HEADER HYDROLASE 25-DEC-17 5Z1A TITLE THE CRYSTAL STRUCTURE OF BACTEROIDES FRAGILIS BETA-GLUCURONIDASE IN TITLE 2 COMPLEX WITH URONIC ISOFAGOMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE BETA-GALACTOSIDASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 38-690; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES FRAGILIS NCTC 9343; SOURCE 3 ORGANISM_TAXID: 272559; SOURCE 4 STRAIN: NCTC 9343; SOURCE 5 GENE: BF9343_0320; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA-GLUCURONIDASE, GH2, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.DASHNYAM,H.Y.LIN,C.H.LIN REVDAT 2 27-MAR-24 5Z1A 1 REMARK REVDAT 1 12-DEC-18 5Z1A 0 JRNL AUTH P.DASHNYAM,R.MUDUDUDDLA,T.J.HSIEH,T.C.LIN,H.Y.LIN,P.Y.CHEN, JRNL AUTH 2 C.Y.HSU,C.H.LIN JRNL TITL DISSECTION OF THE SUBSTRATE PREFERENCE AND STRUCTURE OF GUT JRNL TITL 2 MICROBIAL-GLUCURONIDASES IDENTIFIES THE MAJOR BACTERIA JRNL TITL 3 CAUSING XENOBIOTIC TOXICITY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 66841 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.990 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.4026 - 4.4767 0.99 5012 154 0.1442 0.1659 REMARK 3 2 4.4767 - 3.5553 0.97 4742 147 0.1322 0.1556 REMARK 3 3 3.5553 - 3.1064 0.99 4816 148 0.1427 0.1502 REMARK 3 4 3.1064 - 2.8226 1.00 4837 150 0.1518 0.2011 REMARK 3 5 2.8226 - 2.6205 1.00 4802 148 0.1516 0.2106 REMARK 3 6 2.6205 - 2.4660 1.00 4817 149 0.1575 0.2286 REMARK 3 7 2.4660 - 2.3426 1.00 4794 147 0.1538 0.1724 REMARK 3 8 2.3426 - 2.2407 1.00 4766 147 0.1754 0.2263 REMARK 3 9 2.2407 - 2.1544 1.00 4804 149 0.1644 0.2300 REMARK 3 10 2.1544 - 2.0801 0.99 4750 146 0.1593 0.2105 REMARK 3 11 2.0801 - 2.0151 0.97 4637 143 0.1612 0.2076 REMARK 3 12 2.0151 - 1.9575 0.93 4424 136 0.1697 0.2121 REMARK 3 13 1.9575 - 1.9060 0.84 4025 125 0.2099 0.3186 REMARK 3 14 1.9060 - 1.8595 0.76 3615 111 0.2186 0.2209 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.000 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 5479 REMARK 3 ANGLE : 1.251 7435 REMARK 3 CHIRALITY : 0.060 776 REMARK 3 PLANARITY : 0.007 972 REMARK 3 DIHEDRAL : 13.229 2022 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5Z1A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1300006265. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68429 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.859 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.39100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 250MM DL-MALIC ACID, PH 7.0, 20%(W/V) REMARK 280 PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277.15K 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 40.12650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.56750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 99.57350 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.12650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.56750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 99.57350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.12650 