HEADER ISOMERASE 18-MAR-09 3GO2 TITLE CRYSTAL STRUCTURE OF PUTATIVE L-ALANINE-DL-GLUTAMATE EPIMERASE FROM TITLE 2 BURKHOLDERIA XENOVORANS STRAIN LB400 BOUND TO MAGNESIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE L-ALANINE-DL-GLUTAMATE EPIMERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BURKHOLDERIA XENOVORANS; SOURCE 3 ORGANISM_TAXID: 266265; SOURCE 4 STRAIN: LB400; SOURCE 5 GENE: BXENO_B1104, BXE_B1897; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: MODIFIED PET26 KEYWDS STRUCTURAL GENOMICS, ISOMERASE, PSI-2, PROTEIN STRUCTURE INITIATIVE, KEYWDS 2 NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS, NYSGXRC EXPDTA X-RAY DIFFRACTION AUTHOR J.B.BONANNO,M.DICKEY,K.T.BAIN,S.CHANG,S.OZYURT,S.WASSERMAN, AUTHOR 2 J.M.SAUDER,S.K.BURLEY,S.C.ALMO,NEW YORK SGX RESEARCH CENTER FOR AUTHOR 3 STRUCTURAL GENOMICS (NYSGXRC) REVDAT 6 21-FEB-24 3GO2 1 REMARK REVDAT 5 10-FEB-21 3GO2 1 AUTHOR JRNL REMARK SEQADV REVDAT 5 2 1 LINK REVDAT 4 21-NOV-18 3GO2 1 AUTHOR REVDAT 3 01-NOV-17 3GO2 1 REMARK REVDAT 2 13-JUL-11 3GO2 1 VERSN REVDAT 1 31-MAR-09 3GO2 0 JRNL AUTH J.B.BONANNO,M.DICKEY,K.T.BAIN,S.CHANG,S.OZYURT,S.WASSERMAN, JRNL AUTH 2 J.M.SAUDER,S.K.BURLEY,S.C.ALMO JRNL TITL CRYSTAL STRUCTURE OF PUTATIVE L-ALANINE-DL-GLUTAMATE JRNL TITL 2 EPIMERASE FROM BURKHOLDERIA XENOVORANS STRAIN LB400 BOUND TO JRNL TITL 3 MAGNESIUM. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 44235 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) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.152 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2230 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3020 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.36 REMARK 3 BIN R VALUE (WORKING SET) : 0.1640 REMARK 3 BIN FREE R VALUE SET COUNT : 162 REMARK 3 BIN FREE R VALUE : 0.2020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3069 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 387 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.21000 REMARK 3 B22 (A**2) : -0.21000 REMARK 3 B33 (A**2) : 0.43000 REMARK 3 B12 (A**2) : 0.00000 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): 0.093 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.092 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.052 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.533 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3186 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2144 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4352 ; 1.333 ; 1.941 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5201 ; 0.888 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 395 ; 5.708 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 159 ;36.927 ;23.774 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 487 ;11.387 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;16.815 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 467 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3611 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 677 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1949 ; 0.685 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 781 ; 0.205 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3150 ; 1.243 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1237 ; 2.159 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1198 ; 3.434 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 3GO2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000052101. