PDB Short entry for 2J24 HEADER ISOMERASE 16-AUG-06 2J24 TITLE THE FUNCTIONAL ROLE OF THE CONSERVED ACTIVE SITE PROLINE OF TITLE 2 TRIOSEPHOSPHATE ISOMERASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TIM, TRIOSE-PHOSPHATE ISOMERASE; COMPND 5 EC: 5.3.1.1; COMPND 6 ENGINEERED: YES; COMPND 7 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_VECTOR: PET3A KEYWDS ISOMERASE, PROTEIN ENGINEERING, FATTY ACID BIOSYNTHESIS, KEYWDS 2 GLUCONEOGENESIS, LIPID SYNTHESIS, PENTOSE SHUNT, POINT MUTATION, KEYWDS 3 LOOP7, GLYCOSOME, TIM-BARREL EXPDTA X-RAY DIFFRACTION AUTHOR M.G.CASTELEIJN,M.ALAHUHTA,K.GROEBEL,I.EL-SAYED,K.AUGUSTYNS, AUTHOR 2 A.M.LAMBEIR,P.NEUBAUER,R.K.WIERENGA REVDAT 5 13-DEC-23 2J24 1 REMARK REVDAT 4 28-JUN-17 2J24 1 REMARK REVDAT 3 13-JUL-11 2J24 1 VERSN REVDAT 2 24-FEB-09 2J24 1 VERSN REVDAT 1 02-JAN-07 2J24 0 JRNL AUTH M.G.CASTELEIJN,M.ALAHUHTA,K.GROEBEL,I.EL-SAYED,K.AUGUSTYNS, JRNL AUTH 2 A.M.LAMBEIR,P.NEUBAUER,R.K.WIERENGA JRNL TITL FUNCTIONAL ROLE OF THE CONSERVED ACTIVE SITE PROLINE OF JRNL TITL 2 TRIOSEPHOSPHATE ISOMERASE. JRNL REF BIOCHEMISTRY V. 45 15483 2006 JRNL REFN ISSN 0006-2960 JRNL PMID 17176070 JRNL DOI 10.1021/BI061683J REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.21 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 20995 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) : 0.149 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1106 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1501 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1520 REMARK 3 BIN FREE R VALUE SET COUNT : 79 REMARK 3 BIN FREE R VALUE : 0.2310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3762 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 399 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : UNVERIFIED REMARK 3 FROM WILSON PLOT (A**2) : 17.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 7.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.30000 REMARK 3 B22 (A**2) : 0.15000 REMARK 3 B33 (A**2) : -0.38000 REMARK 3 B12 (A**2) : 0.12000 REMARK 3 B13 (A**2) : 0.21000 REMARK 3 B23 (A**2) : -0.79000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.319 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.220 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.150 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.282 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.883 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3874 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3631 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5260 ; 1.638 ; 1.938 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8435 ; 0.880 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 496 ; 7.264 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 155 ;40.228 ;24.581 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 668 ;16.431 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;13.964 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 625 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4299 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 750 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 931 ; 0.214 