HEADER ISOMERASE 15-APR-14 4PCF TITLE STRUCTURE-BASED PROTEIN ENGINEERING OF A MONOMERIC TRIOSEPHOSPHATE TITLE 2 ISOMERASE TOWARDS CHANGING SUBSTRATE SPECIFICITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: MA18-TIM; COMPND 3 CHAIN: A, B, C; COMPND 4 EC: 5.3.1.1; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI BRUCEI; SOURCE 3 ORGANISM_TAXID: 5702; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PMK KEYWDS TRIOSEPHOSPHATE ISOMERASE, TIM BARREL, PROTEIN ENGINEERING, SUBSTRATE KEYWDS 2 SPECIFICITY, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.KRAUSE,P.NEUBAUER,R.K.WIERENGA REVDAT 3 27-DEC-23 4PCF 1 REMARK REVDAT 2 29-JUN-16 4PCF 1 JRNL REMARK REVDAT 1 22-APR-15 4PCF 0 JRNL AUTH M.KRAUSE,T.R.KIEMA,P.NEUBAUER,R.K.WIERENGA JRNL TITL CRYSTAL STRUCTURES OF TWO MONOMERIC TRIOSEPHOSPHATE JRNL TITL 2 ISOMERASE VARIANTS IDENTIFIED VIA A DIRECTED-EVOLUTION JRNL TITL 3 PROTOCOL SELECTING FOR L-ARABINOSE ISOMERASE ACTIVITY. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 72 490 2016 JRNL REFN ESSN 2053-230X JRNL PMID 27303904 JRNL DOI 10.1107/S2053230X16007548 REMARK 2 REMARK 2 RESOLUTION. 2.71 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 2.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 83.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 19927 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) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1078 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) : 2.71 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.78 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1370 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.10 REMARK 3 BIN R VALUE (WORKING SET) : 0.3120 REMARK 3 BIN FREE R VALUE SET COUNT : 60 REMARK 3 BIN FREE R VALUE : 0.3440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5398 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 147 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.19000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.20000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.11000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.413 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.358 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.335 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.868 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.798 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5503 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5395 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7471 ; 1.481 ; 1.933 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12351 ; 1.277 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 703 ; 6.406 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 223 ;33.984 ;24.350 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 917 ;19.715 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;20.444 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 866 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6254 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1263 ; 0.004 ; 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): 2827 ; 1.125 ; 1.752 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2826 ; 1.126 ; 1.752 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3525 ; 2.023 ; 2.621 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3526 ; 2.022 ; 2.621 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2676 ; 0.841 ; 1.854 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2677 ; 0.841 ; 1.855 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3947 ; 1.548 ; 2.737 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6499 ; 3.642 ;14.151 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6486 ; 3.636 ;14.164 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 3 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 2 249 B 2 249 12773 0.17 0.05 REMARK 3 2 A 2 250 C 2 250 13504 0.14 0.05 REMARK 3 3 B 2 249 C 2 249 13003 0.16 0.05 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 4PCF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000201138. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-AUG-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.2 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.542 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER PLATINUM 135 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19927 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.710 REMARK 200 RESOLUTION RANGE LOW (A) : 83.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.960 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.71 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 56.3 REMARK 200 DATA REDUNDANCY IN SHELL : 1.23 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.490 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.75M (NH4)2HPO4,, PH 8.2, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 24.71000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: MONOMERIC 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 REMARK 350 BIOMOLECULE: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 1 REMARK 465 GLY A 16 REMARK 465 SER A 17 REMARK 465 PRO A 18 REMARK 465 ASP A 19 REMARK 465 MET B 1 REMARK 465 GLY B 16 REMARK 465 GLN B 250 REMARK 465 MET C 1 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 ALA B 9 O LEU B 232 1.86 REMARK 500 O GLY B 216 O HOH B 321 1.89 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 207 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 LEU C 189 CA - CB - CG ANGL. DEV. = 15.7 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 ALA A 49 -62.02 145.17 REMARK 500 ASP A 227 -10.25 69.60 REMARK 500 LYS B 13 37.07 -89.92 REMARK 500 ASP B 19 -57.46 -162.96 REMARK 500 SER B 20 149.67 126.36 REMARK 500 ASP B 227 -11.22 71.10 REMARK 500 ALA B 233 159.05 61.16 REMARK 500 LYS C 13 46.87 -161.58 REMARK 500 SER C 15 78.06 90.30 REMARK 500 SER C 20 160.87 91.14 REMARK 500 ALA C 67 57.51 -103.07 REMARK 500 ASP C 227 -9.02 70.51 REMARK 500 THR C 249 30.74 -82.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO B 18 ASP B 19 -147.84 REMARK 500 GLY C 68 ASN C 69 147.