HEADER HYDROLASE 27-NOV-16 5MI5 TITLE BTGH84 MUTANT WITH COVALENT MODIFICATION BY MA3 IN COMPLEX WITH PUGNAC COMPND MOL_ID: 1; COMPND 2 MOLECULE: O-GLCNACASE BT_4395; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BETA-N-ACETYLGLUCOSAMINIDASE,BETA-N-ACETYLHEXOSAMINIDASE, COMPND 5 BETA-HEXOSAMINIDASE,HEXOSAMINIDASE B,N-ACETYL-BETA-GLUCOSAMINIDASE; COMPND 6 EC: 3.2.1.169,3.2.1.52; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES THETAIOTAOMICRON (STRAIN ATCC 29148 SOURCE 3 / DSM 2079 / NCTC 10582 / E50 / VPI-5482); SOURCE 4 ORGANISM_TAXID: 226186; SOURCE 5 STRAIN: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482; SOURCE 6 GENE: BT_4395; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: YSBLLICPET28 KEYWDS HYDROLASE, ACTIVATOR EXPDTA X-RAY DIFFRACTION AUTHOR J.F.DARBY,G.J.DAVIES,R.E.HUBBARD REVDAT 3 17-JAN-24 5MI5 1 REMARK REVDAT 2 06-DEC-17 5MI5 1 JRNL REVDAT 1 01-NOV-17 5MI5 0 JRNL AUTH J.F.DARBY,M.ATOBE,J.D.FIRTH,P.BOND,G.J.DAVIES,P.O'BRIEN, JRNL AUTH 2 R.E.HUBBARD JRNL TITL INCREASE OF ENZYME ACTIVITY THROUGH SPECIFIC COVALENT JRNL TITL 2 MODIFICATION WITH FRAGMENTS. JRNL REF CHEM SCI V. 8 7772 2017 JRNL REFN ISSN 2041-6520 JRNL PMID 29163914 JRNL DOI 10.1039/C7SC01966A REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 58090 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.235 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 5498 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 51.8299 - 6.6761 0.98 3521 164 0.1815 0.2031 REMARK 3 2 6.6761 - 5.3008 0.99 3556 186 0.2047 0.2419 REMARK 3 3 5.3008 - 4.6312 0.98 3512 173 0.1717 0.2452 REMARK 3 4 4.6312 - 4.2080 0.97 3457 191 0.1703 0.2171 REMARK 3 5 4.2080 - 3.9065 0.99 3519 197 0.1892 0.2083 REMARK 3 6 3.9065 - 3.6762 0.99 3533 185 0.1841 0.2003 REMARK 3 7 3.6762 - 3.4921 0.99 3534 156 0.1961 0.2506 REMARK 3 8 3.4921 - 3.3402 0.99 3554 164 0.2304 0.2641 REMARK 3 9 3.3402 - 3.2116 0.97 3479 202 0.2346 0.2541 REMARK 3 10 3.2116 - 3.1008 0.96 3388 206 0.2209 0.2616 REMARK 3 11 3.1008 - 3.0038 0.97 3480 182 0.2280 0.2934 REMARK 3 12 3.0038 - 2.9180 0.98 3473 209 0.2356 0.2602 REMARK 3 13 2.9180 - 2.8412 0.97 3517 164 0.2307 0.3074 REMARK 3 14 2.8412 - 2.7719 0.98 3521 170 0.2284 0.2335 REMARK 3 15 2.7719 - 2.7088 0.97 3502 181 0.2566 0.2698 REMARK 3 16 2.7088 - 2.6512 0.98 3525 168 0.2562 0.3316 REMARK 3 17 2.6512 - 2.5982 0.98 3448 197 0.2641 0.3512 REMARK 3 18 2.5982 - 2.5491 0.97 3489 173 0.2687 0.2881 REMARK 3 19 2.5491 - 2.5036 0.97 3411 195 0.2860 0.3680 REMARK 3 20 2.5036 - 2.4612 0.95 3447 155 0.3013 0.3426 REMARK 3 21 2.4612 - 2.4215 0.95 3388 171 0.3113 0.3694 REMARK 3 22 2.4215 - 2.3842 0.97 3365 176 0.3209 0.3207 REMARK 3 23 2.3842 - 2.3492 0.96 3468 207 0.3244 0.3751 REMARK 3 24 2.3492 - 2.3161 0.97 3530 174 0.3227 0.4133 REMARK 3 25 2.3161 - 2.2848 0.97 3418 187 0.3484 0.3264 REMARK 3 26 2.2848 - 2.2551 0.97 3422 188 0.3721 0.3863 REMARK 3 27 2.2551 - 2.2269 0.96 3461 195 0.3766 0.4042 REMARK 3 28 2.2269 - 2.2001 0.97 3451 196 0.3740 0.4385 REMARK 3 29 2.2001 - 2.1745 0.98 3347 202 0.4056 0.3968 REMARK 3 30 2.1745 - 2.1501 0.96 3546 184 0.4292 0.4429 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.530 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.004 5667 REMARK 3 ANGLE : 0.634 7666 REMARK 3 CHIRALITY : 0.045 814 REMARK 3 PLANARITY : 0.005 989 REMARK 3 DIHEDRAL : 4.983 4787 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 4:128) REMARK 3 ORIGIN FOR THE GROUP (A): 15.2049 -4.3992 47.7601 REMARK 3 T TENSOR REMARK 3 T11: 0.5379 T22: 0.3354 REMARK 3 T33: 0.2757 T12: -0.0362 REMARK 3 T13: -0.1226 T23: 0.0410 REMARK 3 L TENSOR REMARK 3 L11: 0.9894 L22: 2.0160 REMARK 3 L33: 2.1169 L12: -0.1185 REMARK 3 L13: -0.0079 L23: 0.2457 REMARK 3 S TENSOR REMARK 3 S11: 0.1301 S12: -0.2156 S13: -0.1198 REMARK 3 S21: 0.3139 S22: -0.0994 S23: 0.0085 REMARK 3 S31: 0.1047 S32: -0.3101 S33: -0.0554 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 129:407) REMARK 3 ORIGIN FOR THE GROUP (A): 30.0548 8.6293 22.4968 REMARK 3 T TENSOR REMARK 3 T11: 0.1815 T22: 0.2449 REMARK 3 T33: 0.2499 T12: 0.0086 REMARK 3 T13: 0.0184 T23: -0.0036 REMARK 3 L TENSOR REMARK 3 L11: 0.9162 L22: 1.4015 REMARK 3 L33: 0.9724 L12: 0.3358 REMARK 3 L13: 0.1492 L23: 0.3002 REMARK 3 S TENSOR REMARK 3 S11: 0.0078 S12: 0.0376 S13: -0.0516 REMARK 3 S21: -0.0286 S22: 0.0093 S23: -0.2537 REMARK 3 S31: -0.0399 S32: 0.1234 S33: -0.0124 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 408:523) REMARK 3 ORIGIN FOR THE GROUP (A): 11.9649 -17.2697 5.2540 REMARK 3 T TENSOR REMARK 3 T11: 0.4210 T22: 0.2372 REMARK 3 T33: 0.2585 T12: 0.0639 REMARK 3 T13: -0.0865 T23: 0.0035 REMARK 3 L TENSOR REMARK 3 L11: 0.9712 L22: 1.2143 REMARK 3 L33: 1.3014 L12: 0.3770 REMARK 3 L13: 0.2654 L23: 0.3245 REMARK 3 S TENSOR REMARK 3 S11: 0.1631 S12: 0.0516 S13: -0.1693 REMARK 3 S21: -0.1895 S22: 0.0013 S23: -0.0751 REMARK 3 S31: 0.4770 S32: 0.0350 S33: -0.1505 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 524:645) REMARK 3 ORIGIN FOR THE GROUP (A): 15.6660 -8.3589 -12.3214 REMARK 3 T TENSOR REMARK 3 T11: 0.3641 T22: 0.3375 REMARK 3 T33: 0.3037 T12: 0.0583 REMARK 3 T13: 0.0631 T23: -0.0203 REMARK 3 L TENSOR REMARK 3 L11: 0.3573 L22: 1.6596 REMARK 3 L33: 0.6630 L12: 0.0506 REMARK 3 L13: 0.0610 