HEADER HYDROLASE 02-DEC-14 4X4A TITLE CRYSTAL STRUCTURE OF THE INTRAMOLECULAR TRANS-SIALIDASE FROM TITLE 2 RUMINOCOCCUS GNAVUS IN COMPLEX WITH 2,7-ANHYDRO-NEU5AC COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANHYDROSIALIDASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 243-723; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RUMINOCOCCUS GNAVUS ATCC 29149; SOURCE 3 ORGANISM_TAXID: 411470; SOURCE 4 GENE: HMPREF1201_01421; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INTRAMOLECULAR, TRANS-SIALIDASE, SIALIDASE, NEURAMINIDASE, 2-7- KEYWDS 2 ANHYDRO-NEU5AC, REACTION PRODUCT, HYDROLASE, ANHYDROSIALDIASE EXPDTA X-RAY DIFFRACTION AUTHOR C.D.OWEN,L.E.TAILFORD,G.L.TAYLOR,N.JUGE REVDAT 4 08-MAY-24 4X4A 1 REMARK REVDAT 3 21-NOV-18 4X4A 1 SOURCE REVDAT 2 30-AUG-17 4X4A 1 REMARK SITE ATOM REVDAT 1 22-JUL-15 4X4A 0 JRNL AUTH L.E.TAILFORD,C.D.OWEN,J.WALSHAW,E.H.CROST,J.HARDY-GODDARD, JRNL AUTH 2 G.LE GALL,W.M.DE VOS,G.L.TAYLOR,N.JUGE JRNL TITL DISCOVERY OF INTRAMOLECULAR TRANS-SIALIDASES IN HUMAN GUT JRNL TITL 2 MICROBIOTA SUGGESTS NOVEL MECHANISMS OF MUCOSAL ADAPTATION. JRNL REF NAT COMMUN V. 6 7624 2015 JRNL REFN ESSN 2041-1723 JRNL PMID 26154892 JRNL DOI 10.1038/NCOMMS8624 REMARK 2 REMARK 2 RESOLUTION. 1.71 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 45702 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) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 2250 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) : 1.71 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.76 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2015 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 54.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE SET COUNT : 86 REMARK 3 BIN FREE R VALUE : 0.2960 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3779 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 529 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.73000 REMARK 3 B22 (A**2) : 0.73000 REMARK 3 B33 (A**2) : -2.36000 REMARK 3 B12 (A**2) : 0.36000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.101 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.104 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.077 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.420 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.980 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3972 ; 0.019 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 3589 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5397 ; 1.891 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8308 ; 0.883 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 497 ; 7.781 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 185 ;37.169 ;25.459 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 644 ;12.388 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;18.251 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 577 ; 0.122 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4594 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 898 ; 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): 1974 ; 2.516 ; 2.755 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1975 ; 2.515 ; 2.756 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2475 ; 3.238 ; 4.121 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 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 : 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4X4A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1000205061. