PDB Short entry for 2GN1 HEADER LYASE 09-APR-06 2GN1 TITLE CRYSTAL STRUCTURE OF DIMERIC BIODEGRADATIVE THREONINE DEAMINASE (TDCB) TITLE 2 FROM SALMONELLA TYPHIMURIUM AT 2.2A RESOLUTION (TRICLINIC FORM WITH TITLE 3 ONE DIMER OF TDCB IN THE ASYMMETRIC UNIT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: THREONINE DEHYDRATASE CATABOLIC; COMPND 3 CHAIN: A, B; 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 2GN1 1 REMARK REVDAT 5 30-AUG-23 2GN1 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 2GN1 1 VERSN REVDAT 3 24-FEB-09 2GN1 1 VERSN REVDAT 2 23-JAN-07 2GN1 1 JRNL REVDAT 1 07-NOV-06 2GN1 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. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 26557 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) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1405 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1637 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.08 REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE SET COUNT : 79 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4789 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 274 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 31.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.76000 REMARK 3 B22 (A**2) : 2.50000 REMARK 3 B33 (A**2) : -1.87000 REMARK 3 B12 (A**2) : 2.34000 REMARK 3 B13 (A**2) : 0.94000 REMARK 3 B23 (A**2) : 0.92000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.431 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.253 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.185 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.718 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.909 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4857 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 4564 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6575 ; 1.025 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10598 ; 0.741 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 648 ; 5.470 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 180 ;36.666 ;24.722 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 837 ;12.703 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;12.482 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 779 ; 0.056 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5444 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 891 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1143 ; 0.180 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4955 ; 0.157 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2424 ; 0.163 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2884 ; 0.079 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 257 ; 0.145 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.043 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 18 ; 0.175 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 38 ; 0.168 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.088 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 1 ; 0.104 ; 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): 3195 ; 0.312 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1347 ; 0.057 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5127 ; 0.563 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1684 ; 0.885 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1447 ; 1.538 ; 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 : 2 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 -1 A 325 REMARK 3 ORIGIN FOR THE GROUP (A): 0.4177 -0.2097 0.4593 REMARK 3 T TENSOR REMARK 3 T11: -0.1815 T22: -0.1626 REMARK 3 T33: -0.1877 T12: -0.0086 REMARK 3 T13: -0.0295 T23: -0.0234 REMARK 3 L TENSOR REMARK 3 L11: 1.2319 L22: 2.7504 REMARK 3 L33: 3.1334 L12: 0.2534 REMARK 3 L13: -0.9049 L23: -1.1316 REMARK 3 S TENSOR REMARK 3 S11: -0.0617 S12: 0.0611 S13: -0.0893 REMARK 3 S21: -0.1726 S22: 0.1548 S23: 0.0252 REMARK 3 S31: 0.2789 S32: -0.0934 S33: -0.0931 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 5 B 325 REMARK 3 ORIGIN FOR THE GROUP (A): -13.2263 5.8540 32.7834 REMARK 3 T TENSOR REMARK 3 T11: -0.0931 T22: -0.0570 REMARK 3 T33: -0.0855 T12: 0.0193 REMARK 3 T13: 0.0225 T23: 0.0215 REMARK 3 L TENSOR REMARK 3 L11: 1.5448 L22: 1.6241 REMARK 3 L33: 2.6857 L12: -0.7612 REMARK 3 L13: -0.1733 L23: -0.2166 REMARK 3 S TENSOR REMARK 3 S11: 0.0839 S12: 0.0212 S13: 0.2004 REMARK 3 S21: -0.0405 S22: 0.0793 S23: 0.0143 REMARK 3 S31: -0.2448 S32: -0.2145 S33: -0.1632 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 2GN1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000037314. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-DEC-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 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 : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.542 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29556 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 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 (%) : 94.7 REMARK 200 DATA REDUNDANCY : 12.19 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.1800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.22200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.980 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 (%): 40.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CITRATE BUFFER PH 6.0, 20% PEG REMARK 280 3350 AND 10% 2-PROPANOL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 LEU A 326 REMARK 465 VAL A 327 REMARK 465 ASP A 328 REMARK 465 ALA A 329 REMARK 465 MET B -12 REMARK 465 ARG B -11 REMARK 465 GLY B -10 REMARK 465 SER B -9 REMARK 465 HIS B -8 REMARK 465 HIS B -7 REMARK 465 HIS B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 GLY B -2 REMARK 465 MET B -1 REMARK 465 ALA B 0 REMARK 465 SER B 1 REMARK 465 HIS B 2 REMARK 465 ILE B 3 REMARK 465 THR B 4 REMARK 465 LEU B 326 REMARK 465 VAL B 327 REMARK 465 ASP B 328 REMARK 465 ALA B 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 TYR A 5 CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 19 CD CE NZ REMARK 470 LYS A 24 CE NZ REMARK 470 GLU A 38 CD OE1 OE2 REMARK 470 LYS A 107 CG CD CE NZ REMARK 470 LYS A 111 CG CD CE NZ REMARK 470 ASP A 129 CG OD1 OD2 REMARK 470 LYS A 137 CG CD CE NZ REMARK 470 LYS A 204 CE NZ REMARK 470 THR A 324 OG1 CG2 REMARK 470 TYR B 5 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASP B 6 CG OD1 OD2 REMARK 470 GLU B 38 CD OE1 OE2 REMARK 470 LYS B 41 CE NZ REMARK 470 GLU B 71 CG CD OE1 OE2 REMARK 470 ARG B 75 NE CZ NH1 NH2 REMARK 470 LEU B 92 CD1 CD2 REMARK 470 LYS B 107 CG CD CE NZ REMARK 470 LYS B 111 CG CD CE NZ REMARK 470 LYS B 113 CG CD CE NZ REMARK 470 VAL B 114 CG1 CG2 REMARK 470 VAL B 125 CG1 CG2 REMARK 470 ASP B 129 CG OD1 OD2 REMARK 470 LYS B 204 CE NZ REMARK 470 ILE B 274 CG2 CD1 REMARK 470 THR B 324 OG1 CG2 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 THR A 54 -8.26 79.57 REMARK 500 LYS A 107 78.84 -64.98 REMARK 500 TYR A 120 -80.17 -62.10 REMARK 500 SER A 121 -49.86 -163.91 REMARK 500 TYR A 153 -41.18 -155.13 REMARK 500 HIS A 214 65.46 -150.47 REMARK 500 THR A 324 -153.84 -84.97 REMARK 500 LYS B 24 -51.62 -131.20 REMARK 500 MET B 30 58.79 -143.21 REMARK 500 THR