HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 16-MAR-06 2GDQ TITLE CRYSTAL STRUCTURE OF MANDELATE RACEMASE/MUCONATE LACTONIZING ENZYME TITLE 2 FROM BACILLUS SUBTILIS AT 1.8 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: YITF; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: MANDELATE RACEMASE/MUCONATE LACTONIZING ENZYME; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS SUBSP. SUBTILIS; SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: YITF; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MANDELATE RACEMASE/MUCONATE LACTONIZING ENZYME, TIM-BARREL, ENOLASE, KEYWDS 2 OCTAMER, STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE INITIATIVE, NEW KEYWDS 3 YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS, NYSGXRC, UNKNOWN KEYWDS 4 FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR V.N.MALASHKEVICH,R.TORO,J.M.SAUDER,K.D.SCHWINN,S.EMTAGE,D.A.THOMPSON, AUTHOR 2 M.E.RUTTER,M.DICKEY,C.GROSHONG,K.T.BAIN,J.M.ADAMS,C.REYES,I.ROONEY, AUTHOR 3 A.POWELL,A.BOICE,T.GHEYI,S.OZYURT,S.ATWELL,S.R.WASSERMAN,S.K.BURLEY, AUTHOR 4 A.SALI,P.BABBITT,U.PIEPER,J.A.GERLT,S.C.ALMO,NEW YORK SGX RESEARCH AUTHOR 5 CENTER FOR STRUCTURAL GENOMICS (NYSGXRC) REVDAT 7 30-AUG-23 2GDQ 1 REMARK REVDAT 6 03-FEB-21 2GDQ 1 AUTHOR JRNL SEQADV REVDAT 5 14-NOV-18 2GDQ 1 AUTHOR REVDAT 4 18-OCT-17 2GDQ 1 REMARK REVDAT 3 13-JUL-11 2GDQ 1 VERSN REVDAT 2 24-FEB-09 2GDQ 1 VERSN REVDAT 1 04-APR-06 2GDQ 0 JRNL AUTH V.N.MALASHKEVICH,R.TORO,J.M.SAUDER,K.D.SCHWINN,S.EMTAGE, JRNL AUTH 2 D.A.THOMPSON,M.E.RUTTER,M.DICKEY,C.GROSHONG,K.T.BAIN, JRNL AUTH 3 J.M.ADAMS,C.REYES,I.ROONEY,A.POWELL,A.BOICE,T.GHEYI, JRNL AUTH 4 S.OZYURT,S.ATWELL,S.R.WASSERMAN,S.K.BURLEY,A.SALI,P.BABBITT, JRNL AUTH 5 U.PIEPER,J.A.GERLT,S.C.ALMO JRNL TITL CRYSTAL STRUCTURE OF MANDELATE RACEMASE/MUCONATE LACTONIZING JRNL TITL 2 ENZYME FROM BACILLUS SUBTILIS AT 1.8 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.46 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 70202 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) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3548 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3965 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.3270 REMARK 3 BIN FREE R VALUE SET COUNT : 212 REMARK 3 BIN FREE R VALUE : 0.3830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5958 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 741 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.150 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.148 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.116 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.822 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6123 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8301 ; 1.436 ; 1.944 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 746 ; 5.778 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 284 ;33.491 ;23.380 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1033 ;14.496 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 44 ;19.608 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 877 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4694 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3084 ; 0.208 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4212 ; 0.307 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 