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5TIM RELATED DB: PDB REMARK 900 TRIOSEPHOSPHATE ISOMERASE COMPLEX WITH SULFATE REMARK 900 RELATED ID: 1TRI RELATED DB: PDB REMARK 900 TRIOSEPHOSPHATE ISOMERASE MUTANT WITH 15 RESIDUES (68 - 82) REMARK 900 REPLACED BY 8 RESIDUES REMARK 900 RELATED ID: 2VEK RELATED DB: PDB REMARK 900 STRUCTURE-BASED ENZYME ENGINEERING EFFORTS WITH AN INACTIVE REMARK 900 MONOMERIC TIM VARIANT: THE IMPORTANCE OF A SINGLE POINT MUTATION REMARK 900 FOR GENERATING AN ACTIVE SITE WITH SUITABLE BINDING PROPERTIES REMARK 900 RELATED ID: 1AG1 RELATED DB: PDB REMARK 900 MONOHYDROGEN PHOSPHATE BINDING TO TRYPANOSOMAL TRIOSEPHOSPHATE REMARK 900 ISOMERASE REMARK 900 RELATED ID: 1DKW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TRIOSE-PHOSPHATE ISOMERASE WITH MODIFIED REMARK 900 SUBSTRATE BINDING SITE REMARK 900 RELATED ID: 1IIG RELATED DB: PDB REMARK 900 STRUCTURE OF TRYPANOSOMA BRUCEI BRUCEI TRIOSEPHOSPHATE ISOMERASE REMARK 900 COMPLEXED WITH 3- PHOSPHONOPROPIONATE REMARK 900 RELATED ID: 1ML1 RELATED DB: PDB REMARK 900 PROTEIN ENGINEERING WITH MONOMERIC TRIOSEPHOSPHATEISOMERASE: THE REMARK 900 MODELLING AND STRUCTURE VERIFICATION OFA SEVEN RESIDUE LO REMARK 900 RELATED ID: 1MSS RELATED DB: PDB REMARK 900 TRIOSEPHOSPHATE ISOMERASE MUTANT WITH PHE 45 REPLACED BY SER, VAL REMARK 900 46 REPLACED BY SER, AND RESIDUES 68 - 82 REPLACED BY THE REMARK 900 RELATED ID: 2V5L RELATED DB: PDB REMARK 900 STRUCTURES OF THE OPEN AND CLOSED STATE OF TRYPANOSOMAL REMARK 900 TRIOSEPHOSPHATE ISOMERASE: AS OBSERVED IN A NEW CRYSTAL FORM: REMARK 900 IMPLICATIONS FOR THE REACTION MECHANISM REMARK 900 RELATED ID: 6TIM RELATED DB: PDB REMARK 900 TRIOSEPHOSPHATE ISOMERASE COMPLEX WITH GLYCEROL -3-PHOSPHATE REMARK 900 RELATED ID: 2VEM RELATED DB: PDB REMARK 900 STRUCTURE-BASED ENZYME ENGINEERING EFFORTS WITH AN INACTIVE REMARK 900 MONOMERIC TIM VARIANT: THE IMPORTANCE OF A SINGLE POINT MUTATION REMARK 900 FOR GENERATING AN ACTIVE SITE WITH SUITABLE BINDING PROPERTIES REMARK 900 RELATED ID: 2VEN RELATED DB: PDB REMARK 900 STRUCTURE-BASED ENZYME ENGINEERING EFFORTS WITH AN INACTIVE REMARK 900 MONOMERIC TIM VARIANT: THE IMPORTANCE OF A SINGLE POINT MUTATION REMARK 900 FOR GENERATING AN ACTIVE SITE WITH SUITABLE BINDING PROPERTIES REMARK 900 RELATED ID: 2VEI RELATED DB: PDB REMARK 900 STRUCTURE-BASED ENZYME ENGINEERING EFFORTS WITH AN INACTIVE REMARK 900 MONOMERIC TIM VARIANT: THE IMPORTANCE OF A SINGLE POINT MUTATION REMARK 900 FOR GENERATING AN ACTIVE SITE WITH SUITABLE BINDING PROPERTIES REMARK 900 RELATED ID: 3TIM RELATED DB: PDB REMARK 900 TRIOSEPHOSPHATE ISOMERASE REMARK 900 RELATED ID: 2VEL RELATED DB: PDB REMARK 900 STRUCTURE-BASED ENZYME ENGINEERING EFFORTS WITH AN INACTIVE REMARK 900 MONOMERIC TIM VARIANT: THE IMPORTANCE OF A SINGLE POINT MUTATION REMARK 900 FOR GENERATING AN ACTIVE SITE WITH SUITABLE BINDING PROPERTIES REMARK 900 RELATED ID: 2V0T RELATED DB: PDB REMARK 900 THE A178L MUTATION IN THE C-TERMINAL HINGE OF THE FLEXIBLE LOOP-6 REMARK 900 OF TRIOSEPHOSPHATE ISOMERASE (TIM) INDUCES A MORE CLOSED REMARK 900 CONFORMATION OF THIS HINGE REGION IN DIMERIC AND MONOMERIC TIM DBREF 4PCF A 1 249 PDB 4PCF 4PCF 1 249 DBREF 4PCF B 1 249 PDB 4PCF 4PCF 1 249 DBREF 4PCF C 1 249 PDB 4PCF 4PCF 1 249 SEQRES 1 A 239 MET SER LYS PRO GLN PRO ILE ALA ALA ALA ASN TRP LYS SEQRES 2 A 239 SER GLY SER PRO ASP SER LEU SER GLY LEU ILE ASP LEU SEQRES 3 A 239 PHE ASN SER THR SER ILE ASN HIS ASP VAL GLN CYS VAL SEQRES 4 A 239 VAL ALA SER THR PHE VAL HIS LEU ALA MET THR LYS GLU SEQRES 5 A 239 ARG LEU SER HIS PRO LYS PHE VAL ILE ALA ALA GLN ASN SEQRES 6 A 239 ALA GLY ASN THR ASP ALA LEU ALA SER LEU LYS ASP PHE SEQRES 7 A 239 GLY VAL ASN TRP ILE