HEADER HYDROLASE 27-JUL-05 2AH2 TITLE TRYPANOSOMA CRUZI TRANS-SIALIDASE IN COMPLEX WITH 2,3-DIFLUOROSIALIC TITLE 2 ACID (COVALENT INTERMEDIATE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANS-SIALIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.18; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA CRUZI; SOURCE 3 ORGANISM_TAXID: 5693; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: TOP10F'; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PTRCHISA KEYWDS TRANSGLYCOSIDASE, COVALENT INTERMEDIATE, TRYPANOSOMA CRUZI, SIALIC KEYWDS 2 ACID, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.F.AMAYA,A.G.WATTS,I.DAMAGER,A.WEHENKEL,T.NGUYEN,A.BUSCHIAZZO, AUTHOR 2 G.PARIS,A.C.FRASCH,S.G.WITHERS,P.M.ALZARI REVDAT 6 20-OCT-21 2AH2 1 SEQADV HETSYN REVDAT 5 29-JUL-20 2AH2 1 COMPND REMARK SEQADV HETNAM REVDAT 5 2 1 LINK SITE REVDAT 4 11-OCT-17 2AH2 1 REMARK REVDAT 3 13-JUL-11 2AH2 1 VERSN REVDAT 2 24-FEB-09 2AH2 1 VERSN REVDAT 1 23-AUG-05 2AH2 0 SPRSDE 23-AUG-05 2AH2 1S0K JRNL AUTH M.F.AMAYA,A.G.WATTS,I.DAMAGER,A.WEHENKEL,T.NGUYEN, JRNL AUTH 2 A.BUSCHIAZZO,G.PARIS,A.C.FRASCH,S.G.WITHERS,P.M.ALZARI JRNL TITL STRUCTURAL INSIGHTS INTO THE CATALYTIC MECHANISM OF JRNL TITL 2 TRYPANOSOMA CRUZI TRANS-SIALIDASE JRNL REF STRUCTURE V. 12 775 2004 JRNL REFN ISSN 0969-2126 JRNL PMID 15130470 JRNL DOI 10.1016/J.STR.2004.02.036 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0003 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 3 NUMBER OF REFLECTIONS : 82504 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) : 0.099 REMARK 3 R VALUE (WORKING SET) : 0.099 REMARK 3 FREE R VALUE : 0.152 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4134 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5424 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.63 REMARK 3 BIN R VALUE (WORKING SET) : 0.1030 REMARK 3 BIN FREE R VALUE SET COUNT : 274 REMARK 3 BIN FREE R VALUE : 0.2220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4849 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 850 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.83000 REMARK 3 B22 (A**2) : -0.50000 REMARK 3 B33 (A**2) : 0.41000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.16000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.080 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.070 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.039 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.382 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.984 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.968 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5147 ; 0.019 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 4579 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7004 ; 1.768 ; 1.937 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10667 ; 0.898 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 652 ; 7.185 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 220 ;33.744 ;23.636 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 847 ;12.851 