PDB Short entry for 2YFN HEADER HYDROLASE 07-APR-11 2YFN TITLE GALACTOSIDASE DOMAIN OF ALPHA-GALACTOSIDASE-SUCROSE KINASE, TITLE 2 AGASK COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-GALACTOSIDASE-SUCROSE KINASE AGASK; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.22; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RUMINOCOCCUS GNAVUS E1; SOURCE 3 ORGANISM_TAXID: 935582; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.SULZENBACHER,L.BRUEL,M.TISON-CERVERA,A.PUJOL,C.NICOLETTI,J.PERRIER, AUTHOR 2 A.GALINIER,D.ROPARTZ,M.FONS,F.POMPEO,T.GIARDINA REVDAT 3 07-DEC-11 2YFN 1 JRNL REVDAT 2 23-NOV-11 2YFN 1 JRNL REMARK HELIX SHEET REVDAT 1 28-SEP-11 2YFN 0 JRNL AUTH L.BRUEL,G.SULZENBACHER,M.TISON-CERVERA,A.PUJOL,C.NICOLETTI, JRNL AUTH 2 J.PERRIER,A.GALINIER,D.ROPARTZ,M.FONS,F.POMPEO,T.GIARDINA JRNL TITL AGASK, A BIFUNCTIONAL ENZYME FROM THE HUMAN MICROBIOME JRNL TITL 2 COUPLING GALACTOSIDASE AND KINASE ACTIVITIES JRNL REF J.BIOL.CHEM. V. 286 40814 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21931163 JRNL DOI 10.1074/JBC.M111.286039 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.19 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 98.75 REMARK 3 NUMBER OF REFLECTIONS : 150207 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) : 0.13105 REMARK 3 R VALUE (WORKING SET) : 0.13007 REMARK 3 FREE R VALUE : 0.14957 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1 REMARK 3 FREE R VALUE TEST SET COUNT : 8033 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) : 1.450 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.488 REMARK 3 REFLECTION IN BIN (WORKING SET) : 10384 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.240 REMARK 3 BIN FREE R VALUE SET COUNT : 525 REMARK 3 BIN FREE R VALUE : 0.258 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5988 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 1058 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.5 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.825 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.35 REMARK 3 B22 (A**2) : -0.14 REMARK 3 B33 (A**2) : -0.21 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.046 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.048 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.031 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.828 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.978 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6191 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 4210 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8458 ; 1.447 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10266 ; 0.860 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 809 ; 6.720 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 323 ;37.263 ;24.118 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1061 ;11.319 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 44 ;17.030 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 902 