VAL LEU GLY HIS PHE GLU ARG ARG SEQRES 8 A 239 TRP TYR TYR GLY GLU THR ASN GLU ILE VAL ALA ASP LYS SEQRES 9 A 239 VAL ALA ALA ALA VAL ALA SER GLY PHE MET VAL ILE ALA SEQRES 10 A 239 CYS ILE GLY GLU THR LEU GLN GLU ARG GLU SER GLY ARG SEQRES 11 A 239 THR ALA VAL VAL VAL LEU THR GLN ILE ALA ALA ILE ALA SEQRES 12 A 239 LYS LYS LEU LYS LYS ALA ASP TRP ALA LYS VAL VAL ILE SEQRES 13 A 239 ALA TYR GLU PRO VAL TRP ALA ILE GLY THR GLY LYS VAL SEQRES 14 A 239 VAL THR PRO GLN GLN ALA GLN GLU ALA HIS ALA LEU ILE SEQRES 15 A 239 ARG SER TRP VAL SER SER LYS ILE GLY ALA ASP VAL ALA SEQRES 16 A 239 GLY GLU LEU ARG ILE LEU TYR GLY GLY SER VAL ASN GLY SEQRES 17 A 239 LYS ASN ALA ARG THR LEU TYR GLN GLN ARG ASP VAL ASN SEQRES 18 A 239 GLY PHE LEU ALA GLY LEU LYS PRO GLU PHE VAL ASP ILE SEQRES 19 A 239 ILE LYS ALA THR GLN SEQRES 1 B 239 MET SER LYS PRO GLN PRO ILE ALA ALA ALA ASN TRP LYS SEQRES 2 B 239 SER GLY SER PRO ASP SER LEU SER GLY LEU ILE ASP LEU SEQRES 3 B 239 PHE ASN SER THR SER ILE ASN HIS ASP VAL GLN CYS VAL SEQRES 4 B 239 VAL ALA SER THR PHE VAL HIS LEU ALA MET THR LYS GLU SEQRES 5 B 239 ARG LEU SER HIS PRO LYS PHE VAL ILE ALA ALA GLN ASN SEQRES 6 B 239 ALA GLY ASN THR ASP ALA LEU ALA SER LEU LYS ASP PHE SEQRES 7 B 239 GLY VAL ASN TRP ILE VAL LEU GLY HIS PHE GLU ARG ARG SEQRES 8 B 239 TRP TYR TYR GLY GLU THR ASN GLU ILE VAL ALA ASP LYS SEQRES 9 B 239 VAL ALA ALA ALA VAL ALA SER GLY PHE MET VAL ILE ALA SEQRES 10 B 239 CYS ILE GLY GLU THR LEU GLN GLU ARG GLU SER GLY ARG SEQRES 11 B 239 THR ALA VAL VAL VAL LEU THR GLN ILE ALA ALA ILE ALA SEQRES 12 B 239 LYS LYS LEU LYS LYS ALA ASP TRP ALA LYS VAL VAL ILE SEQRES 13 B 239 ALA TYR GLU PRO VAL TRP ALA ILE GLY THR GLY LYS VAL SEQRES 14 B 239 VAL THR PRO GLN GLN ALA GLN GLU ALA HIS ALA LEU ILE SEQRES 15 B 239 ARG SER TRP VAL SER SER LYS ILE GLY ALA ASP VAL ALA SEQRES 16 B 239 GLY GLU LEU ARG ILE LEU TYR GLY GLY SER VAL ASN GLY SEQRES 17 B 239 LYS ASN ALA ARG THR LEU TYR GLN GLN ARG ASP VAL ASN SEQRES 18 B 239 GLY PHE LEU ALA GLY LEU LYS PRO GLU PHE VAL ASP ILE SEQRES 19 B 239 ILE LYS ALA THR GLN SEQRES 1 C 239 MET SER LYS PRO GLN PRO ILE ALA ALA ALA ASN TRP LYS SEQRES 2 C 239 SER GLY SER PRO ASP SER LEU SER GLY LEU ILE ASP LEU SEQRES 3 C 239 PHE ASN SER THR SER ILE ASN HIS ASP VAL GLN CYS VAL SEQRES 4 C 239 VAL ALA SER THR PHE VAL HIS LEU ALA MET THR LYS GLU SEQRES 5 C 239 ARG LEU SER HIS PRO LYS PHE VAL ILE ALA ALA GLN ASN SEQRES 6 C 239 ALA GLY ASN THR ASP ALA LEU ALA SER LEU LYS ASP PHE SEQRES 7 C 239 GLY VAL ASN TRP ILE VAL LEU GLY HIS PHE GLU ARG ARG SEQRES 8 C 239 TRP TYR TYR GLY GLU THR ASN GLU ILE VAL ALA ASP LYS SEQRES 9 C 239 VAL ALA ALA ALA VAL ALA SER GLY PHE MET VAL ILE ALA SEQRES 10 C 239 CYS ILE GLY GLU THR LEU GLN GLU ARG GLU SER GLY ARG SEQRES 11 C 239 THR ALA VAL VAL VAL LEU THR GLN ILE ALA ALA ILE ALA SEQRES 12 C 239 LYS LYS LEU LYS LYS ALA ASP TRP ALA LYS VAL VAL ILE SEQRES 13 C 239 ALA TYR GLU PRO VAL TRP ALA ILE GLY THR GLY LYS VAL SEQRES 14 C 239 VAL THR PRO GLN GLN ALA GLN GLU ALA HIS ALA LEU ILE SEQRES 15 C 239 ARG SER TRP VAL SER SER LYS ILE GLY ALA ASP VAL ALA SEQRES 16 C 239 GLY GLU LEU ARG ILE LEU TYR GLY GLY SER VAL ASN GLY SEQRES 17 C 239 LYS ASN ALA ARG THR LEU TYR GLN GLN ARG ASP VAL ASN SEQRES 18 C 239 GLY PHE LEU ALA GLY LEU LYS PRO GLU PHE