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4018 ; 0.192 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1951 ; 0.182 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2429 ; 0.087 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 310 ; 0.201 ; 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): 22 ; 0.172 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 100 ; 0.233 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 36 ; 0.222 ; 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): 3144 ; 0.792 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3990 ; 1.008 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1625 ; 1.833 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1270 ; 2.567 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 2 A 250 5 REMARK 3 1 B 2 B 250 5 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 1468 ; 0.14 ; 0.50 REMARK 3 MEDIUM POSITIONAL 1 B (A): 1468 ; 0.14 ; 0.50 REMARK 3 LOOSE POSITIONAL 1 A (A): 2121 ; 0.54 ; 5.00 REMARK 3 LOOSE POSITIONAL 1 B (A): 2121 ; 0.54 ; 5.00 REMARK 3 MEDIUM THERMAL 1 A (A**2): 1468 ; 0.50 ; 2.00 REMARK 3 MEDIUM THERMAL 1 B (A**2): 1468 ; 0.50 ; 2.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 2121 ; 0.92 ; 10.00 REMARK 3 LOOSE THERMAL 1 B (A**2): 2121 ; 0.92 ; 10.00 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 2 A 250 REMARK 3 ORIGIN FOR THE GROUP (A): -0.0610 0.3710 -0.8270 REMARK 3 T TENSOR REMARK 3 T11: -0.0771 T22: -0.0590 REMARK 3 T33: -0.0563 T12: 0.0033 REMARK 3 T13: -0.0066 T23: 0.0093 REMARK 3 L TENSOR REMARK 3 L11: 0.6075 L22: 0.8921 REMARK 3 L33: 1.2280 L12: -0.3538 REMARK 3 L13: -0.2490 L23: 0.1874 REMARK 3 S TENSOR REMARK 3 S11: -0.0299 S12: -0.0880 S13: -0.0207 REMARK 3 S21: 0.1180 S22: 0.0639 S23: 0.0300 REMARK 3 S31: 0.0471 S32: 0.0171 S33: -0.0340 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 2 B 250 REMARK 3 ORIGIN FOR THE GROUP (A): 8.3460 0.3320 -35.2630 REMARK 3 T TENSOR REMARK 3 T11: -0.0850 T22: -0.0663 REMARK 3 T33: -0.0455 T12: 0.0062 REMARK 3 T13: -0.0009 T23: -0.0018 REMARK 3 L TENSOR REMARK 3 L11: 0.6408 L22: 0.8407 REMARK 3 L33: 1.1670 L12: 0.3441 REMARK 3 L13: -0.2130 L23: -0.2053 REMARK 3 S TENSOR REMARK 3 S11: -0.0107 S12: 0.0900 S13: -0.0122 REMARK 3 S21: -0.1121 S22: 0.0346 S23: -0.0636 REMARK 3 S31: 0.0486 S32: -0.0079 S33: -0.0240 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 2J24 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-AUG-06. REMARK 100 THE DEPOSITION ID IS D_1290029642. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-AUG-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.00 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 : ENRAF-NONIUS FR591 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MONTEL MIRRORS REMARK 200 OPTICS : MONTEL MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22102 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 2.650 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.63 REMARK 200 R MERGE FOR SHELL (I) : 0.13000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 8.670 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: PDB ENTRY 