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 51.56750 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 99.57350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 40.12650 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 51.56750 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 99.57350 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 91720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 206.27000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 206.27000 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 A1039 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1303 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1490 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1529 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 16 REMARK 465 GLY A 17 REMARK 465 SER A 18 REMARK 465 SER A 19 REMARK 465 HIS A 20 REMARK 465 HIS A 21 REMARK 465 HIS A 22 REMARK 465 HIS A 23 REMARK 465 HIS A 24 REMARK 465 HIS A 25 REMARK 465 SER A 26 REMARK 465 SER A 27 REMARK 465 GLY A 28 REMARK 465 LEU A 29 REMARK 465 VAL A 30 REMARK 465 PRO A 31 REMARK 465 ARG A 32 REMARK 465 GLY A 33 REMARK 465 SER A 34 REMARK 465 MET A 35 REMARK 465 GLU A 691 REMARK 465 ASP A 692 REMARK 465 ARG A 693 REMARK 465 GLU A 694 REMARK 465 GLY A 695 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 1521 O HOH A 1534 1.84 REMARK 500 O HOH A 1572 O HOH A 1602 1.85 REMARK 500 O HOH A 915 O HOH A 1536 1.89 REMARK 500 O LYS A 679 O HOH A 801 1.90 REMARK 500 O HOH A 810 O HOH A 1092 1.93 REMARK 500 O HOH A 1133 O HOH A 1216 1.95 REMARK 500 O HOH A 1567 O HOH A 1612 1.96 REMARK 500 O HOH A 847 O HOH A 1466 2.03 REMARK 500 O HOH A 977 O HOH A 1281 2.04 REMARK 500 O HOH A 999 O HOH A 1346 2.04 REMARK 500 O HOH A 854 O HOH A 1083 2.05 REMARK 500 O HOH A 801 O HOH A 810 2.05 REMARK 500 O HOH A 1590 O HOH A 1593 2.07 REMARK 500 O HOH A 1555 O HOH A 1615 2.07 REMARK 500 O HOH A 1040 O HOH A 1281 2.07 REMARK 500 OE1 GLU A 472 O HOH A 802 2.08 REMARK 500 O HOH A 1327 O HOH A 1338 2.09 REMARK 500 O HOH A 1056 O HOH A 1450 2.10 REMARK 500 NH1 ARG A 300 O PRO A 419 2.10 REMARK 500 O HOH A 1328 O HOH A 1525 2.13 REMARK 500 O HOH A 1450 O HOH A 1493 2.13 REMARK 500 O HOH A 1445 O HOH A 1456 2.16 REMARK 500 O LYS A 690 O HOH A 803 2.16 REMARK 500 O HOH A 1564 O HOH A 1618 2.18 REMARK 500 O HOH A 1324 O HOH A 1528 2.18 REMARK 500 O HOH A 1250 O HOH A 1433 2.18 REMARK 500 O HOH A 1155 O HOH A 1402 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 1456 O HOH A 1535 7545 1.83 REMARK 500 O HOH A 1265 O HOH A 1417 8575 1.86 REMARK 500 O HOH A 997 O HOH A 1393 2585 2.15 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 ARG A 300 CG ARG A 300 CD -0.157 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 300 NH1 - CZ - NH2 ANGL. DEV. = 7.9 DEGREES REMARK 500 ARG A 300 NE - CZ - NH1 ANGL. DEV. = -15.4 DEGREES REMARK 500 ARG A 300 NE - CZ - NH2 ANGL. DEV. = 6.