HEADER OXIDOREDUCTASE 06-JUL-07 2V5L TITLE STRUCTURES OF THE OPEN AND CLOSED STATE OF TRYPANOSOMAL TITLE 2 TRIOSEPHOSPHATE ISOMERASE: AS OBSERVED IN A NEW CRYSTAL FORM: TITLE 3 IMPLICATIONS FOR THE REACTION MECHANISM COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRIOSEPHOSPHATE ISOMERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TRIOSE-PHOSPHATE ISOMERASE GLYCOSOMSAL, TIM; COMPND 5 EC: 5.3.1.1; COMPND 6 ENGINEERED: 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: 562 KEYWDS OXIDOREDUCTASE, TRIOSEPHOSPHATE ISOMERASE, PENTOSE SHUNT, KEYWDS 2 GLUCONEOGENESIS, BINDING STUDIES, TIM, ISOMERASE, GLYCOSOME, KEYWDS 3 GLYCOLYSIS, ENGINEERING, LIPID SYNTHESIS, FATTY ACID BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR M.E.M.NOBLE,J.P.ZEELEN,R.K.WIERENGA REVDAT 6 04-APR-18 2V5L 1 REMARK REVDAT 5 01-SEP-09 2V5L 1 REMARK REVDAT 4 24-FEB-09 2V5L 1 VERSN REVDAT 3 20-MAY-08 2V5L 1 REMARK MASTER REVDAT 2 19-FEB-08 2V5L 1 JRNL REVDAT 1 31-JUL-07 2V5L 0 JRNL AUTH M.E.M.NOBLE,J.P.ZEELEN,R.K.WIERENGA JRNL TITL STRUCTURES OF THE OPEN AND CLOSED STATE OF TRYPANOSOMAL JRNL TITL 2 TRIOSEPHOSPHATE ISOMERASE: AS OBSERVED IN A NEW CRYSTAL JRNL TITL 3 FORM: IMPLICATIONS FOR THE REACTION MECHANISM JRNL REF PROTEINS: STRUCT.,FUNCT., V. 16 311 1993 JRNL REF 2 GENET. JRNL REFN ISSN 0887-3585 JRNL PMID 8356028 JRNL DOI 10.1002/PROT.340160402 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 999.00 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 39764 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.1580 REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3766 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 81 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : NULL ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: X-PLOR USED IN THE INITIAL STAGES OF REMARK 3 REFINEMENT REMARK 4 REMARK 4 2V5L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1290033062. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 290 REMARK 200 PH : 8.8 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 : ELLIOTT GX-21 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : GRONINGEN BIOMOL PACKAGE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20429 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 99.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 81.8 REMARK 200 DATA REDUNDANCY : 1.950 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 41.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG6000, 200 MM TRIS PH 8.8, 1MM REMARK 280 EDTA, 1MM DTT AND 1MM NAN3 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 47.30000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.10000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 47.30000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.10000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.5 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 24.04244 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -128.46965 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 A2018 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 MET B 301 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 GLU A 23 CD GLU A 23 OE2 0.072 REMARK 500 GLU A 53 CD GLU A 53 OE2 0.077 REMARK 500 GLU A 77 CD GLU A 77 OE2 0.069 REMARK 500 GLU A 129 