HEADER HYDROLASE 15-APR-20 6YPD TITLE CRYSTAL STRUCTURE OF AMPC FROM E. COLI WITH CYCLIC BORONATE 3 (CB3 / TITLE 2 APC308) COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CEPHALOSPORINASE; COMPND 5 EC: 3.5.2.6; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: AMPC, AMPA, B4150, JW4111; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI STR. K-12 SUBSTR. W3110; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 316407 KEYWDS BETA LACTAMASE, ANTIBIOTIC RESISTANCE, BICYCLIC BORONATE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.A.LANG,J.BREM,C.J.SCHOFIELD REVDAT 5 06-NOV-24 6YPD 1 REMARK REVDAT 4 24-JAN-24 6YPD 1 REMARK REVDAT 3 30-SEP-20 6YPD 1 JRNL REVDAT 2 01-JUL-20 6YPD 1 JRNL REVDAT 1 24-JUN-20 6YPD 0 JRNL AUTH P.A.LANG,A.PARKOVA,T.M.LEISSING,K.CALVOPINA,R.CAIN,A.KRAJNC, JRNL AUTH 2 T.D.PANDUWAWALA,J.PHILIPPE,C.W.G.FISHWICK,P.TRAPENCIERIS, JRNL AUTH 3 M.G.P.PAGE,C.J.SCHOFIELD,J.BREM JRNL TITL BICYCLIC BORONATES AS POTENT INHIBITORS OF AMPC, THE CLASS C JRNL TITL 2 BETA-LACTAMASE FROM ESCHERICHIA COLI . JRNL REF BIOMOLECULES V. 10 2020 JRNL REFN ESSN 2218-273X JRNL PMID 32545682 JRNL DOI 10.3390/BIOM10060899 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 60656 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.280 REMARK 3 FREE R VALUE TEST SET COUNT : 1990 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 49.1340 - 3.8531 1.00 4541 154 0.1549 0.1708 REMARK 3 2 3.8531 - 3.0585 1.00 4310 147 0.1576 0.1513 REMARK 3 3 3.0585 - 2.6719 1.00 4259 145 0.1549 0.1761 REMARK 3 4 2.6719 - 2.4276 1.00 4214 143 0.1555 0.1850 REMARK 3 5 2.4276 - 2.2536 1.00 4179 142 0.1692 0.2010 REMARK 3 6 2.2536 - 2.1207 0.99 4166 142 0.1868 0.1979 REMARK 3 7 2.1207 - 2.0145 1.00 4136 138 0.1937 0.2030 REMARK 3 8 2.0145 - 1.9268 0.99 4115 138 0.1896 0.2061 REMARK 3 9 1.9268 - 1.8527 0.98 4079 139 0.2659 0.2779 REMARK 3 10 1.8527 - 1.7887 1.00 4158 141 0.1870 0.2317 REMARK 3 11 1.7887 - 1.7328 1.00 4125 140 0.1974 0.2263 REMARK 3 12 1.7328 - 1.6833 1.00 4128 140 0.2034 0.2508 REMARK 3 13 1.6833 - 1.6389 1.00 4129 141 0.2115 0.2592 REMARK 3 14 1.6389 - 1.6000 1.00 4127 140 0.2392 0.2828 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.01 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 THROUGH 23 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.1991 -0.4765 6.4347 REMARK 3 T TENSOR REMARK 3 T11: 0.2107 T22: 0.2439 REMARK 3 T33: 0.1926 T12: 0.0119 REMARK 3 T13: 0.0183 T23: 0.0054 REMARK 3 L TENSOR REMARK 3 L11: 2.6720 L22: 6.6840 REMARK 3 L33: 3.1456 L12: -0.8965 REMARK 3 L13: -1.3547 L23: 1.3878 REMARK 3 S TENSOR REMARK 3 S11: 0.0623 S12: 0.1534 S13: -0.0423 REMARK 3 S21: -0.3345 S22: -0.1838 S23: -0.1663 REMARK 3 S31: 0.0962 S32: -0.0972 S33: 0.1150 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 24 THROUGH 79 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.3129 2.8558 23.0206 REMARK 3 T TENSOR REMARK 3 T11: 0.1665 T22: 0.1372 REMARK 3 T33: 0.1339 T12: 0.0013 REMARK 3 T13: -0.0275 T23: 0.0089 REMARK 3 L TENSOR REMARK 3 L11: 3.0720 L22: 1.4098 REMARK 3 L33: 2.2141 L12: 0.8659 REMARK 3 L13: -2.1199 L23: -0.5618 REMARK 3 S TENSOR REMARK 3 S11: 0.1235 S12: -0.2061 S13: 0.1134 REMARK 3 S21: 0.1224 S22: -0.0216 S23: -0.0951 REMARK 3 S31: -0.1125 S32: 0.1507 S33: -0.1169 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 80 THROUGH 98 ) REMARK 3 ORIGIN FOR THE GROUP (A): -30.5287 8.3709 43.7818 REMARK 3 T TENSOR REMARK 3 T11: 0.3969 T22: 0.2862 REMARK 3 T33: 0.2849 T12: 0.0474 REMARK 3 T13: 0.1664 T23: -0.0165 REMARK 3 L TENSOR REMARK 3 L11: 1.3691 L22: 3.4195 REMARK 3 L33: 0.5930 L12: -0.0992 REMARK 3 L13: 0.5950 L23: -0.8965 REMARK 3 S TENSOR REMARK 3 S11: 0.1357 S12: -0.2499 S13: 0.2701 REMARK 3 S21: 0.5172 S22: -0.0152 S23: 