587 ; 0.175 ; 0.200 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): 92 ; 0.236 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 56 ; 0.185 ; 0.200 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): 3832 ; 1.029 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5991 ; 1.533 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2688 ; 2.426 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2310 ; 3.594 ; 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 : 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 2GDQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAR-06. REMARK 100 THE DEPOSITION ID IS D_1000036991. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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) : 0.9793 REMARK 200 MONOCHROMATOR : SGX-CAT REMARK 200 OPTICS : SGX-CAT REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70561 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.84500 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: PHASER REMARK 200 STARTING MODEL: 1MUC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M LITHIUM SULFATE, 0.1M TRIS, PH REMARK 280 8.5, 25% W/V PEG 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 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 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 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 1.000000 0.000000 0.000000 41.18700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 56.62300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 84.30600 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 41.18700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 56.62300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 84.30600 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 41.18700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 56.62300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 84.30600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 41.18700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 56.62300 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 84.30600 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 BIOLOGICAL ASSEMBLY IS A OCTAMER GENERATED FROM THE REMARK 300 DIMER IN THE ASYMMETRIC UNIT BY THE OPERATIONS: -X,1-Y,Z; X,1-Y,-Z; REMARK 300 -X,Y,-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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 27170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 99180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -101.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 113.24600 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 113.24600 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 HOH A1153 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1167 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 1 REMARK 465 ALA A 2 REMARK 465 GLY A 376 REMARK 465 HIS A 377 REMARK 465 HIS A 378 REMARK 465 HIS A 379 REMARK 465 HIS A 380 REMARK 465 HIS A 381 REMARK 465 HIS A 382 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 GLY B 376 REMARK 465 HIS B 377 REMARK 465 HIS B 378 REMARK 465 HIS B 379 REMARK 465 HIS B 380 REMARK 465 HIS B 381 REMARK 465 HIS B 382 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 OD1 ASN A 271 O HOH A 1009 1.96 REMARK 500 O HOH