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;17.281 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 767 ; 0.119 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5799 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1069 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 922 ; 0.227 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4789 ; 0.201 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2578 ; 0.179 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 3149 ; 0.084 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 611 ; 0.207 ; 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): 16 ; 0.228 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 62 ; 0.271 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 44 ; 0.381 ; 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): 4043 ; 2.187 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1314 ; 0.655 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5150 ; 2.657 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2336 ; 4.305 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1854 ; 5.514 ; 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): 11879 ; 2.413 ;20.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 852 ;26.686 ;12.500 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 9599 ; 6.919 ;12.500 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 2AH2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUL-05. REMARK 100 THE DEPOSITION ID IS D_1000033885. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-APR-03 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : DIAMOND (111), LAUE GEOMETRY, REMARK 200 150 MICRONS THIN REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 82813 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 28.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04200 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) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.20100 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, TRIS-HCL, ISOPROPANOL, PH REMARK 280 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 64.34500 REMARK 290 SMTRY3 2 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A MONOMER 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 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 -13 REMARK 465 GLY A -12 REMARK 465 GLY A -11 REMARK 465 SER A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 GLY A -3 REMARK 465 MET A -2 REMARK 465 ALA A -1 REMARK 465 SER A 0 REMARK 465 ASP A 400 REMARK 465 PRO A 401 REMARK 465 ALA A 402 REMARK 465 ALA A 403 REMARK 465 SER A 404 REMARK 465 SER A 405 REMARK 465 SER A 406 REMARK 465 GLU A 407 REMARK 465 ARG A 408 REMARK 465 ASP A 634 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MET A 633 CB CG SD CE 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 NZ LYS A 215 O HOH A 2720 1.77 REMARK 500 O HOH A 2129 O HOH A 2699 1.80 REMARK 500 O HOH A 2228 O HOH A 2717 1.86 REMARK 500 OE2 GLU A 576 O HOH A 2495 1.89 REMARK 500 O HOH A 2286 O HOH A 2697 1.89 REMARK 500 