CD GLU A 129 OE2 0.074 REMARK 500 GLU A 133 CD GLU A 133 OE2 0.074 REMARK 500 GLU A 167 CD GLU A 167 OE2 0.073 REMARK 500 GLU A 185 CD GLU A 185 OE2 0.083 REMARK 500 GLU A 205 CD GLU A 205 OE2 0.070 REMARK 500 GLU B 323 CD GLU B 323 OE2 0.071 REMARK 500 GLU B 377 CD GLU B 377 OE1 -0.067 REMARK 500 GLU B 404 CD GLU B 404 OE2 0.076 REMARK 500 GLU B 407 CD GLU B 407 OE2 0.070 REMARK 500 GLU B 429 CD GLU B 429 OE2 0.067 REMARK 500 GLU B 433 CD GLU B 433 OE2 0.072 REMARK 500 GLU B 467 CD GLU B 467 OE2 0.091 REMARK 500 GLU B 485 CD GLU B 485 OE2 0.067 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 ASP A 26 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 36 CB - CG - OD1 ANGL. DEV. = 10.4 DEGREES REMARK 500 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 85 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 111 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 111 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 VAL A 123 CG1 - CB - CG2 ANGL. DEV. = -9.9 DEGREES REMARK 500 ASP A 158 CB - CG - OD2 ANGL. DEV. = -8.8 DEGREES REMARK 500 ARG A 191 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ASP A 201 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP A 201 CB - CG - OD2 ANGL. DEV. = -7.8 DEGREES REMARK 500 ASP A 227 CB - CG - OD1 ANGL. DEV. = 7.8 DEGREES REMARK 500 ASP A 227 CB - CG - OD2 ANGL. DEV. = -9.0 DEGREES REMARK 500 PRO A 240 C - N - CD ANGL. DEV. = -12.7 DEGREES REMARK 500 ASP A 244 CB - CG - OD1 ANGL. DEV. = 7.5 DEGREES REMARK 500 ASP B 336 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG B 354 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG B 354 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP B 385 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ASP B 385 CB - CG - OD2 ANGL. DEV. = -10.2 DEGREES REMARK 500 ASP B 411 CB - CG - OD2 ANGL. DEV. = -6.4 DEGREES REMARK 500 ARG B 434 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ASP B 458 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP B 458 CB - CG - OD2 ANGL. DEV. = -9.7 DEGREES REMARK 500 ARG B 491 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ASP B 501 CB - CG - OD2 ANGL. DEV. = -7.5 DEGREES REMARK 500 ARG B 507 NH1 - CZ - NH2 ANGL. DEV. = -8.1 DEGREES REMARK 500 ARG B 507 NE - CZ - NH1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP B 527 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP B 544 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ASP B 544 CB - CG - OD2 ANGL. DEV. = -9.2 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 LYS A 13 -140.53 55.24 REMARK 500 ASN A 34 57.50 -109.41 REMARK 500 ASP A 36 85.76 -59.14 REMARK 500 LYS B 313 -146.85 54.14 REMARK 500 ASN B 366 171.82 178.40 REMARK 500 THR B 474 16.88 -141.90 REMARK 500 GLU B 541 -9.21 -56.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR B 466 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1251 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1551 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: 2J24 RELATED DB: PDB REMARK 900 THE FUNCTIONAL ROLE OF THE CONSERVED ACTIVE SITE PROLINE OF REMARK 900 TRIOSEPHOSPHATE ISOMERASE REMARK 900 RELATED ID: 2J27 RELATED DB: PDB REMARK 900 THE FUNCTIONAL ROLE OF THE CONSERVED ACTIVE SITE PROLINE OF REMARK 900 TRIOSEPHOSPHATE