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-DEC-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97958 REMARK 200 MONOCHROMATOR : DIAMOND REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALA 3.2.25, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44736 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 85.126 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 9.000 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : 0.05800 REMARK 200 FOR THE DATA SET : 26.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.00 REMARK 200 R MERGE FOR SHELL (I) : 0.25100 REMARK 200 R SYM FOR SHELL (I) : 0.25100 REMARK 200 FOR SHELL : 6.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXCD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM SODIUM ACETATE PH 4.8, 2.4M REMARK 280 SODIUM FORMATE, VAPOR DIFFUSION, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 52.34850 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 52.34850 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 72.91400 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 52.34850 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 52.34850 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 72.91400 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 52.34850 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 52.34850 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 72.91400 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 52.34850 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 52.34850 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 72.91400 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 52.34850 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 52.34850 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 72.91400 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 52.34850 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 52.34850 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 72.91400 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 52.34850 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 52.34850 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 72.91400 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 52.34850 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 52.34850 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 72.91400 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: AUTHORS STATE THAT THE ASSEMBLY OF THE BIOLOGICAL UNIT THAT REMARK 300 IS SHOWN IN REMARK 350 IS PUTATIVE. 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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 35790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 85300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -96.6 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 104.69700 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 104.69700 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 104.69700 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 104.69700 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 -1.000000 0.000000 0.000000 104.69700 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 6 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 6 0.000000 -1.000000 0.000000 104.69700 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 7 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 7 