5TIM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: WELL SOLUTION: 0.1 M TEA PH 7.0, 27% REMARK 280 PEG 2K MME AND 0.2 M KSCN PROTEIN SOLUTION: 11 MG/ML PROTEIN, REMARK 280 0.02 M TRIS/HCL PH 7.0, 0.1 M NACL, 1 MM DTT, 1 MM EDTA AND 1 MM REMARK 280 NAN3., PH 7.00 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: 3030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, PRO 168 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN B, PRO 168 TO ALA 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 MET B 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 VAL A 177 NE2 GLN A 182 2.03 REMARK 500 O HOH A 2088 O HOH A 2114 2.03 REMARK 500 OD1 ASP A 85 O HOH A 2085 2.09 REMARK 500 OE1 GLU B 135 O HOH B 2147 2.10 REMARK 500 OG SER B 196 O HOH B 2186 2.11 REMARK 500 O HOH B 2006 O HOH B 2016 2.16 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 2072 O HOH B 2073 1455 2.13 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 134 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ASP A 201 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG B 134 NE - CZ - NH1 ANGL. DEV. = 3.5 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 PRO A 4 -177.51 -69.73 REMARK 500 LYS A 13 -144.80 52.36 REMARK 500 CYS A 14 66.76 -100.59 REMARK 500 ASN A 66 161.47 179.56 REMARK 500 SER A 213 102.03 -57.41 REMARK 500 LYS B 13 -143.66 53.16 REMARK 500 ALA B 248 -8.03 -59.11 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 SER B 2 LYS B 3 -145.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2009 DISTANCE = 6.80 ANGSTROMS REMARK 525 HOH A2023 DISTANCE = 6.75 ANGSTROMS REMARK 700 REMARK 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" REMARK 700 AND "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9- REMARK 700 STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN REMARK 700 WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. REMARK 900 REMARK 900 RELATED ENTRIES 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 TRIOSEPHOSPHATEISOMERASE REMARK 900 COMPLEXED WITH 3- PHOSPHONOPROPIONATE REMARK 900 RELATED ID: 1IIH RELATED DB: PDB REMARK 900 STRUCTURE OF TRYPANOSOMA BRUCEI BRUCEI TRIOSEPHOSPHATEISOMERASE REMARK 900 COMPLEXED WITH 3- PHOSPHOGLYCERATE REMARK 900 RELATED ID: 1KV5 RELATED DB: PDB REMARK 900 STRUCTURE OF TRYPANOSOMA BRUCEI BRUCEI TIM WITH THE SALT-BRIDGE- REMARK 900 FORMING RESIDUE ARG191 MUTATED TO SER 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 LOOP 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 RESIDUES REMARK 900 GNADALAS (F45S,V46S,68-82:GNADALAS) REMARK 900 RELATED ID: 1MTM RELATED DB: PDB REMARK 900 LOOP-1 MODELING OF MONOTIM-A100W MUTANT REMARK 900 RELATED ID: 1TPD RELATED DB: PDB REMARK 900 TRIOSEPHOSPHATE ISOMERASE REMARK 900 RELATED ID: 1TPE RELATED DB: PDB REMARK 900 TRIOSEPHOSPHATE ISOMERASE REMARK 900 RELATED ID: 1TPF RELATED DB: PDB REMARK 900 TRIOSEPHOSPHATE ISOMERASE REMARK 900 RELATED ID: 1TRD RELATED DB: PDB REMARK 900 TRIOSEPHOSPHATE ISOMERASE 1 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: 1TSI RELATED DB: PDB REMARK 900 TRIOSEPHOSPHATE ISOMERASE COMPLEX WITH N- HYDROXY-4-PHOSPHONO- REMARK 900 BUTANAMIDE