ISOMERASE 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 REMARK 900 RELATED ID: 2V2C 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 REMARK 900 RELATED ID: 2V2D 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 REMARK 900 RELATED ID: 2V2H 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 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 REMARK 999 REMARK 999 SEQUENCE REMARK 999 IN HOUSE NAME P4MAS_W3TB.PDB (RESIDUES 203 AND 503 ARE REMARK 999 NOW AN ALANINE) RELATED PDB'S 1TPD AND 1TRD. REMARK 999 THIS IS AN OLD STRUCTURE THAT WAS ALREADY USED IN REMARK 999 PUBLICATION NOBLE, M.E.M., ZEELEN, J.P., WIERENGA, R.K. REMARK 999 (1993) PROTEINS, 16, 311-326. IN THAT ARTICLE IT WAS REMARK 999 REFERRED WITH IN-HOUSE NAME P4MAS_W3TB.PDB. WE WANT TO REMARK 999 DEPOSIT THIS STRUCTURE, BECAUSE SOME DETAILS OF IT HAVE REMARK 999 BECOME RELEVANT FOR OUR FORTHCOMING PUBLICATION. ONLY THE REMARK 999 COORDINATES AND THE INFORMATION ON THE ARTICLE FROM 1993 REMARK 999 ARE AVAILABLE FOR US. THIS MEANS THAT MOST OF THE REMARK 999 INFORMATION FOR THE HEADER FILES IS NOT AVAILABLE. DBREF 2V5L A 1 250 UNP P04789 TPIS_TRYBB 1 250 DBREF 2V5L B 301 550 UNP P04789 TPIS_TRYBB 1 250 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 PRO 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 PRO 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 HET SO4 A1251 5 HET SO4 B1551 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *81(H2 O) HELIX 1 1 SER A 17 SER A 30 1 14 HELIX 2 2 HIS A 47 LEU A 55 1 9 HELIX 3 3 SER A 79 GLY A 87 1 9 HELIX 4 4 HIS A 95 TYR A 102 1 8 HELIX 5 5 THR A 105 SER A 119 1 15 HELIX 6 6 THR A 130 SER A 136 1 7 HELIX 7 7 ARG A 138 LYS A 152 1 15 HELIX 8 8 LYS A 155 ALA A 160 5 6 HELIX 9 9 PRO A 168 ILE A 172 5 5 HELIX 10 10 THR A 179 GLY A 199 1 21 HELIX 11 11 GLY A 199 LEU A 206 1 8 HELIX 12 12 ASN A 218 GLN A 224 1 7 HELIX 13 13 GLY A 234 LYS A 239 5 6 HELIX 14 14 PRO A 240 THR A 249 1 10 HELIX 15 15 SER B 317 SER B 330 1 14 HELIX 16 16 HIS B 347 LEU B 355 1 9 HELIX 17 17 SER B 379 PHE B 386 1 8 HELIX 18 18 HIS B 395 TYR B 402 1 8 HELIX 19 19 THR B 405 SER B 419 1 15 HELIX 20 20 THR B 430 SER B 436 1 7 HELIX 21 21 ARG B 438 LYS B 453 1 16 HELIX 22 22 LYS B 456 ALA B 460 5 5 HELIX 23 23 PRO B 468 ILE B 472 5 5 HELIX 24 24 THR B 479 ILE B 498 1 20 HELIX 25 25 GLY B 499 LEU B 506 1 8 HELIX 26 26 ASN B 518 GLN B 525 1 8 HELIX 27 27 GLY B 534 LYS B 539 5 6 HELIX 28 28 PRO B 540 ALA B 548 1 9 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 BA 4 PHE B 360 ALA B 364 0 SHEET 2 BA 4 GLN B 338 SER B 343 1 O CYS B 339 N VAL B 361 SHEET 3 BA 4 ILE B 307 ASN B 311 1 O ALA B 308 N VAL B 340 SHEET 4 BA 4 GLY B 530 VAL B 533 1 O PHE B 531 N ALA B 309 SHEET 1 BB 4 TRP B 390 LEU B 393 0 SHEET 2 BB 4 MET B 422 ILE B 427 1 O MET B 422 N ILE B 391 SHEET 3 BB 4 VAL B 462 TYR B 466 1 O VAL B 463 N ALA B 425 SHEET 4 BB 4 ARG B 507 TYR B 510 1 O ARG B 507 N ILE B 464 SITE 1 AC1 5 SER A 213 GLY A 234 GLY A 235 HOH A2044 SITE 2 AC1 5 HOH A2045 SITE 1 AC2 2 GLY B 535 HOH B2036 CRYST1 94.600 48.200 130.700 90.00 100.60 90.00 C 1 2 1 8 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 0.010571 0.000000 0.001978 0.00000 SCALE2 0.000000 0.020747 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007784 0.00000