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7087 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1323 ; 0.001 ; 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): 3708 ; 0.752 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1517 ; 0.235 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6015 ; 1.303 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2483 ; 2.080 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2395 ; 3.359 ; 4.500 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 : NULL 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 626 REMARK 3 ORIGIN FOR THE GROUP (A): 38.3170 15.0330 51.4330 REMARK 3 T TENSOR REMARK 3 T11: 0.0341 T22: 0.0428 REMARK 3 T33: 0.0331 T12: 0.0039 REMARK 3 T13: 0.0042 T23: 0.0157 REMARK 3 L TENSOR REMARK 3 L11: 0.2231 L22: 0.0703 REMARK 3 L33: 0.0771 L12: 0.0023 REMARK 3 L13: 0.0229 L23: -0.0085 REMARK 3 S TENSOR REMARK 3 S11: 0.0138 S12: 0.0092 S13: 0.0211 REMARK 3 S21: -0.0237 S22: 0.0121 S23: 0.0107 REMARK 3 S31: -0.0252 S32: -0.0129 S33: -0.0259 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 : A 627 A 720 REMARK 3 ORIGIN FOR THE GROUP (A): 32.0230 20.2610 81.8430 REMARK 3 T TENSOR REMARK 3 T11: 0.0426 T22: 0.0445 REMARK 3 T33: 0.0383 T12: 0.0122 REMARK 3 T13: 0.0132 T23: 0.0082 REMARK 3 L TENSOR REMARK 3 L11: 0.3140 L22: 0.7342 REMARK 3 L33: 1.1582 L12: 0.4185 REMARK 3 L13: -0.1557 L23: -0.5507 REMARK 3 S TENSOR REMARK 3 S11: 0.0288 S12: -0.0332 S13: 0.0376 REMARK 3 S21: 0.0686 S22: -0.0090 S23: 0.0684 REMARK 3 S31: -0.1335 S32: -0.0043 S33: -0.0198 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 : 1.40 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 REMARK 3 RIDING POSITIONS. DISORDERED SIDE CHAINS WERE MODELED REMARK 3 STEREOCHEMICALLY REMARK 4 REMARK 4 2YFN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-APR-11. REMARK 100 THE PDBE ID CODE IS EBI-47954. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 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) : 0.933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 158241 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.45 REMARK 200 RESOLUTION RANGE LOW (A) : 36.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 2.9 REMARK 200 R MERGE (I) : 0.08 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.00 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.6 REMARK 200 R MERGE FOR SHELL (I) : 0.46 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.20 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3MI6 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG 8000, 0.1M HEPES PH REMARK 280 7.5, PROTEIN CONCENTRATION 7MG/ML REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 52.52900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 55.82500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 77.44300 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 52.52900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 55.82500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 