O HOH A 2400 O HOH A 2742 2.05 REMARK 500 O HOH A 2397 O HOH A 2652 2.10 REMARK 500 OG SER A 394 O HOH A 2648 2.10 REMARK 500 O HOH A 2562 O HOH A 2726 2.12 REMARK 500 O HOH A 2147 O HOH A 2723 2.13 REMARK 500 O HOH A 2368 O HOH A 2576 2.14 REMARK 500 O HOH A 2475 O HOH A 2631 2.16 REMARK 500 O HOH A 2351 O HOH A 2578 2.17 REMARK 500 O HOH A 2271 O HOH A 2716 2.17 REMARK 500 O HOH A 2257 O HOH A 2625 2.18 REMARK 500 O HOH A 2431 O HOH A 2633 2.19 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 1919 O HOH A 2724 1556 1.40 REMARK 500 O HOH A 2103 O HOH A 2752 1554 1.86 REMARK 500 O HOH A 2264 O HOH A 2687 2555 2.03 REMARK 500 O HOH A 1994 O HOH A 2644 1556 2.10 REMARK 500 O HOH A 2111 O HOH A 2333 2555 2.15 REMARK 500 O HOH A 2612 O HOH A 2723 2545 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 21 CD GLU A 21 OE1 0.067 REMARK 500 LYS A 102 CD LYS A 102 CE -0.174 REMARK 500 GLU A 235 CD GLU A 235 OE2 -0.094 REMARK 500 GLU A 255 CD GLU A 255 OE1 0.076 REMARK 500 VAL A 420 CB VAL A 420 CG1 -0.135 REMARK 500 GLU A 566 CD GLU A 566 OE1 0.087 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 LYS A 12 CD - CE - NZ ANGL. DEV. = 15.1 DEGREES REMARK 500 ASP A 51 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 7.9 DEGREES REMARK 500 ARG A 117 NE - CZ - NH2 ANGL. DEV. = -7.2 DEGREES REMARK 500 ARG A 250 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 250 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 376 NE - CZ - NH1 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG A 376 NE - CZ - NH2 ANGL. DEV. = 3.7 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 SER A 15 -58.74 -149.99 REMARK 500 ASN A 60 67.92 -100.30 REMARK 500 ASN A 60 67.92 -110.41 REMARK 500 THR A 142 49.30 -146.94 REMARK 500 ASN A 173 -76.20 -126.32 REMARK 500 ALA A 179 170.56 71.21 REMARK 500 ALA A 182 -163.62 -102.77 REMARK 500 GLU A 230 62.38 34.49 REMARK 500 THR A 269 -79.65 -139.52 REMARK 500 ARG A 311 -134.53 51.20 REMARK 500 ARG A 316 64.00 64.09 REMARK 500 GLN A 325 -67.74 -134.17 REMARK 500 SER A 340 80.79 -157.36 REMARK 500 ALA A 341 -72.12 -88.37 REMARK 500 SER A 424 -126.32 -142.08 REMARK 500 VAL A 466 -96.13 -116.58 REMARK 500 ASP A 575 31.62 -158.30 REMARK 500 GLU A 576 -19.03 77.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 THE COVALENT SIALO-TYROSINE ADDUCT IS THE PRODUCT OF THE REMARK 600 REACTION OF 2,3-DIFLUOROSIALIC ACID WITH THE ENZYME REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2AGS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TRYPANOSOMA RANGELI SIALIDASE IN INCOMPLEX REMARK 900 WITH 2-KETO-3-DEOXY-D-GLYCERO-D-GALACTO-2,3_DIFLUORO-NONONIC ACID REMARK 900 (2,3-DIFLUORO-KDN) REMARK 900 RELATED ID: 2A75 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TRYPANOSOMA RANGELI SIALIDASE IN COMPLEX WITH REMARK 900 2,3- DIFLUOROSIALIC ACID (COVALENT INTERMEDIATE) REMARK 999 REMARK 999 SEQUENCE REMARK 999 AUTHORS INDICATE THAT THE SEQUENCE IN THE DATABASE IS REMARK 999 INCORRECT DBREF 2AH2 A 1 634 UNP Q26966 Q26966_TRYCR 2 635 SEQADV 2AH2 MET A -13 