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 8 0.000000 -1.000000 0.000000 104.69700 REMARK 350 BIOMT2 8 -1.000000 0.000000 0.000000 104.69700 REMARK 350 BIOMT3 8 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 LYS A 388 REMARK 465 VAL A 389 REMARK 465 MET A 390 REMARK 465 GLY A 391 REMARK 465 GLY A 392 REMARK 465 LEU A 393 REMARK 465 LEU A 394 REMARK 465 GLN A 395 REMARK 465 TYR A 396 REMARK 465 LYS A 397 REMARK 465 ARG A 398 REMARK 465 SER A 399 REMARK 465 GLU A 400 REMARK 465 GLY A 401 REMARK 465 HIS A 402 REMARK 465 HIS A 403 REMARK 465 HIS A 404 REMARK 465 HIS A 405 REMARK 465 HIS A 406 REMARK 465 HIS A 407 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 O HOH A 433 O HOH A 448 1.99 REMARK 500 NE2 GLN A 361 O HOH A 751 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 498 O HOH A 767 4565 2.09 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 ASN A 163 -155.14 -124.84 REMARK 500 GLN A 184 76.51 -152.80 REMARK 500 ASN A 219 -131.24 47.55 REMARK 500 CYS A 266 3.43 97.74 REMARK 500 PHE A 318 33.90 -147.91 REMARK 500 TYR A 319 -142.18 -119.95 REMARK 500 ILE A 339 165.27 178.92 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 MG A 408 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 217 OD2 REMARK 620 2 HOH A 410 O 85.5 REMARK 620 3 HOH A 431 O 96.1 105.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 409 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 247 OH REMARK 620 2 THR A 268 O 132.4 REMARK 620 3 HOH A 414 O 114.0 113.5 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 409 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2OO6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PUTATIVE L-ALANINE-DL-GLUTAMATE EPIMERASE FROM REMARK 900 BURKHOLDERIA XENOVORANS STRAIN LB400, APO-FORM REMARK 900 RELATED ID: NYSGXRC-9228C RELATED DB: TARGETDB DBREF 3GO2 A 2 399 UNP Q13PB7 Q13PB7_BURXL 2 399 SEQADV 3GO2 MET A -1 UNP Q13PB7 EXPRESSION TAG SEQADV 3GO2 SER A 0 UNP Q13PB7 EXPRESSION TAG SEQADV 3GO2 LEU A 1 UNP Q13PB7 EXPRESSION TAG SEQADV 3GO2 GLU A 400 UNP Q13PB7 EXPRESSION TAG SEQADV 3GO2 GLY A 401 UNP Q13PB7 EXPRESSION TAG SEQADV 3GO2 HIS A 402 UNP Q13PB7 EXPRESSION TAG SEQADV 3GO2 HIS A 403 UNP Q13PB7 EXPRESSION TAG SEQADV 3GO2 HIS A 404 UNP Q13PB7 EXPRESSION TAG SEQADV 3GO2 HIS A 405 UNP Q13PB7 EXPRESSION TAG SEQADV 3GO2 HIS A 406 UNP Q13PB7 EXPRESSION TAG SEQADV 3GO2 HIS A 407 UNP Q13PB7 EXPRESSION TAG SEQRES 1 A 409 MET SER LEU LYS VAL VAL SER VAL ASP THR LEU CYS CYS SEQRES 2 A 409 ASP ALA GLY TRP ARG ASN TYR HIS PHE VAL LYS LEU THR SEQRES 3 A 409 THR ASP GLU GLY ILE VAL GLY TRP SER GLU PHE ASP GLU SEQRES 4 A 409 GLY PHE GLY SER PRO GLY VAL THR ALA VAL ILE GLU GLN SEQRES 5 A 409 LEU GLY LYS ARG LEU VAL GLY ALA SER VAL MET GLU HIS SEQRES 6 A 409 GLU ARG PHE PHE ALA GLU ALA TYR CYS LEU THR ARG PRO SEQRES 7 A 409 ALA THR GLY GLY VAL VAL SER GLU GLY ILE GLY ALA ILE SEQRES 8 A 409 GLU ASN ALA LEU LEU ASP ALA LYS ALA LYS THR LEU ASN SEQRES 9 A 409 VAL PRO CYS TYR GLU LEU LEU GLY GLY LYS LEU ARG ASP SEQRES 10 A 409 ARG VAL PRO VAL TYR TRP SER HIS CYS PRO THR TRP ARG SEQRES 11 A 409 ILE ASN HIS PRO LYS PHE PHE GLY PRO PRO VAL THR ASP SEQRES 12 A 409 LEU ASP GLY VAL LYS ARG THR ALA GLU GLU ALA ARG GLU SEQRES 13 A 409 ARG GLN PHE ARG ALA ILE LYS THR ASN ILE PHE ILE HIS SEQRES 14 A 409 ASP ASP GLY PRO LEU HIS ALA TRP ARG PRO GLY PHE ALA SEQRES 15 A 409 VAL PRO PHE GLN PRO ALA LEU ASN VAL ASP ARG LYS