 3 A 342 ILE LEU GLU ALA LYS LYS ARG LEU ALA GLY LYS ILE TYR SEQRES 4 A 342 LYS THR GLY MET PRO ARG SER ASN TYR PHE SER GLU ARG SEQRES 5 A 342 CYS LYS GLY GLU ILE PHE LEU LYS PHE GLU ASN MET GLN SEQRES 6 A 342 ARG THR GLY SER PHE LLP ILE ARG GLY ALA PHE ASN LYS SEQRES 7 A 342 LEU SER SER LEU THR GLU ALA GLU LYS ARG LYS GLY VAL SEQRES 8 A 342 VAL ALA CYS SER ALA GLY ASN HIS ALA GLN GLY VAL SER SEQRES 9 A 342 LEU SER CYS ALA MET LEU GLY ILE ASP GLY LYS VAL VAL SEQRES 10 A 342 MET PRO LYS GLY ALA PRO LYS SER LYS VAL ALA ALA THR SEQRES 11 A 342 CYS ASP TYR SER ALA GLU VAL VAL LEU HIS GLY ASP ASN SEQRES 12 A 342 PHE ASN ASP THR ILE ALA LYS VAL SER GLU ILE VAL GLU SEQRES 13 A 342 THR GLU GLY ARG ILE PHE ILE PRO PRO TYR ASP ASP PRO SEQRES 14 A 342 LYS VAL ILE ALA GLY GLN GLY THR ILE GLY LEU GLU ILE SEQRES 15 A 342 MET GLU ASP LEU TYR ASP VAL ASP ASN VAL ILE VAL PRO SEQRES 16 A 342 ILE GLY GLY GLY GLY LEU ILE ALA GLY ILE ALA ILE ALA SEQRES 17 A 342 ILE LYS SER ILE ASN PRO THR ILE LYS VAL ILE GLY VAL SEQRES 18 A 342 GLN ALA GLU ASN VAL HIS GLY MET ALA ALA SER TYR TYR SEQRES 19 A 342 THR GLY GLU ILE THR THR HIS ARG THR THR GLY THR LEU SEQRES 20 A 342 ALA ASP GLY CYS ASP VAL SER ARG PRO GLY ASN LEU THR SEQRES 21 A 342 TYR GLU ILE VAL ARG GLU LEU VAL ASP ASP ILE VAL LEU SEQRES 22 A 342 VAL SER GLU ASP GLU ILE ARG ASN SER MET ILE ALA LEU SEQRES 23 A 342 ILE GLN ARG ASN LYS VAL ILE THR GLU GLY ALA GLY ALA SEQRES 24 A 342 LEU ALA CYS ALA ALA LEU LEU SER GLY LYS LEU ASP SER SEQRES 25 A 342 HIS ILE GLN ASN ARG LYS THR VAL SER ILE ILE SER GLY SEQRES 26 A 342 GLY ASN ILE ASP LEU SER ARG VAL SER GLN ILE THR GLY SEQRES 27 A 342 LEU VAL ASP ALA MODRES 2GN2 LLP A 58 LYS HET LLP A 58 24 HET NA A 401 1 HET C5P A 400 21 HETNAM LLP (2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5- HETNAM 2 LLP (PHOSPHONOOXYMETHYL)PYRIDIN-4- HETNAM 3 LLP YL]METHYLIDENEAMINO]HEXANOIC ACID HETNAM NA SODIUM ION HETNAM C5P CYTIDINE-5'-MONOPHOSPHATE HETSYN LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE FORMUL 1 LLP C14 H22 N3 O7 P FORMUL 2 NA NA 1+ FORMUL 3 C5P C9 H14 N3 O8 P FORMUL 4 HOH *62(H2 O) HELIX 1 1 ALA A 10 ALA A 22 1 13 HELIX 2 2 SER A 33 LYS A 41 1 9 HELIX 3 3 ASN A 50 PHE A 57 5 8 HELIX 4 4 LLP A 58 LEU A 69 1 12 HELIX 5 5 THR A 70 LYS A 76 1 7 HELIX 6 6 GLY A 84 GLY A 98 1 15 HELIX 7 7 PRO A 110 TYR A 120 1 11 HELIX 8 8 ASN A 130 GLY A 146 1 17 HELIX 9 9 ASP A 155 GLY A 163 1 9 HELIX 10 10 GLY A 163 LEU A 173 1 11 HELIX 11 11 GLY A 186 ASN A 200 1 15 HELIX 12 12 HIS A 214 GLY A 223 1 10 HELIX 13 13 ALA A 235 ASP A 239 5 5 HELIX 14 14 GLY A 244 VAL A 255 1 12 HELIX 15 15 SER A 262 LYS A 278 1 17 HELIX 16 16 GLY A 283 GLY A 285 5 3 HELIX 17 17 ALA A 286 GLY A 295 1 10 HELIX 18 18 LEU A 297 GLN A 302 1 6 HELIX 19 19 ASP A 316 LEU A 326 1 11 SHEET 1 A 5 GLU A 43 PHE A 48 0 SHEET 2 A 5 LYS A 305 ILE A 310 1 O SER A 308 N PHE A 45 SHEET 3 A 5 ASN A 178 PRO A 182 1 N ILE A 180 O VAL A 307 SHEET 4 A 5 LYS A 204 ALA A 210 1 O ILE A 206 N VAL A 179 SHEET 5 A 5 ASP A 257 VAL A 261 1 O ASP A 257 N GLY A 207 SHEET 1 B 4 GLU A 123 LEU A 126 0 SHEET 2 B 4 GLY A 101 MET A 105 1 N VAL A 103 O GLU A 123 SHEET 3 B 4 VAL A 78 CYS A 81 1 N ALA A 80 O VAL A 104 SHEET 4 B 4 ILE A 148 PHE A 149 1 O ILE A 148 N VAL A 79 SSBOND 1 CYS A 118 CYS A 118 1555 11554 2.86 LINK C PHE A 57 N LLP A 58 1555 1555 1.34 LINK C LLP A 58 N ILE A 59 1555 1555 1.33 LINK O GLU A 171 NA NA A 401 1555 1555 2.31 LINK O GLU A 171 NA NA A 401 4445 1555 2.35 SITE 1 AC1 1 GLU A 171 SITE 1 AC2 16 ASN A 34 ARG A 53 THR A 54 GLY A 55 SITE 2 AC2 16 GLN A 88 ALA A 116 ASP A 119 TYR A 120 SITE 3 AC2 16 GLN A 275 ARG A 276 LYS A 278 ASN A 314 SITE 4 AC2 16 HOH A 412 HOH A 424 HOH A 425 HOH A 441 CRYST1 161.145 161.145 68.723 90.00 90.00 120.00 P 6 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 0.006206 0.003583 0.000000 0.00000 SCALE2 0.000000 0.007166 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014551 0.00000