UNP Q26966 CLONING ARTIFACT SEQADV 2AH2 GLY A -12 UNP Q26966 CLONING ARTIFACT SEQADV 2AH2 GLY A -11 UNP Q26966 CLONING ARTIFACT SEQADV 2AH2 SER A -10 UNP Q26966 CLONING ARTIFACT SEQADV 2AH2 HIS A -9 UNP Q26966 EXPRESSION TAG SEQADV 2AH2 HIS A -8 UNP Q26966 EXPRESSION TAG SEQADV 2AH2 HIS A -7 UNP Q26966 EXPRESSION TAG SEQADV 2AH2 HIS A -6 UNP Q26966 EXPRESSION TAG SEQADV 2AH2 HIS A -5 UNP Q26966 EXPRESSION TAG SEQADV 2AH2 HIS A -4 UNP Q26966 EXPRESSION TAG SEQADV 2AH2 GLY A -3 UNP Q26966 CLONING ARTIFACT SEQADV 2AH2 MET A -2 UNP Q26966 CLONING ARTIFACT SEQADV 2AH2 ALA A -1 UNP Q26966 CLONING ARTIFACT SEQADV 2AH2 SER A 0 UNP Q26966 CLONING ARTIFACT SEQADV 2AH2 PHE A 58 UNP Q26966 ASN 59 ENGINEERED MUTATION SEQADV 2AH2 THR A 262 UNP Q26966 SER 263 SEE REMARK 999 SEQADV 2AH2 HIS A 476 UNP Q26966 ARG 477 SEE REMARK 999 SEQADV 2AH2 LEU A 484 UNP Q26966 VAL 485 SEE REMARK 999 SEQADV 2AH2 LYS A 495 UNP Q26966 SER 496 ENGINEERED MUTATION SEQADV 2AH2 GLY A 496 UNP Q26966 VAL 497 ENGINEERED MUTATION SEQADV 2AH2 LYS A 520 UNP Q26966 GLU 521 ENGINEERED MUTATION SEQADV 2AH2 VAL A 558 UNP Q26966 GLU 559 SEE REMARK 999 SEQADV 2AH2 GLY A 593 UNP Q26966 ASP 594 ENGINEERED MUTATION SEQADV 2AH2 ASP A 597 UNP Q26966 ILE 598 ENGINEERED MUTATION SEQADV 2AH2 ARG A 599 UNP Q26966 HIS 600 ENGINEERED MUTATION SEQRES 1 A 648 MET GLY GLY SER HIS HIS HIS HIS HIS HIS GLY MET ALA SEQRES 2 A 648 SER LEU ALA PRO GLY SER SER ARG VAL GLU LEU PHE LYS SEQRES 3 A 648 ARG GLN SER SER LYS VAL PRO PHE GLU LYS ASP GLY LYS SEQRES 4 A 648 VAL THR GLU ARG VAL VAL HIS SER PHE ARG LEU PRO ALA SEQRES 5 A 648 LEU VAL ASN VAL ASP GLY VAL MET VAL ALA ILE ALA ASP SEQRES 6 A 648 ALA ARG TYR GLU THR SER PHE ASP ASN SER LEU ILE ASP SEQRES 7 A 648 THR VAL ALA LYS TYR SER VAL ASP ASP GLY GLU THR TRP SEQRES 8 A 648 GLU THR GLN ILE ALA ILE LYS ASN SER ARG ALA SER SER SEQRES 9 A 648 VAL SER ARG VAL VAL ASP PRO THR VAL ILE VAL LYS GLY SEQRES 10 A 648 ASN LYS LEU TYR VAL LEU VAL GLY SER TYR ASN SER SER SEQRES 11 A 648 ARG SER TYR TRP THR SER HIS GLY ASP ALA ARG ASP TRP SEQRES 12 A 648 ASP ILE LEU LEU ALA VAL GLY GLU VAL THR LYS SER THR SEQRES 13 A 648 ALA GLY GLY LYS ILE THR ALA SER ILE LYS TRP GLY SER SEQRES 14 A 648 PRO VAL SER LEU LYS GLU PHE PHE PRO ALA GLU MET GLU SEQRES 15 A 648 GLY MET HIS THR ASN GLN PHE LEU GLY GLY ALA GLY VAL SEQRES 16 A 648 ALA ILE VAL ALA SER ASN GLY ASN LEU VAL TYR PRO VAL SEQRES 17 A 648 GLN VAL THR ASN LYS LYS LYS GLN VAL PHE SER LYS ILE SEQRES 18 A 648 PHE TYR SER GLU ASP GLU GLY LYS THR TRP LYS PHE GLY SEQRES 19 A 648 LYS GLY ARG SER ALA PHE GLY CYS SER GLU PRO VAL ALA SEQRES 20 A 648 LEU GLU TRP GLU GLY LYS LEU ILE ILE ASN THR ARG VAL SEQRES 21 A 648 ASP TYR ARG ARG ARG LEU VAL TYR GLU SER SER ASP MET SEQRES 22 A 648 GLY ASN THR TRP LEU GLU ALA VAL GLY THR LEU SER ARG SEQRES 23 A 648 VAL TRP GLY PRO SER PRO LYS SER ASN GLN PRO GLY SER SEQRES 24 A 648 GLN SER SER PHE THR ALA VAL THR ILE GLU GLY MET ARG SEQRES 25 A 648 VAL MET LEU PHE THR HIS PRO LEU ASN PHE LYS GLY ARG SEQRES 26 A 648 TRP LEU ARG ASP ARG LEU