L23: -0.3017 REMARK 3 S TENSOR REMARK 3 S11: -0.0224 S12: 0.1338 S13: 0.0487 REMARK 3 S21: -0.5044 S22: 0.0491 S23: -0.3046 REMARK 3 S31: 0.0752 S32: 0.1252 S33: 0.0034 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 646:707) REMARK 3 ORIGIN FOR THE GROUP (A): 27.1509 9.1265 -24.5512 REMARK 3 T TENSOR REMARK 3 T11: 0.7615 T22: 0.9081 REMARK 3 T33: 0.8602 T12: 0.0161 REMARK 3 T13: 0.3761 T23: 0.1086 REMARK 3 L TENSOR REMARK 3 L11: 0.8817 L22: 0.6041 REMARK 3 L33: 0.1067 L12: -0.1590 REMARK 3 L13: 0.0656 L23: 0.2281 REMARK 3 S TENSOR REMARK 3 S11: 0.0499 S12: 0.1677 S13: 0.0291 REMARK 3 S21: -0.6949 S22: -0.1634 S23: -0.6400 REMARK 3 S31: -0.0902 S32: 0.4674 S33: -0.0920 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 708:715) REMARK 3 ORIGIN FOR THE GROUP (A): 21.2713 8.1767 -15.0743 REMARK 3 T TENSOR REMARK 3 T11: 0.3337 T22: 0.5725 REMARK 3 T33: 0.7033 T12: -0.0185 REMARK 3 T13: 0.2406 T23: 0.0091 REMARK 3 L TENSOR REMARK 3 L11: 2.3972 L22: 3.9643 REMARK 3 L33: 2.0312 L12: -1.1555 REMARK 3 L13: 0.5357 L23: -0.2246 REMARK 3 S TENSOR REMARK 3 S11: -0.0600 S12: -0.2271 S13: -0.1000 REMARK 3 S21: -0.0023 S22: 0.0777 S23: -0.2854 REMARK 3 S31: 0.0597 S32: 0.2927 S33: 0.0321 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 5MI5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1200002096. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58090 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 51.815 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.13100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.58800 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: MOLREP REMARK 200 STARTING MODEL: 2CHO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4% PEG 8K, 125MM IMIDAZOLE, 3% TMAO, REMARK 280 15% ETHYLENE GLYCOL, PH 8.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 99.11050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.06000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 99.11050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.06000 REMARK 290 SMTRY3 4 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 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: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 MET A -10 REMARK 465 GLY A -9 REMARK 465 SER A -8 REMARK 465 SER A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 GLN A 0 REMARK 465 TRP A 1 REMARK 465 ASN A 2 REMARK 465 VAL A 3 REMARK 465 ILE A 596 REMARK 465 SER A 597 REMARK 465 ASN A 598 REMARK 465 VAL A 599 REMARK 465 GLU A 600 REMARK 465 GLN A 601 REMARK 465 ILE A 602 REMARK 465 ASN A 620 REMARK 465 GLU A 621 REMARK 465 VAL A 622 REMARK 465 VAL A 