77.44300 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 52.52900 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 55.82500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 77.44300 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 52.52900 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 55.82500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 77.44300 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 26650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 83260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -114.9 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 154.88600 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 105.05800 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 154.88600 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 105.05800 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 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 A2058 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2463 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2521 LIES ON A SPECIAL POSITION. REMARK 375 HOH A3034 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 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 SG CYS A 458 O HOH A 2342 2.12 REMARK 500 NZ LYS A 677 O HOH A 2996 2.00 REMARK 500 OE2 GLU A 684 O HOH A 3002 2.13 REMARK 500 O HOH A 2226 O HOH A 2227 1.86 REMARK 500 O HOH A 2234 O HOH A 3055 2.19 REMARK 500 O HOH A 2310 O HOH A 2354 2.16 REMARK 500 O HOH A 2358 O HOH A 2360 2.08 REMARK 500 O HOH A 2367 O HOH A 2823 2.05 REMARK 500 O HOH A 2456 O HOH A 2997 2.15 REMARK 500 O HOH A 2732 O HOH A 2783 2.01 REMARK 500 O HOH A 2753 O HOH A 2759 1.99 REMARK 500 O HOH A 2766 O HOH A 2767 2.09 REMARK 500 O HOH A 2978 O HOH A 2980 2.07 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 577 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 ARG A 577 NE - CZ - NH2 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 TYR A 77 71.38 -152.26 REMARK 500 MET A 201 70.93 -163.45 REMARK 500 SER A 225 156.49 100.10 REMARK 500 VAL A 319 -62.05 -123.96 REMARK 500 TYR A 340 -126.07 51.01 REMARK 500 ASP A 366 -156.02 -85.01 REMARK 500 ASP A 376 33.22 -93.05 REMARK 500 SER A 379 -12.15 89.99 REMARK 500 ASP A 382 73.89 -107.65 REMARK 500 TRP A 383 48.90 -87.24 REMARK 500 MET A 479 103.04 -168.15 REMARK 500 SER A 519 82.67 -156.62 REMARK 500 ARG A 524 58.48 -141.51 REMARK 500 PHE A 593 -178.30 64.47 REMARK 500 GLU A 596 75.57 -154.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1725 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 176 OE1 REMARK 620 2 GLU A 176 O 100.7 REMARK 620 3 GLU A 277 O 160.6 98.2 REMARK 620 4 PHE A 280 O 80.5 91.0 95.0 REMARK 620 5 HOH A2513 O 80.3 88.6 104.4 160.4 REMARK 620 6 HOH A2516 O 101.7 151.2 62.0 110.3 77.