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 46 74.96 58.19 REMARK 500 ASP A 79 50.06 -102.39 REMARK 500 ASP A 223 133.56 -38.37 REMARK 500 ASP A 273 83.56 -167.80 REMARK 500 GLN A 326 43.07 -91.51 REMARK 500 GLU A 330 -35.06 72.16 REMARK 500 PRO A 382 45.69 -83.80 REMARK 500 ASP A 391 -156.27 69.31 REMARK 500 ASP A 452 88.55 -156.21 REMARK 500 TYR A 483 35.60 -91.18 REMARK 500 SER A 485 -157.76 63.85 REMARK 500 ASP A 582 33.10 -99.08 REMARK 500 ASN A 605 70.96 -116.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 GLN A 201 0.10 SIDE CHAIN 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 A1632 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH A1633 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A1634 DISTANCE = 6.07 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SJ5 A 701 DBREF 5Z1A A 38 690 UNP Q5LIC7 Q5LIC7_BACFN 38 690 SEQADV 5Z1A MET A 16 UNP Q5LIC7 INITIATING METHIONINE SEQADV 5Z1A GLY A 17 UNP Q5LIC7 EXPRESSION TAG SEQADV 5Z1A SER A 18 UNP Q5LIC7 EXPRESSION TAG SEQADV 5Z1A SER A 19 UNP Q5LIC7 EXPRESSION TAG SEQADV 5Z1A HIS A 20 UNP Q5LIC7 EXPRESSION TAG SEQADV 5Z1A HIS A 21 UNP Q5LIC7 EXPRESSION TAG SEQADV 5Z1A HIS A 22 UNP Q5LIC7 EXPRESSION TAG SEQADV 5Z1A HIS A 23 UNP Q5LIC7 EXPRESSION TAG SEQADV 5Z1A HIS A 24 UNP Q5LIC7 EXPRESSION TAG SEQADV 5Z1A HIS A 25 UNP Q5LIC7 EXPRESSION TAG SEQADV 5Z1A SER A 26 UNP Q5LIC7 EXPRESSION TAG SEQADV 5Z1A SER A 27 UNP Q5LIC7 EXPRESSION TAG SEQADV 5Z1A GLY A 28 UNP Q5LIC7 EXPRESSION TAG SEQADV 5Z1A LEU A 29 UNP Q5LIC7 EXPRESSION TAG SEQADV 5Z1A VAL A 30 UNP Q5LIC7 EXPRESSION TAG SEQADV 5Z1A PRO A 31 UNP Q5LIC7 EXPRESSION TAG SEQADV 5Z1A ARG A 32 UNP Q5LIC7 EXPRESSION TAG SEQADV 5Z1A GLY A 33 UNP Q5LIC7 EXPRESSION TAG SEQADV 5Z1A SER A 34 UNP Q5LIC7 EXPRESSION TAG SEQADV 5Z1A MET A 35 UNP Q5LIC7 EXPRESSION TAG SEQADV 5Z1A SER A 36 UNP Q5LIC7 EXPRESSION TAG SEQADV 5Z1A LEU A 37 UNP Q5LIC7 EXPRESSION TAG SEQADV 5Z1A GLU A 691 UNP Q5LIC7 EXPRESSION TAG SEQADV 5Z1A ASP A 692 UNP Q5LIC7 EXPRESSION TAG SEQADV 5Z1A ARG A 693 UNP Q5LIC7 EXPRESSION TAG SEQADV 5Z1A GLU A 694 UNP Q5LIC7 EXPRESSION TAG SEQADV 5Z1A GLY A 695 UNP Q5LIC7 EXPRESSION TAG SEQRES 1 A 680 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 680 LEU VAL PRO ARG GLY SER MET SER LEU ARG GLN ASP ILE SEQRES 3 A 680 LEU LEU ASN ASN ASN TRP ASN PHE ARG PHE SER HIS GLN SEQRES 4 A 680 VAL GLN GLY ASP THR ARG ARG VAL ASP LEU PRO HIS THR SEQRES 5 A 680 TRP ASN ALA GLN ASP ALA LEU ALA GLY LYS ILE ASP TYR SEQRES 6 A 680 LYS ARG GLY ILE GLY ASN TYR GLU LYS ALA LEU TYR ILE SEQRES 7 A 680 ARG PRO GLU TRP LYS GLY LYS ARG LEU PHE LEU ARG PHE SEQRES 8 A 680 ASP GLY VAL ASN SER ILE ALA ASP VAL PHE ILE ASN ARG SEQRES 9 A 680 LYS HIS ILE GLY GLU HIS ARG GLY GLY TYR GLY ALA PHE SEQRES 10 A 680 ILE PHE GLU ILE THR ASP LEU VAL LYS TYR GLY GLU LYS SEQRES 11 A 680 ASN SER VAL LEU VAL ARG ALA ASN ASN GLY GLU GLN LEU SEQRES 12 A 680 ASP ILE MET PRO LEU VAL GLY ASP PHE ASN PHE TYR GLY SEQRES 13 A 680 GLY ILE TYR ARG ASP VAL HIS LEU LEU ILE THR ASP GLU SEQRES 14 A 680 THR CYS ILE SER PRO LEU ASP TYR ALA SER PRO GLY VAL SEQRES 15 A 680 TYR LEU VAL