623 REMARK 465 LYS A 624 REMARK 465 TRP A 625 REMARK 465 ALA A 626 REMARK 465 ALA A 627 REMARK 465 VAL A 631 REMARK 465 GLY A 649 REMARK 465 LYS A 650 REMARK 465 ASP A 651 REMARK 465 ALA A 652 REMARK 465 PRO A 653 REMARK 465 SER A 654 REMARK 465 THR A 655 REMARK 465 TRP A 656 REMARK 465 GLY A 657 REMARK 465 ARG A 658 REMARK 465 GLU A 677 REMARK 465 ASN A 696 REMARK 465 GLU A 700 REMARK 465 GLU A 701 REMARK 465 GLN A 702 REMARK 465 GLN A 703 REMARK 465 VAL A 704 REMARK 465 TYR A 705 REMARK 465 LEU A 706 REMARK 465 LYS A 716 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 OD2 ASP A 442 O HOH A 901 1.87 REMARK 500 NH2 ARG A 693 O HOH A 902 2.11 REMARK 500 CB CYS A 550 C7 7NQ A 802 2.17 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 959 O HOH A 959 2555 1.90 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 693 NE - CZ - NH2 ANGL. DEV. = -4.3 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 172 -148.31 -126.34 REMARK 500 ASP A 243 60.14 60.64 REMARK 500 PHE A 265 -56.57 -131.18 REMARK 500 ASP A 271 39.92 -150.23 REMARK 500 ASN A 273 -94.68 -105.18 REMARK 500 ASN A 290 35.63 -79.94 REMARK 500 ASN A 292 26.54 -155.40 REMARK 500 LEU A 411 69.50 -151.23 REMARK 500 ALA A 414 50.86 -152.10 REMARK 500 SER A 426 -20.03 -140.60 REMARK 500 ARG A 519 -74.96 -76.88 REMARK 500 ALA A 611 -128.09 58.26 REMARK 500 GLU A 642 -67.41 -109.98 REMARK 500 ARG A 679 83.47 69.18 REMARK 500 LYS A 690 -30.66 -134.05 REMARK 500 PHE A 709 94.45 -167.35 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 CA A 803 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 32 O REMARK 620 2 GLU A 61 OE1 94.0 REMARK 620 3 ASP A 64 OD1 101.1 115.4 REMARK 620 4 ASP A 64 OD2 81.1 74.6 47.4 REMARK 620 5 HOH A1068 O 93.1 83.8 154.9 157.0 REMARK 620 6 HOH A1111 O 90.1 170.0 72.6 115.1 86.9 REMARK 620 7 HOH A1118 O 167.2 85.3 90.6 110.9 74.1 88.6 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OAN A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 7NQ A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 803 DBREF 5MI5 A 2 716 UNP Q89ZI2 OGA_BACTN 23 737 SEQADV 5MI5 MET A -10 UNP Q89ZI2 INITIATING METHIONINE SEQADV 5MI5 GLY A -9 UNP Q89ZI2 EXPRESSION TAG SEQADV 5MI5 SER A -8 UNP Q89ZI2 EXPRESSION TAG SEQADV 5MI5 SER A -7 UNP Q89ZI2 EXPRESSION TAG SEQADV 5MI5 HIS A -6 UNP Q89ZI2 EXPRESSION TAG SEQADV 5MI5 HIS A -5 UNP Q89ZI2 EXPRESSION TAG SEQADV 5MI5 HIS A -4 UNP Q89ZI2 EXPRESSION TAG SEQADV 5MI5 HIS A -3 UNP Q89ZI2 EXPRESSION TAG SEQADV 5MI5 HIS A -2 UNP Q89ZI2 EXPRESSION TAG SEQADV 5MI5 HIS A -1 UNP Q89ZI2 EXPRESSION TAG SEQADV 5MI5 GLN A 0 UNP Q89ZI2 EXPRESSION TAG SEQADV 5MI5 TRP A 1 