REMARK 900 RELATED ID: 1TTI RELATED DB: PDB REMARK 900 MOL_ID: 1; MOLECULE: TRIOSEPHOSPHATE ISOMERASE ; CHAIN: NULL; EC: REMARK 900 5.3.1.1; ENGINEERED: YES; MUTATION: I68G, A69N, K70A, S71D, DEL( 73- REMARK 900 79), P81A, A100W; OTHER_DETAILS: MONOTIM WITH A110W MUTATION REMARK 900 RELATED ID: 1TTJ RELATED DB: PDB REMARK 900 MOL_ID: 1; MOLECULE: TRIOSEPHOSPHATE ISOMERASE ; CHAIN: NULL; EC: REMARK 900 5.3.1.1; MUTATION: VARIANT OF MONOTIM WITH PHE 45 REPLACED BY SER REMARK 900 AND VAL 46 REPLACED BY SER (F45S, V46S) AND 73 - 79 DELETED REMARK 900 RELATED ID: 3TIM RELATED DB: PDB REMARK 900 TRIOSEPHOSPHATE ISOMERASE REMARK 900 RELATED ID: 4TIM RELATED DB: PDB REMARK 900 TRIOSEPHOSPHATE ISOMERASE COMPLEX WITH 2- PHOSPHOGLYCERATE REMARK 900 RELATED ID: 5TIM RELATED DB: PDB REMARK 900 TRIOSEPHOSPHATE ISOMERASE COMPLEX WITH SULFATE REMARK 900 RELATED ID: 6TIM RELATED DB: PDB REMARK 900 TRIOSEPHOSPHATE ISOMERASE COMPLEX WITH GLYCEROL -3-PHOSPHATE DBREF 2J24 A 1 250 UNP P04789 TPIS_TRYBB 1 250 DBREF 2J24 B 1 250 UNP P04789 TPIS_TRYBB 1 250 SEQADV 2J24 ALA A 168 UNP P04789 PRO 168 ENGINEERED MUTATION SEQADV 2J24 ALA B 168 UNP P04789 PRO 168 ENGINEERED MUTATION SEQRES 1 A 250 MET SER LYS PRO GLN PRO ILE ALA ALA ALA ASN TRP LYS SEQRES 2 A 250 CYS ASN GLY SER GLN GLN SER LEU SER GLU LEU ILE ASP SEQRES 3 A 250 LEU PHE ASN SER THR SER ILE ASN HIS ASP VAL GLN CYS SEQRES 4 A 250 VAL VAL ALA SER THR PHE VAL HIS LEU ALA MET THR LYS SEQRES 5 A 250 GLU ARG LEU SER HIS PRO LYS PHE VAL ILE ALA ALA GLN SEQRES 6 A 250 ASN ALA ILE ALA LYS SER GLY ALA PHE THR GLY GLU VAL SEQRES 7 A 250 SER LEU PRO ILE LEU LYS ASP PHE GLY VAL ASN TRP ILE SEQRES 8 A 250 VAL LEU GLY HIS SER GLU ARG ARG ALA TYR TYR GLY GLU SEQRES 9 A 250 THR ASN GLU ILE VAL ALA ASP LYS VAL ALA ALA ALA VAL SEQRES 10 A 250 ALA SER GLY PHE MET VAL ILE ALA CYS ILE GLY GLU THR SEQRES 11 A 250 LEU GLN GLU ARG GLU SER GLY ARG THR ALA VAL VAL VAL SEQRES 12 A 250 LEU THR GLN ILE ALA ALA ILE ALA LYS LYS LEU LYS LYS SEQRES 13 A 250 ALA ASP TRP ALA LYS VAL VAL ILE ALA TYR GLU ALA VAL SEQRES 14 A 250 TRP ALA ILE GLY THR GLY LYS VAL ALA THR PRO GLN GLN SEQRES 15 A 250 ALA GLN GLU ALA HIS ALA LEU ILE ARG SER TRP VAL SER SEQRES 16 A 250 SER LYS ILE GLY ALA ASP VAL ALA GLY GLU LEU ARG ILE SEQRES 17 A 250 LEU TYR GLY GLY SER VAL ASN GLY LYS ASN ALA ARG THR SEQRES 18 A 250 LEU TYR GLN GLN ARG ASP VAL ASN GLY PHE LEU VAL GLY SEQRES 19 A 250 GLY ALA SER LEU LYS PRO GLU PHE VAL ASP ILE ILE LYS SEQRES 20 A 250 ALA THR GLN SEQRES 1 B 250 MET SER LYS PRO GLN PRO ILE ALA ALA ALA ASN TRP LYS SEQRES 2 B 250 CYS ASN GLY SER GLN GLN SER LEU SER GLU LEU ILE ASP SEQRES 3 B 250 LEU PHE ASN SER THR SER ILE ASN HIS ASP VAL GLN CYS SEQRES 4 B 250 VAL VAL ALA SER THR PHE VAL HIS LEU ALA MET THR LYS SEQRES 5 B 250 GLU ARG LEU SER HIS PRO LYS PHE VAL ILE ALA ALA GLN SEQRES 6 B 250 ASN ALA ILE ALA LYS SER GLY ALA PHE THR GLY GLU VAL SEQRES 7 B 250 SER LEU PRO ILE LEU LYS ASP PHE GLY VAL ASN TRP ILE SEQRES 8 B 250 VAL LEU GLY HIS SER GLU ARG ARG ALA TYR TYR GLY GLU SEQRES 9 B 250 THR ASN GLU ILE VAL ALA ASP LYS VAL ALA ALA ALA VAL SEQRES 10 B 250 ALA SER GLY PHE MET VAL ILE ALA CYS