ASN LEU TRP LEU THR ASP ASN SEQRES 27 A 648 GLN ARG ILE TYR ASN VAL GLY GLN VAL SER ILE GLY ASP SEQRES 28 A 648 GLU ASN SER ALA TYR SER SER VAL LEU TYR LYS ASP ASP SEQRES 29 A 648 LYS LEU TYR CYS LEU HIS GLU ILE ASN SER ASN GLU VAL SEQRES 30 A 648 TYR SER LEU VAL PHE ALA ARG LEU VAL GLY GLU LEU ARG SEQRES 31 A 648 ILE ILE LYS SER VAL LEU GLN SER TRP LYS ASN TRP ASP SEQRES 32 A 648 SER HIS LEU SER SER ILE CYS THR PRO ALA ASP PRO ALA SEQRES 33 A 648 ALA SER SER SER GLU ARG GLY CYS GLY PRO ALA VAL THR SEQRES 34 A 648 THR VAL GLY LEU VAL GLY PHE LEU SER HIS SER ALA THR SEQRES 35 A 648 LYS THR GLU TRP GLU ASP ALA TYR ARG CYS VAL ASN ALA SEQRES 36 A 648 SER THR ALA ASN ALA GLU ARG VAL PRO ASN GLY LEU LYS SEQRES 37 A 648 PHE ALA GLY VAL GLY GLY GLY ALA LEU TRP PRO VAL SER SEQRES 38 A 648 GLN GLN GLY GLN ASN GLN ARG TYR HIS PHE ALA ASN HIS SEQRES 39 A 648 ALA PHE THR LEU VAL ALA SER VAL THR ILE HIS GLU VAL SEQRES 40 A 648 PRO LYS GLY ALA SER PRO LEU LEU GLY ALA SER LEU ASP SEQRES 41 A 648 SER SER GLY GLY LYS LYS LEU LEU GLY LEU SER TYR ASP SEQRES 42 A 648 LYS ARG HIS GLN TRP GLN PRO ILE TYR GLY SER THR PRO SEQRES 43 A 648 VAL THR PRO THR GLY SER TRP GLU MET GLY LYS ARG TYR SEQRES 44 A 648 HIS VAL VAL LEU THR MET ALA ASN LYS ILE GLY SER VAL SEQRES 45 A 648 TYR ILE ASP GLY GLU PRO LEU GLU GLY SER GLY GLN THR SEQRES 46 A 648 VAL VAL PRO ASP GLU ARG THR PRO ASP ILE SER HIS PHE SEQRES 47 A 648 TYR VAL GLY GLY TYR LYS ARG SER GLY MET PRO THR ASP SEQRES 48 A 648 SER ARG VAL THR VAL ASN ASN VAL LEU LEU TYR ASN ARG SEQRES 49 A 648 GLN LEU ASN ALA GLU GLU ILE ARG THR LEU PHE LEU SER SEQRES 50 A 648 GLN ASP LEU ILE GLY THR GLU ALA HIS MET ASP HET CL A1001 1 HET FSI A 700 21 HET GOL A1800 6 HET GOL A1801 6 HET GOL A1802 6 HET IPA A1903 4 HETNAM CL CHLORIDE ION HETNAM FSI 5-ACETAMIDO-3,5-DIDEOXY-3-FLUORO-D-ERYTHRO-ALPHA-L- HETNAM 2 FSI MANNO-NON-2-ULOPYRANOSONIC ACID HETNAM GOL GLYCEROL HETNAM IPA ISOPROPYL ALCOHOL HETSYN FSI 5-(ACETYLAMINO)-3,5-DIDEOXY-3-FLUORO-D-ERYTHRO-ALPHA-L- HETSYN 2 FSI MANNO-NON-2-ULOPYRANOSONIC ACID; 3-FLUOROSIALIC ACID; HETSYN 3 FSI 5-ACETAMIDO-3,5-DIDEOXY-3-FLUORO-D-ERYTHRO-ALPHA-L- HETSYN 4 FSI MANNO-NON-2-ULOSONIC ACID; 5-ACETAMIDO-3,5-DIDEOXY-3- HETSYN 5 FSI FLUORO-D-ERYTHRO-L-MANNO-NON-2-ULOSONIC ACID; 5- HETSYN 6 FSI ACETAMIDO-3,5-DIDEOXY-3-FLUORO-D-ERYTHRO-MANNO-NON-2- HETSYN 7 FSI ULOSONIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN IPA 2-PROPANOL FORMUL 2 CL CL 1- FORMUL 3 FSI C11 H18 F N O9 FORMUL 4 GOL 3(C3 H8 O3) FORMUL 7 IPA C3 H8 O FORMUL 8 HOH *850(H2 O) HELIX 1 1 TYR A 119 HIS A 123 5 5 HELIX 2 2 THR A 142 LYS A 146 5 5 HELIX 3 3 LYS A 160 PHE A 163 5 4 HELIX 4 4 LEU A 371 ILE A 395 1 25 HELIX 5 5 SER A 467 GLY A 470 5 4 HELIX 6 6 TYR A 475 ASN A 479 5 5 HELIX 7 7 ASN A 613 SER A 623 1 11 HELIX 8 8 THR A 629 MET A 633 5 5 SHEET 1 A 4 SER A 6 PHE A 11 0 SHEET 2 A 4 VAL A 363 ARG A 370 -1 O ARG A 370 N SER A 6 SHEET 3 A 4 LYS A 351 SER A 360 -1 N CYS A 354 O ALA A 369 SHEET 4 A 4 SER A 343 LYS A 348 -1 N LYS A 348 O LYS A 351 SHEET 1 B 2 LYS A 17 LYS A 22 