0.3252 REMARK 3 S31: -0.2855 S32: -0.2705 S33: -0.1057 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 99 THROUGH 162 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.7984 16.5618 34.1821 REMARK 3 T TENSOR REMARK 3 T11: 0.3901 T22: 0.2207 REMARK 3 T33: 0.2992 T12: 0.0738 REMARK 3 T13: 0.1626 T23: 0.0089 REMARK 3 L TENSOR REMARK 3 L11: 1.7873 L22: 2.4184 REMARK 3 L33: 3.5465 L12: -0.3443 REMARK 3 L13: -0.6543 L23: 0.3689 REMARK 3 S TENSOR REMARK 3 S11: 0.2720 S12: -0.1154 S13: 0.5063 REMARK 3 S21: 0.3526 S22: 0.0578 S23: 0.0906 REMARK 3 S31: -0.7504 S32: -0.2787 S33: -0.1899 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 163 THROUGH 275 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.5715 1.6327 31.0669 REMARK 3 T TENSOR REMARK 3 T11: 0.2319 T22: 0.1734 REMARK 3 T33: 0.1555 T12: -0.0002 REMARK 3 T13: 0.0076 T23: 0.0040 REMARK 3 L TENSOR REMARK 3 L11: 2.1937 L22: 1.0278 REMARK 3 L33: 1.2889 L12: 0.6703 REMARK 3 L13: -0.9522 L23: -0.1399 REMARK 3 S TENSOR REMARK 3 S11: 0.0363 S12: -0.1577 S13: 0.0181 REMARK 3 S21: 0.1915 S22: -0.0209 S23: -0.0370 REMARK 3 S31: -0.0743 S32: 0.0809 S33: -0.0140 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 276 THROUGH 362 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.4717 1.8820 15.6950 REMARK 3 T TENSOR REMARK 3 T11: 0.1909 T22: 0.2109 REMARK 3 T33: 0.1828 T12: 0.0025 REMARK 3 T13: 0.0021 T23: 0.0078 REMARK 3 L TENSOR REMARK 3 L11: 1.6383 L22: 0.6974 REMARK 3 L33: 1.6285 L12: -0.0809 REMARK 3 L13: -0.8477 L23: -0.3102 REMARK 3 S TENSOR REMARK 3 S11: -0.0057 S12: 0.2294 S13: 0.0106 REMARK 3 S21: 0.0008 S22: 0.0431 S23: 0.1326 REMARK 3 S31: -0.0088 S32: -0.2732 S33: -0.0382 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 6YPD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292108044. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAY-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60941 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.599 REMARK 200 RESOLUTION RANGE LOW (A) : 138.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 77.30 REMARK 200 R MERGE (I) : 0.16500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 67.40 REMARK 200 R MERGE FOR SHELL (I) : 4.50400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.1 REMARK 200 STARTING MODEL: 1IEM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% (W/V) PEG6000, 0.01 M ZNCL2, 0.1 M REMARK 280 MES PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 REMARK 290 13555 Y+1/4,X+3/4,-Z+3/4 REMARK 290 14555 -Y+1/4,-X+1/4,-Z+1/4 REMARK 290 15555 Y+3/4,-X+3/4,Z+1/4 REMARK 290 16555 -Y+3/4,X+1/4,Z+3/4 REMARK 290 17555 X+1/4,Z+3/4,-Y+3/4 REMARK 290 18555 -X+3/4,Z+1/4,Y+3/4 REMARK 290 19555 -X+1/4,-Z+1/4,-Y+1/4 REMARK 290 20555 X+3/4,-Z+3/4,Y+1/4 REMARK 290 21555 Z+1/4,Y+3/4,-X+3/4 REMARK 290 22555 Z+3/4,-Y+3/4,X+1/4 REMARK 290 23555 -Z+3/4,Y+1/4,X+3/4 REMARK 290 24555 -Z+1/4,-Y+1/4,-X+1/4 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 69.48550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 69.48550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 69.48550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 69.48550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 69.48550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 69.48550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 69.48550 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 69.48550 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 69.48550 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 69.48550 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 69.48550 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 69.48550 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 69.48550 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 