UNP Q89ZI2 EXPRESSION TAG SEQADV 5MI5 SER A 420 UNP Q89ZI2 CYS 441 ENGINEERED MUTATION SEQADV 5MI5 CYS A 550 UNP Q89ZI2 TYR 571 ENGINEERED MUTATION SEQADV 5MI5 SER A 654 UNP Q89ZI2 CYS 675 ENGINEERED MUTATION SEQRES 1 A 727 MET GLY SER SER HIS HIS HIS HIS HIS HIS GLN TRP ASN SEQRES 2 A 727 VAL SER LEU GLN PRO PRO PRO GLN GLN LEU ILE VAL GLN SEQRES 3 A 727 ASN LYS THR ILE ASP LEU PRO ALA VAL TYR GLN LEU ASN SEQRES 4 A 727 GLY GLY GLU GLU ALA ASN PRO HIS ALA VAL LYS VAL LEU SEQRES 5 A 727 LYS GLU LEU LEU SER GLY LYS GLN SER SER LYS LYS GLY SEQRES 6 A 727 MET LEU ILE SER ILE GLY GLU LYS GLY ASP LYS SER VAL SEQRES 7 A 727 ARG LYS TYR SER ARG GLN ILE PRO ASP HIS LYS GLU GLY SEQRES 8 A 727 TYR TYR LEU SER VAL ASN GLU LYS GLU ILE VAL LEU ALA SEQRES 9 A 727 GLY ASN ASP GLU ARG GLY THR TYR TYR ALA LEU GLN THR SEQRES 10 A 727 PHE ALA GLN LEU LEU LYS ASP GLY LYS LEU PRO GLU VAL SEQRES 11 A 727 GLU ILE LYS ASP TYR PRO SER VAL ARG TYR ARG GLY VAL SEQRES 12 A 727 VAL GLU GLY PHE TYR GLY THR PRO TRP SER HIS GLN ALA SEQRES 13 A 727 ARG LEU SER GLN LEU LYS PHE TYR GLY LYS ASN LYS MET SEQRES 14 A 727 ASN THR TYR ILE TYR GLY PRO LYS ASP ASP PRO TYR HIS SEQRES 15 A 727 SER ALA PRO ASN TRP ARG LEU PRO TYR PRO ASP LYS GLU SEQRES 16 A 727 ALA ALA GLN LEU GLN GLU LEU VAL ALA VAL ALA ASN GLU SEQRES 17 A 727 ASN GLU VAL ASP PHE VAL TRP ALA ILE HIS PRO GLY GLN SEQRES 18 A 727 ASP ILE LYS TRP ASN LYS GLU ASP ARG ASP LEU LEU LEU SEQRES 19 A 727 ALA LYS PHE GLU LYS MET TYR GLN LEU GLY VAL ARG SER SEQRES 20 A 727 PHE ALA VAL PHE PHE ASP ASP ILE SER GLY GLU GLY THR SEQRES 21 A 727 ASN PRO GLN LYS GLN ALA GLU LEU LEU ASN TYR ILE ASP SEQRES 22 A 727 GLU LYS PHE ALA GLN VAL LYS PRO ASP ILE ASN GLN LEU SEQRES 23 A 727 VAL MET CYS PRO THR GLU TYR ASN LYS SER TRP SER ASN SEQRES 24 A 727 PRO ASN GLY ASN TYR LEU THR THR LEU GLY ASP LYS LEU SEQRES 25 A 727 ASN PRO SER ILE GLN ILE MET TRP THR GLY ASP ARG VAL SEQRES 26 A 727 ILE SER ASP ILE THR ARG ASP GLY ILE SER TRP ILE ASN SEQRES 27 A 727 GLU ARG ILE LYS ARG PRO ALA TYR ILE TRP TRP ASN PHE SEQRES 28 A 727 PRO VAL SER ASP TYR VAL ARG ASP HIS LEU LEU LEU GLY SEQRES 29 A 727 PRO VAL TYR GLY ASN ASP THR THR ILE ALA LYS GLU MET SEQRES 30 A 727 SER GLY PHE VAL THR ASN PRO MET GLU HIS ALA GLU SER SEQRES 31 A 727 SER LYS ILE ALA ILE TYR SER VAL ALA SER TYR ALA TRP SEQRES 32 A 727 ASN PRO ALA LYS TYR ASP THR TRP GLN THR TRP LYS ASP SEQRES 33 A 727 ALA ILE ARG THR ILE LEU PRO SER ALA ALA GLU GLU LEU SEQRES 34 A 727 GLU SER PHE ALA MET HIS ASN SER ASP LEU GLY PRO ASN SEQRES 35 A 727 GLY HIS GLY TYR ARG ARG GLU GLU SER MET ASP ILE GLN SEQRES 36 A 727 PRO ALA ALA GLU ARG PHE