0 SHEET 2 B 2 LYS A 25 VAL A 30 -1 O ARG A 29 N VAL A 18 SHEET 1 C 4 SER A 33 VAL A 42 0 SHEET 2 C 4 VAL A 45 ARG A 53 -1 O VAL A 45 N VAL A 42 SHEET 3 C 4 ILE A 63 SER A 70 -1 O LYS A 68 N ALA A 48 SHEET 4 C 4 GLU A 78 ILE A 83 -1 O GLN A 80 N ALA A 67 SHEET 1 D 3 THR A 148 TRP A 153 0 SHEET 2 D 3 TRP A 129 SER A 141 -1 N THR A 139 O SER A 150 SHEET 3 D 3 VAL A 157 SER A 158 -1 O VAL A 157 N LEU A 133 SHEET 1 E 5 THR A 148 TRP A 153 0 SHEET 2 E 5 TRP A 129 SER A 141 -1 N THR A 139 O SER A 150 SHEET 3 E 5 LYS A 105 TYR A 113 -1 N VAL A 110 O LEU A 132 SHEET 4 E 5 ARG A 93 LYS A 102 -1 N ILE A 100 O TYR A 107 SHEET 5 E 5 GLY A 180 VAL A 181 1 O GLY A 180 N VAL A 99 SHEET 1 F 4 GLU A 166 MET A 167 0 SHEET 2 F 4 MET A 170 GLY A 177 -1 O MET A 170 N MET A 167 SHEET 3 F 4 LEU A 190 ASN A 198 -1 O THR A 197 N ASN A 173 SHEET 4 F 4 ILE A 183 VAL A 184 -1 N ILE A 183 O VAL A 191 SHEET 1 G 5 GLU A 166 MET A 167 0 SHEET 2 G 5 MET A 170 GLY A 177 -1 O MET A 170 N MET A 167 SHEET 3 G 5 LEU A 190 ASN A 198 -1 O THR A 197 N ASN A 173 SHEET 4 G 5 VAL A 203 SER A 210 -1 O PHE A 204 N VAL A 196 SHEET 5 G 5 LYS A 218 PHE A 219 -1 O LYS A 218 N TYR A 209 SHEET 1 H 4 SER A 229 TRP A 236 0 SHEET 2 H 4 LYS A 239 ARG A 245 -1 O ASN A 243 N VAL A 232 SHEET 3 H 4 VAL A 253 SER A 256 -1 O SER A 256 N LEU A 240 SHEET 4 H 4 LEU A 264 GLU A 265 -1 O LEU A 264 N GLU A 255 SHEET 1 I 4 PHE A 289 ILE A 294 0 SHEET 2 I 4 MET A 297 PRO A 305 -1 O VAL A 299 N VAL A 292 SHEET 3 I 4 LEU A 317 THR A 322 -1 O THR A 322 N MET A 300 SHEET 4 I 4 ILE A 327 GLN A 332 -1 O TYR A 328 N LEU A 321 SHEET 1 J 7 ALA A 446 VAL A 449 0 SHEET 2 J 7 GLY A 452 PHE A 455 -1 O LYS A 454 N GLU A 447 SHEET 3 J 7 VAL A 600 TYR A 608 -1 O VAL A 600 N PHE A 455 SHEET 4 J 7 ALA A 481 ILE A 490 -1 N THR A 483 O TYR A 608 SHEET 5 J 7 ARG A 544 ALA A 552 -1 O VAL A 547 N ALA A 486 SHEET 6 J 7 ILE A 555 ILE A 560 -1 O TYR A 559 N VAL A 548 SHEET 7 J 7 GLU A 563 PRO A 564 -1 O GLU A 563 N ILE A 560 SHEET 1 K13 TRP A 524 TYR A 528 0 SHEET 2 K13 LYS A 512 ASP A 519 -1 N SER A 517 O GLN A 525 SHEET 3 K13 ALA A 497 SER A 504 -1 N LEU A 501 O LEU A 516 SHEET 4 K13 HIS A 583 VAL A 586 -1 O HIS A 583 N SER A 504 SHEET 5 K13 GLY A 461 PRO A 465 -1 N TRP A 464 O PHE A 584 SHEET 6 K13 ALA A 441 ALA A 444 -1 N SER A 442 O LEU A 463 SHEET 7 K13 GLU A 431 ASP A 434 -1 N TRP A 432 O ALA A 441 SHEET 8 K13 LEU A 419 ALA A 427 -1 N SER A 426 O GLU A 433 SHEET 9 K13 VAL A 600 TYR A 608 -1 O LEU A 607 N VAL A 420 SHEET 10 K13 ALA A 481 ILE A 490 -1 N THR A 483 O TYR A 608 SHEET 11 K13 ARG A 544 ALA A 552 -1 O VAL A 547 N ALA A 486 SHEET 12 K13 ILE A 555 ILE A 560 -1 O TYR A 559 N VAL A 548 SHEET 13 K13 GLN A 570 THR A 571 -1 O GLN A 570 N GLY A 556 SSBOND 1 CYS A 396 CYS A 410 1555 1555 2.01 LINK OH TYR A 342 C2 FSI A 700 1555 1555 1.42 CRYST1 54.149 128.690 54.298 90.00 108.74 90.00 P 1 21 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 0.018468 0.000000 0.006265 0.00000 SCALE2 0.000000 0.007771 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019448 0.00000