B 54 -13.88 80.88 REMARK 500 PRO B 110 124.52 -38.08 REMARK 500 SER B 121 -35.61 112.01 REMARK 500 TYR B 153 -33.98 -155.34 REMARK 500 HIS B 214 66.97 -154.48 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 400 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 220 OH REMARK 620 2 ASP A 256 O 79.4 REMARK 620 3 HOH A 465 O 84.7 92.1 REMARK 620 4 HOH A 466 O 161.1 81.6 96.5 REMARK 620 5 HOH A 550 O 96.6 92.8 175.1 83.9 REMARK 620 6 ARG B 229 O 100.8 175.7 92.1 98.1 83.0 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 400 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2GN0 RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN DIFFRENT CRYSTAL FORM (TRICLINIC FORM WITH TWO REMARK 900 DIMERS OF TDCB IN THE ASYMMETRIC UNIT) AND ONE COMPLETE SUBUNIT REMARK 900 BUILT IN ALTERNATE CONFORMATION. REMARK 900 RELATED ID: 2GN2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TETRAMERIC BIODEGRADATIVE THREONINE DEAMINASE REMARK 900 (TDCB) FROM SALMONELLA TYPHIMURIUM IN COMPLEX WITH CMP AT 2.5A REMARK 900 RESOLUTION (HEXAGONAL FORM) DBREF 2GN1 A 2 329 UNP P11954 THD2_SALTY 2 329 DBREF 2GN1 B 2 329 UNP P11954 THD2_SALTY 2 329 SEQADV 2GN1 MET A -12 UNP P11954 CLONING ARTIFACT SEQADV 2GN1 ARG A -11 UNP P11954 CLONING ARTIFACT SEQADV 2GN1 GLY A -10 UNP P11954 CLONING ARTIFACT SEQADV 2GN1 SER A -9 UNP P11954 CLONING ARTIFACT SEQADV 2GN1 HIS A -8 UNP P11954 EXPRESSION TAG SEQADV 2GN1 HIS A -7 UNP P11954 EXPRESSION TAG SEQADV 2GN1 HIS A -6 UNP P11954 EXPRESSION TAG SEQADV 2GN1 HIS A -5 UNP P11954 EXPRESSION TAG SEQADV 2GN1 HIS A -4 UNP P11954 EXPRESSION TAG SEQADV 2GN1 HIS A -3 UNP P11954 EXPRESSION TAG SEQADV 2GN1 GLY A -2 UNP P11954 CLONING ARTIFACT SEQADV 2GN1 MET A -1 UNP P11954 CLONING ARTIFACT SEQADV 2GN1 ALA A 0 UNP P11954 CLONING ARTIFACT SEQADV 2GN1 SER A 1 UNP P11954 CLONING ARTIFACT SEQADV 2GN1 LLP A 58 UNP P11954 LYS 58 MODIFIED RESIDUE SEQADV 2GN1 MET B -12 UNP P11954 CLONING ARTIFACT SEQADV 2GN1 ARG B -11 UNP P11954 CLONING ARTIFACT SEQADV 2GN1 GLY B -10 UNP P11954 CLONING ARTIFACT SEQADV 2GN1 SER B -9 UNP P11954 CLONING ARTIFACT SEQADV 2GN1 HIS B -8 UNP P11954 EXPRESSION TAG SEQADV 2GN1 HIS B -7 UNP P11954 EXPRESSION TAG SEQADV 2GN1 HIS B -6 UNP P11954 EXPRESSION TAG SEQADV 2GN1 HIS B -5 UNP P11954 EXPRESSION TAG SEQADV 2GN1 HIS B -4 UNP P11954 EXPRESSION TAG SEQADV 2GN1 HIS B -3 UNP P11954 EXPRESSION TAG SEQADV 2GN1 GLY B -2 UNP P11954 CLONING ARTIFACT SEQADV 2GN1 MET B -1 UNP P11954 CLONING ARTIFACT SEQADV 2GN1 ALA B 0 UNP P11954 CLONING ARTIFACT SEQADV 2GN1 SER B 1 UNP P11954 CLONING ARTIFACT SEQADV 2GN1 LLP B 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 SEQRES 1 B 342 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY MET ALA SEQRES 2 B 342 SER HIS ILE THR TYR ASP LEU PRO VAL ALA ILE GLU ASP SEQRES 3 B 342 ILE LEU GLU ALA LYS LYS ARG LEU ALA GLY LYS ILE TYR SEQRES 4 B 342 LYS THR GLY MET PRO ARG SER ASN TYR PHE SER GLU ARG SEQRES 5 B 342 CYS LYS GLY GLU ILE PHE LEU LYS PHE GLU ASN MET GLN SEQRES 6 B 342 ARG THR GLY SER PHE LLP ILE ARG GLY ALA PHE ASN LYS SEQRES 7 B 342 LEU SER SER LEU THR GLU ALA GLU LYS ARG LYS GLY VAL SEQRES 8 B 342 VAL ALA CYS SER ALA GLY ASN HIS ALA GLN GLY VAL SER SEQRES 9 B 342 LEU SER CYS ALA MET LEU GLY ILE ASP GLY LYS VAL VAL SEQRES 10 B 342 MET PRO LYS GLY ALA PRO LYS SER LYS VAL ALA ALA THR SEQRES 11 B 342 CYS ASP TYR SER ALA GLU VAL VAL LEU HIS GLY ASP ASN SEQRES 12 B 342 PHE ASN ASP THR ILE ALA LYS VAL SER GLU ILE VAL GLU SEQRES 13 B 342 THR GLU GLY ARG ILE PHE ILE PRO PRO TYR ASP ASP PRO SEQRES 14 B 342 LYS VAL ILE ALA GLY GLN GLY THR ILE GLY LEU GLU ILE