GLN GLU VAL VAL SER PRO GLN GLU ALA LYS SEQRES 16 A 680 VAL CYS ALA LYS VAL ASN LEU SER ASN ARG ALA ALA ASP SEQRES 17 A 680 GLY THR ALA GLU LEU GLN VAL LEU VAL THR ASP GLY THR SEQRES 18 A 680 LYS VAL ILE CYS LYS GLU SER ARG ASN VAL SER LEU LYS SEQRES 19 A 680 GLN GLY ALA ASP ILE LEU GLU GLN LEU PRO LEU LEU ILE SEQRES 20 A 680 GLN LYS PRO ARG LEU TRP ASN GLY CYS GLU ASP PRO PHE SEQRES 21 A 680 MET TYR GLN VAL SER ILE SER LEU HIS LYS ASP GLY LYS SEQRES 22 A 680 GLN ILE ASP SER VAL THR GLN PRO LEU GLY LEU ARG TYR SEQRES 23 A 680 TYR HIS THR ASP PRO ASP LYS GLY PHE PHE LEU ASN GLY SEQRES 24 A 680 LYS HIS LEU PRO LEU HIS GLY VAL CYS ARG HIS GLN ASP SEQRES 25 A 680 ARG ALA GLU VAL GLY ASN ALA LEU ARG PRO GLN HIS HIS SEQRES 26 A 680 GLU GLU ASP VAL ALA LEU MET ARG GLU MET GLY VAL ASN SEQRES 27 A 680 ALA ILE ARG LEU ALA HIS TYR PRO GLN ALA THR TYR MET SEQRES 28 A 680 TYR ASP LEU MET ASP LYS HIS GLY ILE VAL THR TRP ALA SEQRES 29 A 680 GLU ILE PRO PHE VAL GLY PRO GLY GLY TYR ALA ASP LYS SEQRES 30 A 680 GLY PHE VAL ASP GLN ALA SER PHE ARG GLU ASN GLY LYS SEQRES 31 A 680 GLN GLN LEU ILE GLU LEU ILE ARG GLN HIS TYR ASN HIS SEQRES 32 A 680 PRO SER ILE CYS PHE TRP GLY LEU PHE ASN GLU LEU LYS SEQRES 33 A 680 GLU VAL GLY ASP ASN PRO VAL GLU TYR VAL LYS GLU LEU SEQRES 34 A 680 ASN ALA LEU ALA LYS GLN GLU ASP PRO THR ARG PRO THR SEQRES 35 A 680 THR SER ALA SER ASN GLN ASP GLY ASN LEU ASN PHE ILE SEQRES 36 A 680 THR GLU ASN ILE ALA TRP ASN ARG TYR ASP GLY TRP TYR SEQRES 37 A 680 GLY SER THR PRO LYS THR LEU ALA THR PHE LEU ASP ARG SEQRES 38 A 680 THR HIS LYS LYS HIS PRO GLU LEU ARG ILE GLY ILE SER SEQRES 39 A 680 GLU TYR GLY ALA GLY ALA SER ILE TYR HIS GLN GLN ASP SEQRES 40 A 680 SER LEU LYS GLN PRO SER ALA SER GLY TRP TRP HIS PRO SEQRES 41 A 680 GLU ASN TRP GLN THR TYR TYR HIS MET GLU ASN TRP LYS SEQRES 42 A 680 ILE ILE ALA GLU ARG PRO PHE VAL TRP GLY THR PHE VAL SEQRES 43 A 680 TRP ASN MET PHE ASP PHE GLY ALA ALA HIS ARG THR GLU SEQRES 44 A 680 GLY ASP ARG PRO GLY ILE ASN ASP LYS GLY LEU VAL THR SEQRES 45 A 680 PHE ASP ARG LYS VAL ARG LYS ASP ALA PHE TYR PHE TYR SEQRES 46 A 680 LYS ALA ASN TRP ASN LYS GLN GLU PRO MET ILE TYR LEU SEQRES 47 A 680 ALA GLU LYS ARG CYS ARG LEU ARG TYR GLN PRO GLU GLN SEQRES 48 A 680 THR PHE MET ALA PHE THR THR ALA PRO GLU ALA GLU LEU SEQRES 49 A 680 PHE VAL ASN GLY VAL SER CYS GLY LYS GLN LYS ALA ASP SEQRES 50 A 680 THR TYR SER THR VAL VAL TRP LYS ASN VAL LYS LEU THR SEQRES 51 A 680 SER GLY GLU ASN ILE ILE ARG VAL THR THR PRO GLY LYS SEQRES 52 A 680 LYS PRO LEU THR ASP GLU VAL THR VAL GLU TYR LYS GLU SEQRES 53 A 680 ASP ARG GLU GLY HET SJ5 A 701 11 HETNAM SJ5 (3S,4R,5R)-4,5-DIHYDROXYPIPERIDINE-3-CARBOXYLIC ACID FORMUL 2 SJ5 C6 H11 N O4 FORMUL 3 HOH *834(H2 O) HELIX 1 AA1 ASP A 72 GLY A 76 5 5 HELIX 2 AA2 ARG A 94 LYS A 98 5 5 HELIX 3 AA3 ASN A 269 ASP A 273 5 5 HELIX 4 AA4 ARG A 336 MET A 350 1 15 HELIX 5 AA5 ALA A 363 GLY A 374 1 12 HELIX 6 AA6 GLN A 397 HIS A 415 1 19 HELIX 7 AA7 PRO A 437 ASP A 452 1 16 HELIX 8 AA8 GLY A 465 ILE