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-AUG-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48126 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.710 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.71 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 53.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.42100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PHASER 2.5.6 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MICRO SEEDING INTO 0.8 M NAH2PO4, 1.2M REMARK 280 K2HPO4, SODIUM ACETATE 0.1M PH 4.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 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 49.62850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.65303 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 43.53300 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 49.62850 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 28.65303 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 43.53300 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 49.62850 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 28.65303 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 43.53300 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 57.30606 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 87.06600 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 57.30606 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 87.06600 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 57.30606 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 87.06600 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 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 GLY A 235 REMARK 465 ASP A 239 REMARK 465 ILE A 240 REMARK 465 GLY A 241 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 HOH A 971 O HOH A 1080 1.54 REMARK 500 O HOH A 914 O HOH A 1166 1.59 REMARK 500 O HOH A 1217 O HOH A 1312 1.60 REMARK 500 O HOH A 1193 O HOH A 1311 1.61 REMARK 500 O HOH A 1002 O HOH A 1340 1.64 REMARK 500 O HOH A 1161 O HOH A 1345 1.68 REMARK 500 O HOH A 1132 O HOH A 1328 1.69 REMARK 500 O HOH A 960 O HOH A 1166 1.85 REMARK 500 O HOH A 1142 O HOH A 1346 1.88 REMARK 500 O HOH A 922 O HOH A 1242 1.94 REMARK 500 O HOH A 949 O HOH A 963 1.94 REMARK 500 O HOH A 962 O HOH A 1389 1.96 REMARK 500 O HOH A 966 O HOH A 1162 1.98 REMARK 500 O HOH A 964 O HOH A 1311 1.99 REMARK 500 O HOH A 1284 O HOH A 1307 2.00 REMARK 500 O HOH A 1184 O HOH A 1323 2.02 REMARK 500 O HOH A 1025 O HOH A 1191 2.02 REMARK 500 O HOH A 910 O HOH A 1126 2.10 REMARK 500 O HOH A 1250 O HOH A 1340 2.13 REMARK 500 O HOH A 1042 O HOH A 1363 2.14 REMARK 500 O HOH A 1030 O HOH A 1332 2.15 REMARK 500 O HOH A 1206 O HOH A 1224 2.15 REMARK 500 O HOH A 1266 O HOH A 1364 2.18 REMARK 500 O HOH A 905 O HOH A 1080 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 OH TYR A 394 OE1 GLN A 551 2645 1.86 REMARK 500 O HOH A 969 O HOH A 1312 2645 2.09 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 274 CB - CG - OD1 ANGL. DEV. = 8.4 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 ILE A 258 67.38 74.25 REMARK 500 SER A 285 -164.85 -167.88 REMARK 500 ASP A 339 79.70 72.65 REMARK 500 TYR A 394 78.70 -117.52 REMARK 500 ASN A 426 55.76 35.67 REMARK 500 SER A 491 35.37 -92.86 REMARK 500 SER A 528 -165.57 -166.75 REMARK 500 GLU A 531 -72.90 -109.11 REMARK 500 ASP A 669 -169.82 -161.29 REMARK 500 SER A 676 -115.44 -113.92 REMARK 500 LYS A 694 59.29 -97.