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1726 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2521 O REMARK 620 2 HOH A2527 O 75.0 REMARK 620 3 HOH A2511 O 165.1 90.6 REMARK 620 4 HOH A2519 O 101.5 175.1 93.1 REMARK 620 5 HOH A2177 O 90.0 90.9 86.4 92.5 REMARK 620 N 1 2 3 4 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1721 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1722 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1723 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A1724 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1725 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1726 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2YFO RELATED DB: PDB REMARK 900 GALACTOSIDASE DOMAIN OF ALPHA-GALACTOSIDASE-SUCROSE KINASE, REMARK 900 AGASK, IN COMPLEX WITH GALACTOSE REMARK 999 REMARK 999 SEQUENCE REMARK 999 SEQUENCE NOT AVAILABLE IN UNIPROT YET, BUT WILL BE REMARK 999 DEPOSITED SOON. THE TREMBL ACCESSION ID IS FQ790379 DBREF 2YFN A 1 720 PDB 2YFN 2YFN 1 720 SEQRES 1 A 720 MET ALA ILE ILE TYR ASN PRO ASN LYS LYS ILE PHE THR SEQRES 2 A 720 LEU HIS THR ALA HIS THR THR TYR GLN MET GLN VAL ASP SEQRES 3 A 720 PRO LEU GLY TYR LEU LEU HIS LEU TYR TYR GLY GLU LYS SEQRES 4 A 720 THR ASN SER SER MET ASP TYR VAL LEU THR TYR ALA ASP SEQRES 5 A 720 ARG GLY PHE SER GLY ASN PRO TYR ALA ALA GLY MET ASP SEQRES 6 A 720 ARG THR TYR SER LEU ASP ALA LEU PRO GLN GLU TYR PRO SEQRES 7 A 720 SER LEU GLY THR GLY ASP TYR ARG ASN ILE ALA LEU ASN SEQRES 8 A 720 ILE LYS ASN GLU LYS GLY VAL GLU SER ALA ASP LEU LEU SEQRES 9 A 720 PHE LYS SER TYR GLU ILE ARG ASN GLY LYS TYR ARG LEU SEQRES 10 A 720 GLN GLY LEU PRO ALA VAL TRP ALA ASP GLU LYS GLU ALA SEQRES 11 A 720 GLN THR LEU GLU ILE VAL LEU ALA ASP GLU ASN ALA GLN SEQRES 12 A 720 VAL GLU VAL HIS LEU LEU TYR GLY VAL LEU GLU GLU ASN SEQRES 13 A 720 ASP VAL ILE THR ARG SER VAL ARG ILE LYS ASN THR GLY SEQRES 14 A 720 THR GLY GLN ILE THR ILE GLU LYS ALA ALA ALA ALA CYS SEQRES 15 A 720 LEU ASP PHE VAL GLN GLY GLU PHE ASP VAL LEU ARG PHE SEQRES 16 A 720 TYR GLY LYS HIS ALA MET GLU ARG ASN LEU GLU ARG THR SEQRES 17 A 720 PRO LEU GLY HIS GLY THR ILE ALA PHE GLY SER ARG ARG SEQRES 18 A 720 GLY THR SER SER HIS GLN TYR ASN PRO ALA VAL ILE LEU SEQRES 19 A 720 ALA GLU LYS GLY THR THR GLU THR ALA GLY SER CYS TYR SEQRES 20 A 720 GLY MET LEU PHE VAL TYR SER GLY ASN PHE SER CYS GLU SEQRES 21 A 720 ALA GLU LYS ASP GLN PHE ASN GLN THR ARG LEU LEU LEU SEQRES 22 A 720 GLY LEU ASN GLU GLU LEU PHE SER TYR PRO LEU ALA SER SEQRES 23 A 720 GLY GLU THR PHE THR VAL PRO GLU VAL ILE LEU SER TYR SEQRES 24 A 720 SER ALA GLU GLY LEU SER ALA LEU SER GLN GLN TYR HIS SEQRES 25 A 720 ASN CYS ILE ARG ASN HIS VAL CYS ARG SER LYS TYR VAL SEQRES 26 A 720 HIS MET GLN ARG PRO VAL LEU ILE ASN SER TRP GLU ALA SEQRES 27 A 720 ALA TYR PHE ASP PHE THR GLY ASP THR ILE VAL ASP LEU SEQRES 28 A 720 ALA LYS GLU ALA ALA SER LEU GLY ILE ASP MET VAL VAL SEQRES 29 A 720 MET ASP ASP GLY TRP PHE GLY LYS ARG ASN ASP ASP ASN SEQRES 30 A 720 SER SER LEU GLY ASP TRP GLN VAL ASN GLU THR LYS LEU SEQRES 31 A 720 GLY GLY SER LEU ALA GLU LEU ILE THR ARG VAL HIS GLU SEQRES 32 A 720 GLN GLY MET LYS PHE GLY ILE TRP ILE GLU PRO GLU MET SEQRES 33 A 720 