VAL ASP ILE SEQRES 19 C 239 ILE LYS ALA THR GLN FORMUL 4 HOH *147(H2 O) HELIX 1 AA1 LEU A 21 SER A 30 1 10 HELIX 2 AA2 PHE A 45 LEU A 48 5 4 HELIX 3 AA3 ALA A 49 LEU A 55 1 7 HELIX 4 AA4 ASN A 69 GLY A 87 1 12 HELIX 5 AA5 HIS A 95 TYR A 102 1 8 HELIX 6 AA6 THR A 105 SER A 119 1 15 HELIX 7 AA7 THR A 130 SER A 136 1 7 HELIX 8 AA8 ARG A 138 LYS A 153 1 16 HELIX 9 AA9 LEU A 154 ALA A 160 5 7 HELIX 10 AB1 PRO A 168 ILE A 172 5 5 HELIX 11 AB2 THR A 179 ILE A 198 1 20 HELIX 12 AB3 GLY A 199 LEU A 206 1 8 HELIX 13 AB4 ASN A 215 GLN A 225 1 11 HELIX 14 AB5 GLU A 241 ALA A 248 1 8 HELIX 15 AB6 SER B 20 SER B 30 1 11 HELIX 16 AB7 THR B 44 LEU B 55 1 12 HELIX 17 AB8 ASN B 69 GLY B 87 1 12 HELIX 18 AB9 HIS B 95 TYR B 102 1 8 HELIX 19 AC1 THR B 105 SER B 119 1 15 HELIX 20 AC2 THR B 130 SER B 136 1 7 HELIX 21 AC3 ARG B 138 LYS B 153 1 16 HELIX 22 AC4 LEU B 154 ALA B 160 5 7 HELIX 23 AC5 PRO B 168 ILE B 172 5 5 HELIX 24 AC6 THR B 179 ILE B 198 1 20 HELIX 25 AC7 GLY B 199 LEU B 206 1 8 HELIX 26 AC8 GLY B 216 GLN B 225 1 10 HELIX 27 AC9 GLU B 241 ALA B 248 1 8 HELIX 28 AD1 SER C 20 SER C 30 1 11 HELIX 29 AD2 THR C 44 LEU C 55 1 12 HELIX 30 AD3 ASN C 69 ASP C 85 1 10 HELIX 31 AD4 HIS C 95 TYR C 102 1 8 HELIX 32 AD5 THR C 105 SER C 119 1 15 HELIX 33 AD6 THR C 130 SER C 136 1 7 HELIX 34 AD7 ARG C 138 LYS C 153 1 16 HELIX 35 AD8 LEU C 154 ALA C 160 5 7 HELIX 36 AD9 PRO C 168 ILE C 172 5 5 HELIX 37 AE1 THR C 179 ILE C 198 1 20 HELIX 38 AE2 GLY C 199 LEU C 206 1 8 HELIX 39 AE3 ASN C 215 GLN C 225 1 11 HELIX 40 AE4 GLU C 241 ALA C 248 1 8 SHEET 1 AA1 9 ILE A 7 TRP A 12 0 SHEET 2 AA1 9 GLN A 38 SER A 43 1 O ALA A 42 N ALA A 10 SHEET 3 AA1 9 PHE A 60 ALA A 64 1 O ALA A 63 N VAL A 41 SHEET 4 AA1 9 TRP A 90 LEU A 93 1 O TRP A 90 N ALA A 64 SHEET 5 AA1 9 MET A 122 ILE A 127 1 O CYS A 126 N LEU A 93 SHEET 6 AA1 9 VAL A 162 TYR A 166 1 O VAL A 163 N ALA A 125 SHEET 7 AA1 9 ILE A 208 TYR A 210 1 O LEU A 209 N ILE A 164 SHEET 8 AA1 9 GLY A 230 GLY A 234 1 O GLY A 230 N TYR A 210 SHEET 9 AA1 9 ILE A 7 TRP A 12 1 N ALA A 9 O PHE A 231 SHEET 1 AA2 9 ILE B 7 ASN B 11 0 SHEET 2 AA2 9 GLN B 38 ALA B 42 1 O ALA B 42 N ALA B 10 SHEET 3 AA2 9 PHE B 60 ALA B 64 1 O ALA B 63 N VAL B 41 SHEET 4 AA2 9 TRP B 90 LEU B 93 1 O TRP B 90 N ALA B 64 SHEET 5 AA2 9 MET B 122 ILE B 127 1 O CYS B 126 N LEU B 93 SHEET 6 AA2 9 VAL B 162 TYR B 166 1 O VAL B 163 N ALA B 125 SHEET 7 AA2 9 ILE B 208 TYR B 210 1 O LEU B 209 N ILE B 164 SHEET 8 AA2 9 GLY B 230 PHE B 231 1 O GLY B 230 N TYR B 210 SHEET 9 AA2 9 ILE B 7 ASN B 11 1 N ALA B 9 O PHE B 231 SHEET 1 AA3 9 ILE C 7 ASN C 11 0 SHEET 2 AA3 9 GLN C 38 ALA C 42 1 O ALA C 42 N ALA C 10 SHEET 3 AA3 9 PHE C 60 ALA C 64 1 O ALA C 63 N VAL C 41 SHEET 4 AA3 9 TRP C 90 LEU C 93 1 O TRP C 90 N ALA C 64 SHEET 5 AA3 9 MET C 122 ILE C 127 1 O CYS C 126 N LEU C 93 SHEET 6 AA3 9 VAL C 162 TYR C 166 1 O VAL C 163 N ALA C 125 SHEET 7 AA3 9 ILE C 208 TYR C 210 1 O LEU C 209 N ILE C 164 SHEET 8 AA3 9 GLY C 230 GLY C 234 1 O GLY C 230 N TYR C 210 SHEET 9 AA3 9 ILE C 7 ASN C 11 1 N ASN C 11 O ALA C 233 CRYST1 92.920 49.420 95.510 90.00 118.50 90.00 P 1 21 1 6 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 0.010762 0.000000 0.005843 0.00000 SCALE2 0.000000 0.020235 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011914 0.00000