B 803 O HOH B 1064 1.99 REMARK 500 O HOH B 1067 O HOH B 1121 2.09 REMARK 500 O HOH B 1071 O HOH B 1146 2.16 REMARK 500 O HOH B 852 O HOH B 1058 2.19 REMARK 500 O HOH B 802 O HOH B 1047 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 34 CB CYS A 34 SG -0.121 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 119 NE - CZ - NH1 ANGL. DEV. = -3.0 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 ARG A 65 -52.72 -129.15 REMARK 500 SER A 77 56.58 -91.12 REMARK 500 HIS A 89 104.53 -161.92 REMARK 500 SER A 136 139.96 -170.90 REMARK 500 ALA A 294 29.26 -149.26 REMARK 500 SER A 298 -62.77 -144.12 REMARK 500 ASP A 320 69.12 -153.16 REMARK 500 ASN A 332 102.12 -169.86 REMARK 500 ASN A 360 98.53 -69.81 REMARK 500 ARG B 65 -55.65 -134.78 REMARK 500 HIS B 89 105.79 -165.74 REMARK 500 ALA B 294 26.30 -152.60 REMARK 500 SER B 298 -63.20 -139.56 REMARK 500 SER B 298 -62.49 -140.97 REMARK 500 ASP B 320 69.70 -151.94 REMARK 500 ASN B 332 101.04 -171.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MUC RELATED DB: PDB REMARK 900 MUCONATE LACTONIZING ENZYME REMARK 900 RELATED ID: 1YEY RELATED DB: PDB REMARK 900 L-FUCONATE DEHYDRATASE FROM 2 XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS REMARK 900 STR. ATCC 33913 REMARK 900 RELATED ID: NYSGXRC-9293A RELATED DB: TARGETDB DBREF 2GDQ A 5 374 UNP O06741 O06741_BACSU 2 371 DBREF 2GDQ B 5 374 UNP O06741 O06741_BACSU 2 371 SEQADV 2GDQ MET A 1 UNP O06741 CLONING ARTIFACT SEQADV 2GDQ ALA A 2 UNP O06741 CLONING ARTIFACT SEQADV 2GDQ LEU A 3 UNP O06741 CLONING ARTIFACT SEQADV 2GDQ VAL A 4 UNP O06741 CLONING ARTIFACT SEQADV 2GDQ GLU A 375 UNP O06741 CLONING ARTIFACT SEQADV 2GDQ GLY A 376 UNP O06741 CLONING ARTIFACT SEQADV 2GDQ HIS A 377 UNP O06741 EXPRESSION TAG SEQADV 2GDQ HIS A 378 UNP O06741 EXPRESSION TAG SEQADV 2GDQ HIS A 379 UNP O06741 EXPRESSION TAG SEQADV 2GDQ HIS A 380 UNP O06741 EXPRESSION TAG SEQADV 2GDQ HIS A 381 UNP O06741 EXPRESSION TAG SEQADV 2GDQ HIS A 382 UNP O06741 EXPRESSION TAG SEQADV 2GDQ MET B 1 UNP O06741 CLONING ARTIFACT SEQADV 2GDQ ALA B 2 UNP O06741 CLONING ARTIFACT SEQADV 2GDQ LEU B 3 UNP O06741 CLONING ARTIFACT SEQADV 2GDQ VAL B 4 UNP O06741 CLONING ARTIFACT SEQADV 2GDQ GLU B 375 UNP O06741 CLONING ARTIFACT SEQADV 2GDQ GLY B 376 UNP O06741 CLONING ARTIFACT SEQADV 2GDQ HIS B 377 UNP O06741 EXPRESSION TAG SEQADV 2GDQ HIS B 378 UNP O06741 EXPRESSION TAG SEQADV 2GDQ HIS B 379 UNP O06741 EXPRESSION TAG SEQADV 2GDQ HIS B 380 UNP O06741 EXPRESSION TAG SEQADV 2GDQ HIS B 381 UNP O06741 EXPRESSION TAG SEQADV 2GDQ HIS B 382 UNP O06741 EXPRESSION TAG SEQRES 1 A 382 MET ALA LEU VAL LYS ILE VAL ARG ILE GLU THR PHE PRO SEQRES 2 A 382 LEU PHE HIS ARG LEU GLU LYS PRO TYR GLY ASP ALA ASN SEQRES 3 A 382 GLY PHE LYS ARG TYR ARG THR CYS TYR LEU ILE ARG ILE SEQRES 4 A 382 ILE THR GLU SER GLY ILE ASP GLY TRP GLY GLU CYS VAL SEQRES 5 A 382 ASP TRP LEU PRO ALA LEU HIS VAL GLY PHE THR LYS ARG SEQRES 6 A 382 ILE ILE PRO PHE LEU LEU GLY LYS GLN ALA GLY SER ARG SEQRES 7 A 382 LEU SER LEU VAL ARG THR ILE GLN LYS TRP HIS GLN ARG SEQRES 8 A 382 ALA ALA SER ALA VAL SER MET ALA LEU THR GLU ILE ALA SEQRES 9 A 382 ALA LYS ALA ALA ASP CYS SER VAL CYS GLU LEU TRP GLY SEQRES 10 A 382 GLY ARG TYR ARG GLU GLU ILE PRO VAL TYR ALA SER PHE SEQRES 11 A 382 GLN SER TYR SER ASP SER PRO GLN TRP ILE SER ARG SER SEQRES 12 A 382 