SEQRES 15 B 342 MET GLU ASP LEU TYR ASP VAL ASP ASN VAL ILE VAL PRO SEQRES 16 B 342 ILE GLY GLY GLY GLY LEU ILE ALA GLY ILE ALA ILE ALA SEQRES 17 B 342 ILE LYS SER ILE ASN PRO THR ILE LYS VAL ILE GLY VAL SEQRES 18 B 342 GLN ALA GLU ASN VAL HIS GLY MET ALA ALA SER TYR TYR SEQRES 19 B 342 THR GLY GLU ILE THR THR HIS ARG THR THR GLY THR LEU SEQRES 20 B 342 ALA ASP GLY CYS ASP VAL SER ARG PRO GLY ASN LEU THR SEQRES 21 B 342 TYR GLU ILE VAL ARG GLU LEU VAL ASP ASP ILE VAL LEU SEQRES 22 B 342 VAL SER GLU ASP GLU ILE ARG ASN SER MET ILE ALA LEU SEQRES 23 B 342 ILE GLN ARG ASN LYS VAL ILE THR GLU GLY ALA GLY ALA SEQRES 24 B 342 LEU ALA CYS ALA ALA LEU LEU SER GLY LYS LEU ASP SER SEQRES 25 B 342 HIS ILE GLN ASN ARG LYS THR VAL SER ILE ILE SER GLY SEQRES 26 B 342 GLY ASN ILE ASP LEU SER ARG VAL SER GLN ILE THR GLY SEQRES 27 B 342 LEU VAL ASP ALA MODRES 2GN1 LLP A 58 LYS MODRES 2GN1 LLP B 58 LYS HET LLP A 58 24 HET LLP B 58 24 HET NA A 400 1 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 HETSYN LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE FORMUL 1 LLP 2(C14 H22 N3 O7 P) FORMUL 3 NA NA 1+ FORMUL 4 HOH *274(H2 O) HELIX 1 1 MET A -1 LEU A 7 1 9 HELIX 2 2 ALA A 10 ALA A 22 1 13 HELIX 3 3 SER A 33 LYS A 41 1 9 HELIX 4 4 ASN A 50 SER A 56 5 7 HELIX 5 5 PHE A 57 LEU A 69 1 13 HELIX 6 6 THR A 70 ARG A 75 1 6 HELIX 7 7 GLY A 84 GLY A 98 1 15 HELIX 8 8 PRO A 110 SER A 121 1 12 HELIX 9 9 ASN A 130 GLY A 146 1 17 HELIX 10 10 ASP A 155 LEU A 173 1 19 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 ARG A 276 1 15 HELIX 16 16 GLU A 282 SER A 294 1 13 HELIX 17 17 LEU A 297 GLN A 302 1 6 HELIX 18 18 ASP A 316 THR A 324 1 9 HELIX 19 19 ALA B 10 ALA B 22 1 13 HELIX 20 20 SER B 33 LYS B 41 1 9 HELIX 21 21 ASN B 50 SER B 56 5 7 HELIX 22 22 PHE B 57 LEU B 69 1 13 HELIX 23 23 THR B 70 ARG B 75 1 6 HELIX 24 24 GLY B 84 GLY B 98 1 15 HELIX 25 25 PRO B 110 TYR B 120 1 11 HELIX 26 26 ASN B 130 GLY B 146 1 17 HELIX 27 27 ASP B 155 LEU B 173 1 19 HELIX 28 28 GLY B 186 ASN B 200 1 15 HELIX 29 29 HIS B 214 GLY B 223 1 10 HELIX 30 30 ALA B 235 ASP B 239 5 5 HELIX 31 31 GLY B 244 VAL B 255 1 12 HELIX 32 32 SER B 262 LYS B 278 1 17 HELIX 33 33 GLY B 283 GLY B 285 5 3 HELIX 34 34 ALA B 286 GLY B 295 1 10 HELIX 35 35 LEU B 297 GLN B 302 1 6 HELIX 36 36 ASP B 316 THR B 324 1 9 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 181 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 SHEET 1 C 5 GLU B 43 PHE B 48 0 SHEET 2 C 5 LYS B 305 ILE B 310 1 O THR B 306 N GLU B 43 SHEET 3 C 5 ASN B 178 PRO B 182 1 N ASN B 178 O VAL B 307 SHEET 4 C 5 LYS B 204 ALA B 210 1 O ILE B 206 N VAL B 181 SHEET 5 C 5 ASP B 257 VAL B 261 1 O ASP B 257 N GLY B 207 SHEET 1 D 4 GLU B 123 LEU B 126 0 SHEET 2 D 4 GLY B 101 MET B 105 1 N VAL B 103 O VAL B 125 SHEET 3 D 4 VAL B 78 CYS B 81 1 N ALA B 80 O VAL B 104 SHEET 4 D 4 ILE B 148 PHE B 149 1 O ILE B 148 N VAL B 79 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 C PHE B 57 N LLP B 58 1555 1555 1.33 LINK C LLP B 58 N ILE B 59 1555 1555 1.32 LINK OH TYR A 220 NA NA A 400 1555 1555 2.52 LINK O ASP A 256 NA NA A 400 1555 1555 2.35 LINK NA NA A 400 O HOH A 465 1555 1555 2.40 LINK NA NA A 400 O HOH A 466 1555 1555 2.51 LINK NA NA A 400 O HOH A 550 1555 1555 2.52 LINK NA NA A 400 O ARG B 229 1555 1554 2.31 SITE 1 AC1 6 TYR A 220 ASP A 256 HOH A 465 HOH A 466 SITE 2 AC1 6 HOH A 550 ARG B 229 CRYST1 46.317 55.300 67.235 103.09 94.70 112.94 P 1 2 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 0.021590 0.009140 0.004532 0.00000 SCALE2 0.000000 0.019637 0.005764 0.00000 SCALE3 0.000000 0.000000 0.015553 0.00000