ILE GLY GLU THR SEQRES 11 B 250 LEU GLN GLU ARG GLU SER GLY ARG THR ALA VAL VAL VAL SEQRES 12 B 250 LEU THR GLN ILE ALA ALA ILE ALA LYS LYS LEU LYS LYS SEQRES 13 B 250 ALA ASP TRP ALA LYS VAL VAL ILE ALA TYR GLU ALA VAL SEQRES 14 B 250 TRP ALA ILE GLY THR GLY LYS VAL ALA THR PRO GLN GLN SEQRES 15 B 250 ALA GLN GLU ALA HIS ALA LEU ILE ARG SER TRP VAL SER SEQRES 16 B 250 SER LYS ILE GLY ALA ASP VAL ALA GLY GLU LEU ARG ILE SEQRES 17 B 250 LEU TYR GLY GLY SER VAL ASN GLY LYS ASN ALA ARG THR SEQRES 18 B 250 LEU TYR GLN GLN ARG ASP VAL ASN GLY PHE LEU VAL GLY SEQRES 19 B 250 GLY ALA SER LEU LYS PRO GLU PHE VAL ASP ILE ILE LYS SEQRES 20 B 250 ALA THR GLN FORMUL 3 HOH *399(H2 O) HELIX 1 1 SER A 17 THR A 31 1 15 HELIX 2 2 THR A 44 VAL A 46 5 3 HELIX 3 3 HIS A 47 LEU A 55 1 9 HELIX 4 4 SER A 79 PHE A 86 1 8 HELIX 5 5 HIS A 95 TYR A 102 1 8 HELIX 6 6 THR A 105 SER A 119 1 15 HELIX 7 7 THR A 130 SER A 136 1 7 HELIX 8 8 ARG A 138 LYS A 152 1 15 HELIX 9 9 LYS A 155 ALA A 160 5 6 HELIX 10 10 ALA A 168 ILE A 172 5 5 HELIX 11 11 THR A 179 ILE A 198 1 20 HELIX 12 12 GLY A 199 LEU A 206 1 8 HELIX 13 13 ASN A 218 GLN A 224 1 7 HELIX 14 14 GLY A 234 LYS A 239 5 6 HELIX 15 15 PRO A 240 ALA A 248 1 9 HELIX 16 16 SER B 17 THR B 31 1 15 HELIX 17 17 THR B 44 VAL B 46 5 3 HELIX 18 18 HIS B 47 LEU B 55 1 9 HELIX 19 19 SER B 79 PHE B 86 1 8 HELIX 20 20 HIS B 95 TYR B 102 1 8 HELIX 21 21 THR B 105 SER B 119 1 15 HELIX 22 22 THR B 130 SER B 136 1 7 HELIX 23 23 ARG B 138 LYS B 152 1 15 HELIX 24 24 LYS B 155 ALA B 160 5 6 HELIX 25 25 ALA B 168 ILE B 172 5 5 HELIX 26 26 THR B 179 ILE B 198 1 20 HELIX 27 27 GLY B 199 LEU B 206 1 8 HELIX 28 28 ASN B 218 GLN B 224 1 7 HELIX 29 29 GLY B 234 PRO B 240 5 7 HELIX 30 30 GLU B 241 ALA B 248 1 8 SHEET 1 AA10 ILE A 7 ASN A 11 0 SHEET 2 AA10 GLN A 38 ALA A 42 1 O GLN A 38 N ALA A 8 SHEET 3 AA10 PHE A 60 ALA A 64 1 O VAL A 61 N VAL A 41 SHEET 4 AA10 TRP A 90 LEU A 93 1 O TRP A 90 N ALA A 64 SHEET 5 AA10 MET A 122 ILE A 127 1 O MET A 122 N ILE A 91 SHEET 6 AA10 VAL A 162 TYR A 166 1 O VAL A 163 N ALA A 125 SHEET 7 AA10 ARG A 207 TYR A 210 1 O ARG A 207 N ILE A 164 SHEET 8 AA10 GLY A 230 VAL A 233 1 O GLY A 230 N TYR A 210 SHEET 9 AA10 ILE A 7 ASN A 11 1 O ILE A 7 N PHE A 231 SHEET 10 AA10 ILE A 7 ASN A 11 0 SHEET 1 BA10 ILE B 7 ASN B 11 0 SHEET 2 BA10 GLN B 38 ALA B 42 1 O GLN B 38 N ALA B 8 SHEET 3 BA10 PHE B 60 ALA B 64 1 O VAL B 61 N VAL B 41 SHEET 4 BA10 TRP B 90 LEU B 93 1 O TRP B 90 N ALA B 64 SHEET 5 BA10 MET B 122 ILE B 127 1 O MET B 122 N ILE B 91 SHEET 6 BA10 VAL B 162 TYR B 166 1 O VAL B 163 N ALA B 125 SHEET 7 BA10 ARG B 207 TYR B 210 1 O ARG B 207 N ILE B 164 SHEET 8 BA10 GLY B 230 VAL B 233 1 O GLY B 230 N TYR B 210 SHEET 9 BA10 ILE B 7 ASN B 11 1 O ILE B 7 N PHE B 231 SHEET 10 BA10 ILE B 7 ASN B 11 0 CRYST1 37.500 43.720 71.270 80.49 79.61 64.66 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 0.026667 -0.012628 -0.003657 0.00000 SCALE2 0.000000 0.025308 -0.002519 0.00000 SCALE3 0.000000 0.000000 0.014336 0.00000 MTRIX1 1 -1.000000 -0.000139 0.001548 8.32600 1 MTRIX2 1 -0.000144 1.000000 -0.003005 -0.06445 1 MTRIX3 1 -0.001548 -0.003005 -1.000000 -36.06000 1