VAL SER ASN VAL GLU ALA GLN LEU LYS LYS GLY PHE GLU SEQRES 13 A 382 GLN ILE LYS VAL LYS ILE GLY GLY THR SER PHE LYS GLU SEQRES 14 A 382 ASP VAL ARG HIS ILE ASN ALA LEU GLN HIS THR ALA GLY SEQRES 15 A 382 SER SER ILE THR MET ILE LEU ASP ALA ASN GLN SER TYR SEQRES 16 A 382 ASP ALA ALA ALA ALA PHE LYS TRP GLU ARG TYR PHE SER SEQRES 17 A 382 GLU TRP THR ASN ILE GLY TRP LEU GLU GLU PRO LEU PRO SEQRES 18 A 382 PHE ASP GLN PRO GLN ASP TYR ALA MET LEU ARG SER ARG SEQRES 19 A 382 LEU SER VAL PRO VAL ALA GLY GLY GLU ASN MET LYS GLY SEQRES 20 A 382 PRO ALA GLN TYR VAL PRO LEU LEU SER GLN ARG CYS LEU SEQRES 21 A 382 ASP ILE ILE GLN PRO ASP VAL MET HIS VAL ASN GLY ILE SEQRES 22 A 382 ASP GLU PHE ARG ASP CYS LEU GLN LEU ALA ARG TYR PHE SEQRES 23 A 382 GLY VAL ARG ALA SER ALA HIS ALA TYR ASP GLY SER LEU SEQRES 24 A 382 SER ARG LEU TYR ALA LEU PHE ALA GLN ALA CYS LEU PRO SEQRES 25 A 382 PRO TRP SER LYS MET LYS ASN ASP HIS ILE GLU PRO ILE SEQRES 26 A 382 GLU TRP ASP VAL MET GLU ASN PRO PHE THR ASP LEU VAL SEQRES 27 A 382 SER LEU GLN PRO SER LYS GLY MET VAL HIS ILE PRO LYS SEQRES 28 A 382 GLY LYS GLY ILE GLY THR GLU ILE ASN MET GLU ILE VAL SEQRES 29 A 382 ASN ARG TYR LYS TRP ASP GLY SER ALA TYR GLU GLY HIS SEQRES 30 A 382 HIS HIS HIS HIS HIS SEQRES 1 B 382 MET ALA LEU VAL LYS ILE VAL ARG ILE GLU THR PHE PRO SEQRES 2 B 382 LEU PHE HIS ARG LEU GLU LYS PRO TYR GLY ASP ALA ASN SEQRES 3 B 382 GLY PHE LYS ARG TYR ARG THR CYS TYR LEU ILE ARG ILE SEQRES 4 B 382 ILE THR GLU SER GLY ILE ASP GLY TRP GLY GLU CYS VAL SEQRES 5 B 382 ASP TRP LEU PRO ALA LEU HIS VAL GLY PHE THR LYS ARG SEQRES 6 B 382 ILE ILE PRO PHE LEU LEU GLY LYS GLN ALA GLY SER ARG SEQRES 7 B 382 LEU SER LEU VAL ARG THR ILE GLN LYS TRP HIS GLN ARG SEQRES 8 B 382 ALA ALA SER ALA VAL SER MET ALA LEU THR GLU ILE ALA SEQRES 9 B 382 ALA LYS ALA ALA ASP CYS SER VAL CYS GLU LEU TRP GLY SEQRES 10 B 382 GLY ARG TYR ARG GLU GLU ILE PRO VAL TYR ALA SER PHE SEQRES 11 B 382 GLN SER TYR SER ASP SER PRO GLN TRP ILE SER ARG SER SEQRES 12 B 382 VAL SER ASN VAL GLU ALA GLN LEU LYS LYS GLY PHE GLU SEQRES 13 B 382 GLN ILE LYS VAL LYS ILE GLY GLY THR SER PHE LYS GLU SEQRES 14 B 382 ASP VAL ARG HIS ILE ASN ALA LEU GLN HIS THR ALA GLY SEQRES 15 B 382 SER SER ILE THR MET ILE LEU ASP ALA ASN GLN SER TYR SEQRES 16 B 382 ASP ALA ALA ALA ALA PHE LYS TRP GLU ARG TYR PHE SER SEQRES 17 B 382 GLU TRP THR ASN ILE GLY TRP LEU GLU GLU PRO LEU PRO SEQRES 18 B 382 PHE ASP GLN PRO GLN ASP TYR ALA MET LEU ARG SER ARG SEQRES 19 B 382 LEU SER VAL PRO VAL ALA GLY GLY GLU ASN MET LYS GLY SEQRES 20 B 382 PRO ALA GLN TYR VAL PRO LEU LEU SER GLN ARG CYS LEU SEQRES 21 B 382 ASP ILE ILE GLN PRO ASP VAL MET HIS VAL ASN GLY ILE SEQRES 22 B 382 ASP GLU PHE ARG ASP CYS LEU GLN LEU ALA ARG TYR PHE SEQRES 23 B 382 GLY VAL ARG ALA SER ALA HIS ALA TYR ASP GLY SER LEU SEQRES 24 B 382 SER ARG LEU TYR ALA LEU PHE ALA GLN ALA CYS LEU PRO SEQRES 25 B 382 PRO TRP SER LYS MET LYS ASN ASP HIS ILE GLU PRO ILE SEQRES 26 B 382 GLU TRP ASP VAL MET GLU ASN PRO PHE THR ASP LEU VAL SEQRES 27 B 382 SER LEU GLN PRO SER LYS GLY MET VAL HIS ILE PRO LYS SEQRES 28 B 382 GLY LYS GLY ILE GLY THR GLU ILE ASN MET GLU ILE VAL SEQRES 29 B 382 ASN ARG TYR LYS TRP ASP GLY SER ALA TYR GLU GLY HIS SEQRES 30 B 382 HIS HIS HIS HIS HIS FORMUL 3 HOH *741(H2 O) HELIX 1 1 TRP A 54 ARG A 65 1 12 HELIX 2 2 