LEU LYS ALA PHE LYS GLU GLY SEQRES 37 A 727 LYS ASN TYR ASP LYS ALA ASP PHE GLU THR LEU GLN TYR SEQRES 38 A 727 THR PHE GLU ARG MET LYS GLU SER ALA ASP ILE LEU LEU SEQRES 39 A 727 MET ASN THR GLU ASN LYS PRO LEU ILE VAL GLU ILE THR SEQRES 40 A 727 PRO TRP VAL HIS GLN PHE LYS LEU THR ALA GLU MET GLY SEQRES 41 A 727 GLU GLU VAL LEU LYS MET VAL GLU GLY ARG ASN GLU SER SEQRES 42 A 727 TYR PHE LEU ARG LYS TYR ASN HIS VAL LYS ALA LEU GLN SEQRES 43 A 727 GLN GLN MET PHE TYR ILE ASP GLN THR SER ASN GLN ASN SEQRES 44 A 727 PRO CYS GLN PRO GLY VAL LYS THR ALA THR ARG VAL ILE SEQRES 45 A 727 LYS PRO LEU ILE ASP ARG THR PHE ALA THR VAL VAL LYS SEQRES 46 A 727 PHE PHE ASN GLN LYS PHE ASN ALA HIS LEU ASP ALA THR SEQRES 47 A 727 THR ASP TYR MET PRO HIS LYS MET ILE SER ASN VAL GLU SEQRES 48 A 727 GLN ILE LYS ASN LEU PRO LEU GLN VAL LYS ALA ASN ARG SEQRES 49 A 727 VAL LEU ILE SER PRO ALA ASN GLU VAL VAL LYS TRP ALA SEQRES 50 A 727 ALA GLY ASN SER VAL GLU ILE GLU LEU ASP ALA ILE TYR SEQRES 51 A 727 PRO GLY GLU ASN ILE GLN ILE ASN PHE GLY LYS ASP ALA SEQRES 52 A 727 PRO SER THR TRP GLY ARG LEU GLU ILE SER THR ASP GLY SEQRES 53 A 727 LYS GLU TRP LYS THR VAL ASP LEU LYS GLN LYS GLU SER SEQRES 54 A 727 ARG LEU SER ALA GLY LEU GLN LYS ALA PRO VAL LYS PHE SEQRES 55 A 727 VAL ARG PHE THR ASN VAL SER ASP GLU GLU GLN GLN VAL SEQRES 56 A 727 TYR LEU ARG GLN PHE VAL LEU THR ILE GLU LYS LYS HET OAN A 801 25 HET 7NQ A 802 18 HET CA A 803 1 HETNAM OAN O-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE) AMINO-N- HETNAM 2 OAN PHENYLCARBAMATE HETNAM 7NQ ~{N}-(4-ETHOXYQUINAZOLIN-2-YL)PROPANAMIDE HETNAM CA CALCIUM ION HETSYN OAN PUGNAC FORMUL 2 OAN C15 H19 N3 O7 FORMUL 3 7NQ C13 H15 N3 O2 FORMUL 4 CA CA 2+ FORMUL 5 HOH *252(H2 O) HELIX 1 AA1 ASN A 34 LEU A 45 1 12 HELIX 2 AA2 ASP A 64 SER A 71 5 8 HELIX 3 AA3 ASP A 96 LEU A 111 1 16 HELIX 4 AA4 SER A 142 ASN A 156 1 15 HELIX 5 AA5 PRO A 181 ASN A 198 1 18 HELIX 6 AA6 ASN A 215 LEU A 232 1 18 HELIX 7 AA7 GLY A 246 THR A 249 5 4 HELIX 8 AA8 ASN A 250 PHE A 265 1 16 HELIX 9 AA9 ASN A 283 SER A 287 5 5 HELIX 10 AB1 ASN A 292 LEU A 301 1 10 HELIX 11 AB2 THR A 319 LYS A 331 1 13 HELIX 12 AB3 ILE A 362 LYS A 364 5 3 HELIX 13 AB4 ALA A 377 SER A 379 5 3 HELIX 14 AB5 SER A 380 ASN A 393 1 14 HELIX 15 AB6 PRO A 394 TYR A 397 5 4 HELIX 16 AB7 ASP A 398 LEU A 411 1 14 HELIX 17 AB8 ALA A 414 HIS A 424 1 11 HELIX 18 AB9 ILE A 443 GLU A 456 1 14 HELIX 19 AC1 ASP A 461 MET A 484 1 24 HELIX 20 AC2 ASN A 488 GLY A 518 1 31 HELIX 21 AC3 ASN A 520 SER A 545 1 26 HELIX 22 AC4 VAL A 560 ASN A 581 1 22 SHEET 1 AA1 7 GLN A 11 ASP A 20 0 SHEET 2 AA1 7 LYS A 115 ASP A 123 -1 O