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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