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1426 DISTANCE = 6.19 ANGSTROMS REMARK 525 HOH A1427 DISTANCE = 6.44 ANGSTROMS REMARK 525 HOH A1428 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH A1429 DISTANCE = 6.93 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SKD A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 804 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 805 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACE A 806 DBREF 4X4A A 243 723 UNP V8BWT1 V8BWT1_RUMGN 243 723 SEQADV 4X4A GLY A 235 UNP V8BWT1 EXPRESSION TAG SEQADV 4X4A ALA A 236 UNP V8BWT1 EXPRESSION TAG SEQADV 4X4A MET A 237 UNP V8BWT1 EXPRESSION TAG SEQADV 4X4A ALA A 238 UNP V8BWT1 EXPRESSION TAG SEQADV 4X4A ASP A 239 UNP V8BWT1 EXPRESSION TAG SEQADV 4X4A ILE A 240 UNP V8BWT1 EXPRESSION TAG SEQADV 4X4A GLY A 241 UNP V8BWT1 EXPRESSION TAG SEQADV 4X4A SER A 242 UNP V8BWT1 EXPRESSION TAG SEQRES 1 A 489 GLY ALA MET ALA ASP ILE GLY SER ASN ILE PHE TYR ALA SEQRES 2 A 489 GLY ASP ALA THR LYS SER ASN TYR PHE ARG ILE PRO SER SEQRES 3 A 489 LEU LEU ALA LEU ASP SER GLY THR VAL ILE ALA ALA ALA SEQRES 4 A 489 ASP ALA ARG TYR GLY GLY THR HIS ASP ALA LYS SER LYS SEQRES 5 A 489 ILE ASN THR ALA PHE ALA LYS SER THR ASP GLY GLY LYS SEQRES 6 A 489 THR TRP GLY GLN PRO THR LEU PRO LEU LYS PHE ASP ASP SEQRES 7 A 489 TYR VAL ALA LYS ASN ILE ASP TRP PRO ARG ASP SER VAL SEQRES 8 A 489 GLY LYS ASN VAL GLN ILE GLN GLY SER ALA SER TYR ILE SEQRES 9 A 489 ASP PRO VAL LEU LEU GLU ASP LYS GLU THR HIS ARG VAL SEQRES 10 A 489 PHE LEU PHE ALA ASP MET MET PRO ALA GLY ILE GLY SER SEQRES 11 A 489 SER ASN ALA SER VAL GLY SER GLY PHE LYS GLU VAL ASP SEQRES 12 A 489 GLY LYS LYS TYR LEU LYS LEU HIS TRP LYS ASP ASP ALA SEQRES 13 A 489 ALA GLY THR TYR ASP TYR SER VAL ARG GLU ASN GLY THR SEQRES 14 A 489 ILE TYR ASN ASP THR THR ASN SER ALA THR GLU TYR SER SEQRES 15 A 489 VAL ASP GLY GLU TYR ASN LEU TYR LYS ASN GLY ASN ALA SEQRES 16 A 489 MET LEU CYS LYS GLN TYR ASP TYR ASN PHE GLU GLY THR SEQRES 17 A 489 LYS LEU LEU GLU THR GLN THR ASP THR ASP VAL ASN MET SEQRES 18 A 489 ASN VAL PHE TYR LYS ASP ALA ASP PHE LYS VAL PHE PRO SEQRES 19 A 489 THR THR TYR LEU ALA MET LYS TYR SER ASP ASP GLU GLY SEQRES 20 A 489 GLU THR TRP SER ASP LEU GLN ILE VAL SER THR PHE LYS SEQRES 21 A 489 PRO GLU GLU SER LYS PHE LEU VAL LEU GLY PRO GLY VAL SEQRES 22 A 489 GLY LYS GLN ILE ALA ASN GLY GLU HIS ALA GLY ARG LEU SEQRES 23 A 489 ILE VAL PRO LEU TYR SER LYS SER SER ALA GLU LEU GLY SEQRES 24 A 489 PHE MET TYR SER ASP ASP HIS GLY ASN ASN TRP THR TYR SEQRES 25 A 489 VAL GLU ALA ASP GLN ASN THR GLY GLY ALA THR ALA GLU SEQRES 26 A 489 ALA GLN ILE VAL GLU MET PRO ASP GLY SER LEU LYS THR SEQRES 27 A 489 TYR LEU ARG THR GLY SER GLY TYR ILE ALA GLN VAL MET SEQRES 28 A 489 SER THR ASP GLY GLY GLU THR TRP SER GLU ARG VAL PRO SEQRES 29 A 489 LEU THR GLU ILE ALA THR THR GLY TYR GLY THR GLN LEU SEQRES 30 A 489 SER VAL ILE ASN TYR SER GLN PRO VAL ASP GLY LYS PRO SEQRES 31 A 489 ALA ILE LEU LEU SER ALA PRO ASN ALA THR ASN GLY ARG SEQRES 32 A 489 LYS ASN GLY LYS ILE TRP ILE GLY LEU ILE SER GLU THR SEQRES 33 A 489 GLY ASN SER GLY LYS ASP LYS TYR SER VAL ASP TRP LYS SEQRES 34 A 489 TYR CYS TYR SER VAL ASP THR PRO GLN MET GLY TYR SER SEQRES 35 A 489 TYR SER CYS LEU THR GLU LEU PRO ASP GLY GLU ILE GLY SEQRES 36 A 489 LEU LEU TYR GLU LYS TYR ASP SER TRP SER ARG ASN GLU SEQRES 37 A 489 LEU HIS LEU LYS ASN ILE LEU LYS TYR GLU ARG PHE ASN SEQRES 38 A 489 ILE ASP GLU LEU LYS VAL GLN PRO HET SKD A 801 20 HET GOL A 802 6 HET GOL A 803 6 HET GOL A 804 6 HET PO4 A 805 5 HET ACE A 806 3 HETNAM SKD 2-ACETYLAMINO-7-(1,2-DIHYDROXY-ETHYL)-3-HYDROXY-6,8- HETNAM 2 SKD DIOXA-BICYCLO[3.2.1]OCTANE-5-CARBOXYLIC ACID HETNAM