GLU A 118 N LYS A 17 SHEET 3 AA1 7 TYR A 81 VAL A 85 -1 N LEU A 83 O ILE A 121 SHEET 4 AA1 7 GLU A 89 GLY A 94 -1 O ALA A 93 N TYR A 82 SHEET 5 AA1 7 MET A 55 GLU A 61 1 N SER A 58 O LEU A 92 SHEET 6 AA1 7 VAL A 24 ASN A 28 1 N GLN A 26 O ILE A 57 SHEET 7 AA1 7 GLN A 49 SER A 50 1 O GLN A 49 N TYR A 25 SHEET 1 AA2 9 TYR A 129 GLU A 134 0 SHEET 2 AA2 9 THR A 160 TYR A 163 1 O ILE A 162 N VAL A 132 SHEET 3 AA2 9 ASP A 201 ILE A 206 1 O VAL A 203 N TYR A 163 SHEET 4 AA2 9 SER A 236 PHE A 240 1 O PHE A 240 N ILE A 206 SHEET 5 AA2 9 LEU A 275 CYS A 278 1 O VAL A 276 N PHE A 237 SHEET 6 AA2 9 GLN A 306 TRP A 309 1 O GLN A 306 N LEU A 275 SHEET 7 AA2 9 ALA A 334 TRP A 338 1 O TRP A 337 N TRP A 309 SHEET 8 AA2 9 MET A 366 THR A 371 1 O VAL A 370 N TRP A 338 SHEET 9 AA2 9 TYR A 129 GLU A 134 1 N VAL A 133 O THR A 371 SHEET 1 AA3 7 LEU A 607 LYS A 610 0 SHEET 2 AA3 7 ARG A 613 ILE A 616 -1 O LEU A 615 N GLN A 608 SHEET 3 AA3 7 PHE A 709 ILE A 713 -1 O LEU A 711 N VAL A 614 SHEET 4 AA3 7 ILE A 633 ILE A 646 -1 N GLN A 645 O VAL A 710 SHEET 5 AA3 7 PRO A 688 ARG A 693 -1 O VAL A 692 N ILE A 633 SHEET 6 AA3 7 GLU A 660 SER A 662 -1 N SER A 662 O LYS A 690 SHEET 7 AA3 7 TRP A 668 THR A 670 -1 O LYS A 669 N ILE A 661 SHEET 1 AA4 6 LEU A 607 LYS A 610 0 SHEET 2 AA4 6 ARG A 613 ILE A 616 -1 O LEU A 615 N GLN A 608 SHEET 3 AA4 6 PHE A 709 ILE A 713 -1 O LEU A 711 N VAL A 614 SHEET 4 AA4 6 ILE A 633 ILE A 646 -1 N GLN A 645 O VAL A 710 SHEET 5 AA4 6 LEU A 680 GLY A 683 -1 O LEU A 680 N ILE A 646 SHEET 6 AA4 6 LYS A 674 GLN A 675 -1 N LYS A 674 O SER A 681 LINK SG CYS A 550 C7 7NQ A 802 1555 1555 1.66 LINK O GLU A 32 CA CA A 803 1555 1555 2.27 LINK OE1 GLU A 61 CA CA A 803 1555 1555 2.62 LINK OD1 ASP A 64 CA CA A 803 1555 1555 2.82 LINK OD2 ASP A 64 CA CA A 803 1555 1555 2.64 LINK CA CA A 803 O HOH A1068 1555 1555 2.44 LINK CA CA A 803 O HOH A1111 1555 1555 2.65 LINK CA CA A 803 O HOH A1118 1555 1555 2.31 CISPEP 1 GLN A 6 PRO A 7 0 -11.96 CISPEP 2 ALA A 173 PRO A 174 0 -1.54 CISPEP 3 PHE A 340 PRO A 341 0 5.54 SITE 1 AC1 14 GLY A 135 PHE A 136 TYR A 137 LYS A 166 SITE 2 AC1 14 ASP A 242 ASP A 243 TYR A 282 TRP A 286 SITE 3 AC1 14 VAL A 314 ASN A 339 ASP A 344 ASN A 372 SITE 4 AC1 14 7NQ A 802 HOH A 908 SITE 1 AC2 5 TYR A 137 PRO A 549 CYS A 550 OAN A 801 SITE 2 AC2 5 HOH A1040 SITE 1 AC3 6 GLU A 32 GLU A 61 ASP A 64 HOH A1068 SITE 2 AC3 6 HOH A1111 HOH A1118 CRYST1 198.221 52.120 112.779 90.00 113.24 90.00 C 1 2 1 4 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 0.005045 0.000000 0.002166 0.00000 SCALE2 0.000000 0.019187 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009650 0.00000