A 470 5 6 HELIX 9 AA9 PRO A 487 HIS A 501 1 15 HELIX 10 AB1 PRO A 535 GLU A 552 1 18 HELIX 11 AB2 LYS A 594 ASN A 605 1 12 SHEET 1 AA1 4 GLN A 39 LEU A 42 0 SHEET 2 AA1 4 VAL A 177 THR A 182 -1 O LEU A 179 N ILE A 41 SHEET 3 AA1 4 ARG A 101 PHE A 106 -1 N PHE A 103 O LEU A 180 SHEET 4 AA1 4 PHE A 132 GLU A 135 -1 O PHE A 132 N PHE A 106 SHEET 1 AA2 6 ARG A 60 VAL A 62 0 SHEET 2 AA2 6 TRP A 47 PHE A 51 -1 N PHE A 49 O ARG A 60 SHEET 3 AA2 6 ILE A 84 TYR A 92 -1 O GLU A 88 N ASN A 48 SHEET 4 AA2 6 LYS A 145 ASN A 153 -1 O ASN A 146 N LEU A 91 SHEET 5 AA2 6 ILE A 112 ILE A 117 -1 N ASP A 114 O ARG A 151 SHEET 6 AA2 6 LYS A 120 ARG A 126 -1 O ILE A 122 N VAL A 115 SHEET 1 AA3 3 THR A 185 ILE A 187 0 SHEET 2 AA3 3 GLU A 208 ASN A 219 -1 O SER A 218 N CYS A 186 SHEET 3 AA3 3 VAL A 197 VAL A 204 -1 N TYR A 198 O LYS A 214 SHEET 1 AA4 3 THR A 185 ILE A 187 0 SHEET 2 AA4 3 GLU A 208 ASN A 219 -1 O SER A 218 N CYS A 186 SHEET 3 AA4 3 ASP A 253 GLN A 263 -1 O LEU A 260 N VAL A 211 SHEET 1 AA5 4 LYS A 237 LEU A 248 0 SHEET 2 AA5 4 GLY A 224 ASP A 234 -1 N VAL A 232 O ILE A 239 SHEET 3 AA5 4 TYR A 277 LYS A 285 -1 O SER A 280 N LEU A 231 SHEET 4 AA5 4 LYS A 288 LEU A 297 -1 O ILE A 290 N LEU A 283 SHEET 1 AA6 3 TYR A 302 ASP A 305 0 SHEET 2 AA6 3 GLY A 309 LEU A 312 -1 O GLY A 309 N ASP A 305 SHEET 3 AA6 3 LYS A 315 HIS A 316 -1 O LYS A 315 N LEU A 312 SHEET 1 AA7 9 HIS A 320 CYS A 323 0 SHEET 2 AA7 9 ALA A 354 LEU A 357 1 O ARG A 356 N VAL A 322 SHEET 3 AA7 9 VAL A 376 GLU A 380 1 O TRP A 378 N ILE A 355 SHEET 4 AA7 9 ILE A 421 ASN A 428 1 O GLY A 425 N ALA A 379 SHEET 5 AA7 9 THR A 457 SER A 461 1 O ALA A 460 N PHE A 427 SHEET 6 AA7 9 ILE A 474 ASN A 477 1 O ALA A 475 N SER A 461 SHEET 7 AA7 9 ILE A 506 TYR A 511 1 O GLY A 507 N TRP A 476 SHEET 8 AA7 9 THR A 559 VAL A 561 1 O PHE A 560 N ILE A 508 SHEET 9 AA7 9 HIS A 320 CYS A 323 1 N CYS A 323 O VAL A 561 SHEET 1 AA8 2 PHE A 567 GLU A 574 0 SHEET 2 AA8 2 ARG A 577 ASN A 581 -1 O ASN A 581 N PHE A 567 SHEET 1 AA9 3 ILE A 611 LEU A 613 0 SHEET 2 AA9 3 GLN A 626 THR A 632 -1 O PHE A 631 N TYR A 612 SHEET 3 AA9 3 THR A 656 VAL A 662 -1 O VAL A 657 N ALA A 630 SHEET 1 AB1 5 LEU A 620 ARG A 621 0 SHEET 2 AB1 5 THR A 682 TYR A 689 1 O GLU A 688 N ARG A 621 SHEET 3 AB1 5 GLY A 667 THR A 674 -1 N ILE A 671 O VAL A 685 SHEET 4 AB1 5 GLU A 636 VAL A 641 -1 N PHE A 640 O ARG A 672 SHEET 5 AB1 5 VAL A 644 LYS A 650 -1 O CYS A 646 N LEU A 639 CISPEP 1 LEU A 64 PRO A 65 0 -5.47 CISPEP 2 ASN A 110 SER A 111 0 -3.99 CISPEP 3 MET A 161 PRO A 162 0 1.86 CISPEP 4 ALA A 358 HIS A 359 0 -8.08 CISPEP 5 TRP A 562 ASN A 563 0 5.77 SITE 1 AC1 13 ASP A 166 HIS A 359 GLU A 429 TYR A 479 SITE 2 AC1 13 TYR A 483 GLU A 510 TRP A 562 PHE A 567 SITE 3 AC1 13 ARG A 572 ASN A 581 LYS A 583 HOH A1002 SITE 4 AC1 13 HOH A1050 CRYST1 80.253 103.135 199.147 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 0.012461 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009696 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005021 0.00000