VAL SEQRES 16 A 409 LEU ARG ASN LEU ARG ALA HIS LEU GLU ALA LEU ARG ASP SEQRES 17 A 409 GLY ALA GLY PRO ASP VAL GLU ILE LEU LEU ASP LEU ASN SEQRES 18 A 409 PHE ASN ALA LYS PRO GLU GLY TYR LEU LYS ILE LEU ARG SEQRES 19 A 409 GLU LEU ALA ASP PHE ASP LEU PHE TRP VAL GLU ILE ASP SEQRES 20 A 409 SER TYR SER PRO GLN GLY LEU ALA TYR VAL ARG ASN HIS SEQRES 21 A 409 SER PRO HIS PRO ILE SER SER CYS GLU THR LEU PHE GLY SEQRES 22 A 409 ILE ARG GLU PHE LYS PRO PHE PHE ASP ALA ASN ALA VAL SEQRES 23 A 409 ASP VAL ALA ILE VAL ASP THR ILE TRP ASN GLY VAL TRP SEQRES 24 A 409 GLN SER MET LYS ILE ALA ALA PHE ALA ASP ALA HIS ASP SEQRES 25 A 409 ILE ASN VAL ALA PRO HIS ASN PHE TYR GLY HIS LEU CYS SEQRES 26 A 409 THR MET ILE ASN ALA ASN PHE ALA ALA ALA VAL PRO ASN SEQRES 27 A 409 LEU ARG ILE MET GLU THR ASP ILE ASP ARG LEU ALA TRP SEQRES 28 A 409 GLU ASP GLU LEU PHE THR HIS ALA PRO GLU TYR GLN ASN SEQRES 29 A 409 GLY GLU LEU ILE ILE PRO ASP ARG PRO GLY TRP GLY THR SEQRES 30 A 409 ASP PRO VAL GLU GLU ALA ILE LEU ALA HIS PRO PRO LYS SEQRES 31 A 409 VAL MET GLY GLY LEU LEU GLN TYR LYS ARG SER GLU GLY SEQRES 32 A 409 HIS HIS HIS HIS HIS HIS HET MG A 408 1 HET MG A 409 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG 2(MG 2+) FORMUL 4 HOH *387(H2 O) HELIX 1 1 GLY A 43 VAL A 56 1 14 HELIX 2 2 GLU A 62 ARG A 75 1 14 HELIX 3 3 PRO A 76 THR A 78 5 3 HELIX 4 4 GLY A 79 ASN A 102 1 24 HELIX 5 5 PRO A 104 LEU A 109 5 6 HELIX 6 6 PRO A 125 HIS A 131 1 7 HELIX 7 7 ASP A 141 ARG A 155 1 15 HELIX 8 8 ARG A 176 ALA A 180 5 5 HELIX 9 9 ASP A 190 GLY A 209 1 20 HELIX 10 10 LYS A 223 LEU A 234 1 12 HELIX 11 11 SER A 248 HIS A 258 1 11 HELIX 12 12 PHE A 270 ALA A 281 1 12 HELIX 13 13 ASP A 290 GLY A 295 1 6 HELIX 14 14 GLY A 295 HIS A 309 1 15 HELIX 15 15 GLY A 320 VAL A 334 1 15 HELIX 16 16 TRP A 349 PHE A 354 1 6 HELIX 17 17 VAL A 378 HIS A 385 1 8 SHEET 1 A 3 VAL A 3 ASP A 12 0 SHEET 2 A 3 ASN A 17 THR A 25 -1 O THR A 24 N VAL A 4 SHEET 3 A 3 VAL A 30 PHE A 35 -1 O GLY A 31 N LEU A 23 SHEET 1 B 4 MET A 340 THR A 342 0 SHEET 2 B 4 ARG A 116 TRP A 121 1 N TYR A 120 O MET A 340 SHEET 3 B 4 GLU A 364 ILE A 366 -1 O LEU A 365 N VAL A 117 SHEET 4 B 4 TYR A 360 GLN A 361 -1 N GLN A 361 O GLU A 364 SHEET 1 C 6 ALA A 159 THR A 162 0 SHEET 2 C 6 GLU A 213 ASP A 217 1 O LEU A 215 N ILE A 160 SHEET 3 C 6 TRP A 241 GLU A 243 1 O GLU A 243 N LEU A 216 SHEET 4 C 6 ILE A 263 SER A 265 1 O SER A 264 N VAL A 242 SHEET 5 C 6 VAL A 286 VAL A 289 1 O ILE A 288 N SER A 265 SHEET 6 C 6 ASN A 312 PRO A 315 1 O ALA A 314 N VAL A 289 SHEET 1 D 2 PHE A 165 ILE A 166 0 SHEET 2 D 2 HIS A 173 ALA A 174 -1 O HIS A 173 N ILE A 166 LINK OD2 ASP A 217 MG MG A 408 1555 1555 2.30 LINK OH TYR A 247 MG MG A 409 1555 1555 2.46 LINK O THR A 268 MG MG A 409 1555 1555 2.36 LINK MG MG A 408 O HOH A 410 1555 1555 2.38 LINK MG MG A 408 O HOH A 431 1555 1555 1.79 LINK MG MG A 409 O HOH A 414 1555 1555 2.37 CISPEP 1 CYS A 124 PRO A 125 0 12.30 CISPEP 2 GLY A 136 PRO A 137 0 0.20 CISPEP 3 VAL A 181 PRO A 182 0 1.79 SITE 1 AC1 7 LYS A 161 ASP A 217 GLU A 243 GLU A 267 SITE 2 AC1 7 HOH A 410 HOH A 413 HOH A 431 SITE 1 AC2 5 PRO A 76 TYR A 247 THR A 268 HOH A 414 SITE 2 AC2 5 HOH A 415 CRYST1 104.697 104.697 145.828 90.00 90.00 90.00 I 4 2 2 16 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 0.009551 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009551 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006857 0.00000