ILE ASN GLU ASP SER ASP LEU TYR ARG ALA HIS PRO ASP SEQRES 34 A 720 TRP ALA ILE ARG ILE GLN GLY LYS LYS PRO VAL ARG SER SEQRES 35 A 720 ARG ASN GLN LEU LEU LEU ASP PHE SER ARG LYS GLU VAL SEQRES 36 A 720 ARG ASP CYS VAL PHE ASP GLN ILE CYS VAL VAL LEU ASP SEQRES 37 A 720 GLN GLY LYS ILE ASP TYR VAL LYS TRP ASP MET ASN ARG SEQRES 38 A 720 SER MET ALA ASP VAL TYR ALA GLY ASN LEU SER TYR ASP SEQRES 39 A 720 TYR VAL LEU GLY VAL TYR ASP PHE MET GLU ARG LEU CYS SEQRES 40 A 720 SER ARG TYR PRO ASP LEU LEU LEU GLU GLY CYS SER GLY SEQRES 41 A 720 GLY GLY GLY ARG PHE ASP ALA GLY MET LEU TYR TYR SER SEQRES 42 A 720 PRO GLN ILE TRP CYS SER ASP ASN THR ASP ALA ILE ASN SEQRES 43 A 720 ARG THR ARG ILE GLN TYR GLY THR SER PHE PHE TYR PRO SEQRES 44 A 720 VAL SER ALA MET GLY ALA HIS VAL SER ALA VAL PRO ASN SEQRES 45 A 720 HIS GLN THR GLY ARG VAL THR SER PHE HIS THR ARG GLY SEQRES 46 A 720 VAL THR ALA MET ALA GLY THR PHE GLY TYR GLU LEU ASN SEQRES 47 A 720 PRO ALA LEU LEU SER ASP GLU GLU LYS GLN GLN ILE ARG SEQRES 48 A 720 GLU GLN ILE LYS THR TYR LYS LYS TYR GLU THR LEU ILE SEQRES 49 A 720 ASN GLU GLY THR TYR TRP ARG LEU SER ASP PRO PHE THR SEQRES 50 A 720 ASP GLU ILE ALA ALA TRP MET SER VAL SER GLU GLU GLN SEQRES 51 A 720 ASP HIS ALA LEU VAL SER VAL VAL ARG LEU MET ALA GLU SEQRES 52 A 720 ALA ASN GLN ALA THR VAL TYR VAL ARG LEU ARG GLY LEU SEQRES 53 A 720 LYS PRO ASP ALA VAL TYR LEU GLU GLU GLN SER GLY ARG SEQRES 54 A 720 GLN TYR SER GLY ALA ALA LEU MET HIS ALA GLY ILE PRO SEQRES 55 A 720 LEU PRO PRO PHE THR GLU GLU TYR GLU ALA TYR GLN PHE SEQRES 56 A 720 ALA PHE THR GLU LEU HET GOL A1721 8 HET GOL A1722 6 HET EDO A1723 4 HET PO4 A1724 5 HET MG A1725 1 HET MG A1726 1 HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETNAM PO4 PHOSPHATE ION HETNAM MG MAGNESIUM ION HETSYN GOL GLYCERIN HETSYN EDO ETHYLENE GLYCOL FORMUL 2 GOL 2(C3 H8 O3) FORMUL 3 EDO C2 H6 O2 FORMUL 4 PO4 O4 P 3- FORMUL 5 MG 2(MG 2+) FORMUL 6 HOH *1058(H2 O) HELIX 1 1 MET A 44 LEU A 48 1 5 HELIX 2 2 TYR A 60 ALA A 62 5 3 HELIX 3 3 LEU A 304 HIS A 318 1 15 HELIX 4 4 LYS A 323 MET A 327 1 5 HELIX 5 5 TRP A 336 ALA A 338 5 3 HELIX 6 6 THR A 344 SER A 357 1 14 HELIX 7 7 GLU A 387 LEU A 390 1 4 HELIX 8 8 LEU A 394 GLN A 404 1 11 HELIX 9 9 ASP A 422 ALA A 426 1 5 HELIX 10 10 PRO A 428 TRP A 430 5 3 HELIX 11 11 LYS A 453 ASP A 468 1 16 HELIX 12 12 ASN A 490 TYR A 510 1 21 HELIX 13 13 ALA A 527 TYR A 532 1 6 HELIX 14 14 ALA A 544 SER A 555 1 12 HELIX 15 15 VAL A 560 ALA A 562 5 3 HELIX 16 16 PHE A 581 ALA A 590 1 10 HELIX 17 17 PRO A 599 LEU A 602 5 4 HELIX 18 18 ASP A 604 TYR A 620 1 17 HELIX 19 19 THR A 622 GLY A 627 1 6 HELIX 19 20 GLY A 693 ALA A 699 1 7 SHEET 1 AA 4 ILE A 3 ASN A 6 0 SHEET 2 AA 4 ILE A 11 HIS A 15 -1 O ILE A 11 N ASN A 6 SHEET 3 AA 4 THR A 19 VAL A 25 -1 O TYR A 21 N LEU A 14 SHEET 4 AA 4 LEU A 31 GLU A 38 -1 O LEU A 32 N GLN A 24 SHEET 1 AB 3 LEU A 90 LYS A 93 0 SHEET 2 AB 3 ILE A 173 ALA A 178 -1 O THR A 174 N LYS A 93 SHEET 3 AB 3 TYR A 282 LEU A 284 -1 O TYR A 282 N ILE