ARG A 65 LEU A 71 1 7 HELIX 3 3 SER A 77 HIS A 89 1 13 HELIX 4 4 HIS A 89 ALA A 108 1 20 HELIX 5 5 SER A 111 TRP A 116 1 6 HELIX 6 6 GLN A 138 LYS A 152 1 15 HELIX 7 7 SER A 166 GLY A 182 1 17 HELIX 8 8 ASP A 196 LYS A 202 1 7 HELIX 9 9 TRP A 203 SER A 208 1 6 HELIX 10 10 GLN A 224 SER A 233 1 10 HELIX 11 11 GLY A 247 GLN A 257 1 11 HELIX 12 12 ASN A 271 GLY A 287 1 17 HELIX 13 13 SER A 298 CYS A 310 1 13 HELIX 14 14 ASN A 332 VAL A 338 5 7 HELIX 15 15 ASN A 360 TYR A 367 1 8 HELIX 16 16 TRP B 54 ARG B 65 1 12 HELIX 17 17 ARG B 65 LEU B 71 1 7 HELIX 18 18 SER B 77 LYS B 87 1 11 HELIX 19 19 HIS B 89 ALA B 108 1 20 HELIX 20 20 SER B 111 TRP B 116 1 6 HELIX 21 21 GLN B 138 LYS B 153 1 16 HELIX 22 22 SER B 166 GLY B 182 1 17 HELIX 23 23 ASP B 196 LYS B 202 1 7 HELIX 24 24 TRP B 203 SER B 208 1 6 HELIX 25 25 GLN B 224 SER B 233 1 10 HELIX 26 26 GLY B 247 GLN B 257 1 11 HELIX 27 27 GLY B 272 GLY B 287 1 16 HELIX 28 28 SER B 298 CYS B 310 1 13 HELIX 29 29 ASN B 332 LEU B 337 5 6 HELIX 30 30 ASN B 360 TYR B 367 1 8 SHEET 1 A 3 ILE A 6 ASP A 24 0 SHEET 2 A 3 GLY A 27 THR A 41 -1 O ILE A 40 N ARG A 8 SHEET 3 A 3 ASP A 46 CYS A 51 -1 O GLY A 47 N ILE A 39 SHEET 1 B 8 ARG A 289 ALA A 290 0 SHEET 2 B 8 ILE A 262 ILE A 263 1 N ILE A 263 O ARG A 289 SHEET 3 B 8 VAL A 239 GLY A 241 1 N GLY A 241 O ILE A 262 SHEET 4 B 8 ILE A 213 GLU A 217 1 N LEU A 216 O ALA A 240 SHEET 5 B 8 THR A 186 ASP A 190 1 N LEU A 189 O GLU A 217 SHEET 6 B 8 GLN A 157 LYS A 161 1 N ILE A 158 O THR A 186 SHEET 7 B 8 GLU A 123 SER A 129 1 N ALA A 128 O LYS A 159 SHEET 8 B 8 ILE A 325 ASP A 328 1 O TRP A 327 N SER A 129 SHEET 1 C 8 ARG A 289 ALA A 290 0 SHEET 2 C 8 ILE A 262 ILE A 263 1 N ILE A 263 O ARG A 289 SHEET 3 C 8 VAL A 239 GLY A 241 1 N GLY A 241 O ILE A 262 SHEET 4 C 8 ILE A 213 GLU A 217 1 N LEU A 216 O ALA A 240 SHEET 5 C 8 THR A 186 ASP A 190 1 N LEU A 189 O GLU A 217 SHEET 6 C 8 GLN A 157 LYS A 161 1 N ILE A 158 O THR A 186 SHEET 7 C 8 GLU A 123 SER A 129 1 N ALA A 128 O LYS A 159 SHEET 8 C 8 MET A 346 HIS A 348 -1 O VAL A 347 N ILE A 124 SHEET 1 D 3 ILE B 6 ASP B 24 0 SHEET 2 D 3 GLY B 27 THR B 41 -1 O LYS B 29 N TYR B 22 SHEET 3 D 3 ASP B 46 CYS B 51 -1 O GLY B 47 N ILE B 39 SHEET 1 E 8 ARG B 289 ALA B 290 0 SHEET 2 E 8 ILE B 262 ILE B 263 1 N ILE B 263 O ARG B 289 SHEET 3 E 8 VAL B 239 GLY B 241 1 N GLY B 241 O ILE B 262 SHEET 4 E 8 ILE B 213 GLU B 217 1 N LEU B 216 O ALA B 240 SHEET 5 E 8 THR B 186 ASP B 190 1 N LEU B 189 O GLU B 217 SHEET 6 E 8 GLN B 157 LYS B 161 1 N VAL B 160 O ASP B 190 SHEET 7 E 8 GLU B 123 SER B 129 1 N ALA B 128 O LYS B 159 SHEET 8 E 8 ILE B 325 ASP B 328 1 O TRP B 327 N SER B 129 SHEET 1 F 8 ARG B 289 ALA B 290 0 SHEET 2 F 8 ILE B 262 ILE B 263 1 N ILE B 263 O ARG B 289 SHEET 3 F 8 VAL B 239 GLY B 241 1 N GLY B 241 O ILE B 262 SHEET 4 F 8 ILE B 213 GLU B 217 1 N LEU B 216 O ALA B 240 SHEET 5 F 8 THR B 186 ASP B 190 1 N LEU B 189 O GLU B 217 SHEET 6 F 8 GLN B 157 LYS B 161 1 N VAL B 160 O ASP B 190 SHEET 7 F 8 GLU B 123 SER B 129 1 N ALA B 128 O LYS B 159 SHEET 8 F 8 MET B 346 HIS B 348 -1 O VAL B 347 N ILE B 124 CRYST1 82.374 113.246 168.612 90.00 90.00 90.00 I 2 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 0.012140 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008830 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005931 0.00000