GOL GLYCEROL HETNAM PO4 PHOSPHATE ION HETNAM ACE ACETYL GROUP HETSYN SKD 2,7-ANHYDRO-NEU5AC HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 SKD C11 H17 N O8 FORMUL 3 GOL 3(C3 H8 O3) FORMUL 6 PO4 O4 P 3- FORMUL 7 ACE C2 H4 O FORMUL 8 HOH *529(H2 O) HELIX 1 AA1 VAL A 325 VAL A 329 5 5 HELIX 2 AA2 GLY A 363 ALA A 367 5 5 HELIX 3 AA3 SER A 491 LYS A 494 5 4 HELIX 4 AA4 SER A 653 ASP A 656 5 4 HELIX 5 AA5 ASN A 715 LYS A 720 1 6 SHEET 1 AA1 4 TYR A 255 ALA A 263 0 SHEET 2 AA1 4 VAL A 269 ARG A 276 -1 O ILE A 270 N LEU A 262 SHEET 3 AA1 4 ILE A 287 SER A 294 -1 O ASN A 288 N ALA A 275 SHEET 4 AA1 4 THR A 305 LEU A 308 -1 O LEU A 308 N THR A 289 SHEET 1 AA2 5 GLN A 488 ILE A 489 0 SHEET 2 AA2 5 TYR A 471 SER A 477 -1 N MET A 474 O GLN A 488 SHEET 3 AA2 5 ARG A 350 MET A 358 -1 N ALA A 355 O ALA A 473 SHEET 4 AA2 5 SER A 336 ASP A 345 -1 N SER A 336 O MET A 358 SHEET 5 AA2 5 GLY A 506 VAL A 507 1 O GLY A 506 N PRO A 340 SHEET 1 AA3 7 PHE A 373 VAL A 376 0 SHEET 2 AA3 7 LYS A 379 TRP A 386 -1 O LYS A 379 N VAL A 376 SHEET 3 AA3 7 TYR A 396 VAL A 398 -1 O TYR A 396 N LEU A 384 SHEET 4 AA3 7 THR A 403 ASN A 406 -1 O TYR A 405 N SER A 397 SHEET 5 AA3 7 SER A 411 VAL A 417 -1 O THR A 413 N ILE A 404 SHEET 6 AA3 7 LEU A 423 LYS A 425 -1 O TYR A 424 N SER A 416 SHEET 7 AA3 7 ASN A 428 ALA A 429 -1 O ASN A 428 N LYS A 425 SHEET 1 AA4 3 PHE A 373 VAL A 376 0 SHEET 2 AA4 3 LYS A 379 TRP A 386 -1 O LYS A 379 N VAL A 376 SHEET 3 AA4 3 PHE A 464 VAL A 466 -1 O LYS A 465 N HIS A 385 SHEET 1 AA5 2 LEU A 431 GLU A 440 0 SHEET 2 AA5 2 LYS A 443 ASN A 454 -1 O LEU A 445 N ASN A 438 SHEET 1 AA6 3 PHE A 500 LEU A 503 0 SHEET 2 AA6 3 LEU A 520 LYS A 527 -1 O TYR A 525 N VAL A 502 SHEET 3 AA6 3 LYS A 509 GLN A 510 -1 N LYS A 509 O ILE A 521 SHEET 1 AA7 4 PHE A 500 LEU A 503 0 SHEET 2 AA7 4 LEU A 520 LYS A 527 -1 O TYR A 525 N VAL A 502 SHEET 3 AA7 4 LEU A 532 SER A 537 -1 O MET A 535 N VAL A 522 SHEET 4 AA7 4 THR A 545 GLU A 548 -1 O VAL A 547 N PHE A 534 SHEET 1 AA8 4 ALA A 560 GLU A 564 0 SHEET 2 AA8 4 LEU A 570 LEU A 574 -1 O LYS A 571 N VAL A 563 SHEET 3 AA8 4 ILE A 581 SER A 586 -1 O VAL A 584 N THR A 572 SHEET 4 AA8 4 VAL A 597 LEU A 599 -1 O LEU A 599 N ILE A 581 SHEET 1 AA9 4 SER A 612 VAL A 620 0 SHEET 2 AA9 4 LYS A 623 ALA A 630 -1 O SER A 629 N SER A 612 SHEET 3 AA9 4 LYS A 641 GLU A 649 -1 O TRP A 643 N LEU A 628 SHEET 4 AA9 4 TYR A 658 SER A 667 -1 O SER A 659 N SER A 648 SHEET 1 AB1 3 SER A 678 GLU A 682 0 SHEET 2 AB1 3 ILE A 688 GLU A 693 -1 O GLY A 689 N THR A 681 SHEET 3 AB1 3 LEU A 709 PHE A 714 -1 O PHE A 714 N ILE A 688 CISPEP 1 ALA A 283 LYS A 284 0 0.86 SITE 1 AC1 17 ARG A 257 ILE A 258 ARG A 276 ASP A 282 SITE 2 AC1 17 ASP A 339 ASP A 356 SER A 364 THR A 557 SITE 3 AC1 17 GLU A 559 ARG A 575 ARG A 637 TYR A 677 SITE 4 AC1 17 TRP A 698 HOH A1037 HOH A 935 HOH A 910 SITE 5 AC1 17 HOH A1126 SITE 1 AC2 7 LYS A 309 PHE A 310 ASP A 311 TYR A 337 SITE 2 AC2 7 GLU A 420 TYR A 459 LEU A 487 SITE 1 AC3 6 SER A 477 ASP A 478 ASP A 479 THR A 483 SITE 2 AC3 6 HOH A 933 HOH A1063 SITE 1 AC4 7 SER A 242 LYS A 299 GLU A 400 TYR A 711 SITE 2 AC4 7 ARG A 713 HOH A1195 HOH A 907 SITE 1 AC5 9 GLU A 531 ASN A 552 ALA A 556 THR A 576 SITE 2 AC5 9 GLY A 577 SER A 578 ARG A 596 HOH A1065 SITE 3 AC5 9 HOH A1143 SITE 1 AC6 3 LYS A 460 ASP A 461 GLU A 595 CRYST1 99.257 99.257 130.599 90.00 90.00 120.00 H 3 9 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 0.010075 0.005817 0.000000 0.00000 SCALE2 0.000000 0.011633 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007657 0.00000