A 175 SHEET 1 AC 4 ALA A 181 PHE A 185 0 SHEET 2 AC 4 THR A 269 GLY A 274 -1 N THR A 269 O PHE A 185 SHEET 3 AC 4 PHE A 257 LYS A 263 -1 N SER A 258 O GLY A 274 SHEET 4 AC 4 GLY A 213 SER A 219 -1 N GLY A 213 O LYS A 263 SHEET 1 AD 9 LEU A 104 ASN A 112 0 SHEET 2 AD 9 ALA A 130 ASP A 139 -1 O THR A 132 N ARG A 111 SHEET 3 AD 9 VAL A 144 LEU A 153 -1 O VAL A 144 N ASP A 139 SHEET 4 AD 9 VAL A 158 ASN A 167 -1 O VAL A 158 N LEU A 153 SHEET 5 AD 9 THR A 289 SER A 300 -1 O PHE A 290 N ILE A 165 SHEET 6 AD 9 CYS A 246 PHE A 251 -1 O CYS A 246 N SER A 300 SHEET 7 AD 9 ALA A 231 GLU A 236 -1 O VAL A 232 N MET A 249 SHEET 8 AD 9 PHE A 190 LYS A 198 -1 O ASP A 191 N ALA A 235 SHEET 9 AD 9 MET A 201 PRO A 209 -1 O MET A 201 N LYS A 198 SHEET 1 AE 8 VAL A 331 SER A 335 0 SHEET 2 AE 8 MET A 362 ASP A 366 1 O MET A 362 N ILE A 333 SHEET 3 AE 8 LYS A 407 GLU A 413 1 O LYS A 407 N VAL A 363 SHEET 4 AE 8 TYR A 474 MET A 479 1 O TYR A 474 N ILE A 410 SHEET 5 AE 8 LEU A 514 CYS A 518 1 O LEU A 514 N VAL A 475 SHEET 6 AE 8 GLN A 535 TRP A 537 1 O GLN A 535 N GLY A 517 SHEET 7 AE 8 MET A 563 SER A 568 1 N GLY A 564 O ILE A 536 SHEET 8 AE 8 THR A 592 GLU A 596 1 N THR A 592 O MET A 563 SHEET 1 AF 6 THR A 628 ARG A 631 0 SHEET 2 AF 6 ILE A 640 VAL A 646 -1 O MET A 644 N TRP A 630 SHEET 3 AF 6 HIS A 652 ARG A 659 -1 O LEU A 654 N SER A 645 SHEET 4 AF 6 GLU A 711 GLU A 719 -1 O GLU A 711 N ARG A 659 SHEET 5 AF 6 VAL A 681 GLU A 684 -1 O LEU A 683 N THR A 718 SHEET 6 AF 6 GLN A 690 SER A 692 -1 O TYR A 691 N TYR A 682 SHEET 1 AG 2 VAL A 669 ARG A 672 0 SHEET 2 AG 2 GLY A 700 LEU A 703 -1 N ILE A 701 O VAL A 671 LINK MG MG A1725 OE1 GLU A 176 1555 1555 2.94 LINK MG MG A1725 O GLU A 176 1555 1555 2.45 LINK MG MG A1725 O GLU A 277 1555 1555 2.41 LINK MG MG A1725 O PHE A 280 1555 1555 2.25 LINK MG MG A1725 O HOH A2513 1555 1555 2.51 LINK MG MG A1725 O HOH A2516 1555 1555 2.65 LINK MG MG A1726 O HOH A2521 1555 2655 2.46 LINK MG MG A1726 O HOH A2527 1555 1555 2.11 LINK MG MG A1726 O HOH A2511 1555 1555 1.97 LINK MG MG A1726 O HOH A2519 1555 1555 2.12 LINK MG MG A1726 O HOH A2177 1555 1555 2.10 LINK MG MG A1726 O HOH A2521 1555 1555 2.43 CISPEP 1 VAL A 570 PRO A 571 0 -6.12 SITE 1 AC1 12 GLY A 81 THR A 82 GLY A 83 ASP A 84 SITE 2 AC1 12 TYR A 85 ARG A 220 ALA A 484 ASP A 485 SITE 3 AC1 12 VAL A 486 HOH A2183 HOH A2209 HOH A3051 SITE 1 AC2 8 TYR A 36 GLN A 187 GLU A 236 TYR A 247 SITE 2 AC2 8 ARG A 672 HIS A 698 HOH A2457 HOH A3052 SITE 1 AC3 4 PRO A 27 ASP A 65 HOH A2134 HOH A3053 SITE 1 AC4 6 ARG A 111 TYR A 115 ARG A 116 ARG A 164 SITE 2 AC4 6 HOH A3055 HOH A3057 SITE 1 AC5 5 GLU A 176 GLU A 277 PHE A 280 HOH A2513 SITE 2 AC5 5 HOH A2516 SITE 1 AC6 6 GLU A 277 HOH A2177 HOH A2511 HOH A2519 SITE 2 AC6 6 HOH A2521 HOH A2527 CRYST1 105.058 111.650 154.886 90.00 90.00 90.00 I 2 2 2 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 0.009519 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008957 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006456 0.00000