69.48550 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 69.48550 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 69.48550 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 69.48550 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 69.48550 REMARK 290 SMTRY1 13 0.000000 1.000000 0.000000 34.74275 REMARK 290 SMTRY2 13 1.000000 0.000000 0.000000 104.22825 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 104.22825 REMARK 290 SMTRY1 14 0.000000 -1.000000 0.000000 34.74275 REMARK 290 SMTRY2 14 -1.000000 0.000000 0.000000 34.74275 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 34.74275 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 104.22825 REMARK 290 SMTRY2 15 -1.000000 0.000000 0.000000 104.22825 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 34.74275 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 104.22825 REMARK 290 SMTRY2 16 1.000000 0.000000 0.000000 34.74275 REMARK 290 SMTRY3 16 0.000000 0.000000 1.000000 104.22825 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 34.74275 REMARK 290 SMTRY2 17 0.000000 0.000000 1.000000 104.22825 REMARK 290 SMTRY3 17 0.000000 -1.000000 0.000000 104.22825 REMARK 290 SMTRY1 18 -1.000000 0.000000 0.000000 104.22825 REMARK 290 SMTRY2 18 0.000000 0.000000 1.000000 34.74275 REMARK 290 SMTRY3 18 0.000000 1.000000 0.000000 104.22825 REMARK 290 SMTRY1 19 -1.000000 0.000000 0.000000 34.74275 REMARK 290 SMTRY2 19 0.000000 0.000000 -1.000000 34.74275 REMARK 290 SMTRY3 19 0.000000 -1.000000 0.000000 34.74275 REMARK 290 SMTRY1 20 1.000000 0.000000 0.000000 104.22825 REMARK 290 SMTRY2 20 0.000000 0.000000 -1.000000 104.22825 REMARK 290 SMTRY3 20 0.000000 1.000000 0.000000 34.74275 REMARK 290 SMTRY1 21 0.000000 0.000000 1.000000 34.74275 REMARK 290 SMTRY2 21 0.000000 1.000000 0.000000 104.22825 REMARK 290 SMTRY3 21 -1.000000 0.000000 0.000000 104.22825 REMARK 290 SMTRY1 22 0.000000 0.000000 1.000000 104.22825 REMARK 290 SMTRY2 22 0.000000 -1.000000 0.000000 104.22825 REMARK 290 SMTRY3 22 1.000000 0.000000 0.000000 34.74275 REMARK 290 SMTRY1 23 0.000000 0.000000 -1.000000 104.22825 REMARK 290 SMTRY2 23 0.000000 1.000000 0.000000 34.74275 REMARK 290 SMTRY3 23 1.000000 0.000000 0.000000 104.22825 REMARK 290 SMTRY1 24 0.000000 0.000000 -1.000000 34.74275 REMARK 290 SMTRY2 24 0.000000 -1.000000 0.000000 34.74275 REMARK 290 SMTRY3 24 -1.000000 0.000000 0.000000 34.74275 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: 1150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 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 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 CL CL A 407 LIES ON A SPECIAL POSITION. REMARK 375 ZN ZN A 408 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 804 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 7 CD OE1 NE2 REMARK 470 TYR A 45 OH REMARK 470 LYS A 51 CD CE NZ REMARK 470 LYS A 84 NZ REMARK 470 LYS A 99 CG CD CE NZ REMARK 470 LYS A 126 CD CE NZ REMARK 470 ARG A 133 CZ NH1 NH2 REMARK 470 LYS A 164 CE NZ REMARK 470 GLN A 172 CD OE1 NE2 REMARK 470 LYS A 183 CE NZ REMARK 470 ARG A 204 CZ NH1 NH2 REMARK 470 LYS A 207 CD CE NZ REMARK 470 LYS A 290 CG CD CE NZ 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 686 O HOH A 735 2.08 REMARK 500 O HOH A 757 O HOH A 770 2.14 REMARK 500 OG SER A 64 O23 KL8 A 401 2.15 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 154 -67.26 -91.54 REMARK 500 VAL A 178 -58.96 -126.16 REMARK 500 TYR A 221 19.49 -159.06 REMARK 500 ALA A 307 124.70 -39.62 REMARK 500 ASN A 341 41.77 -98.96 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 A 856 DISTANCE = 6.11 ANGSTROMS 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 ZN A 408 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 13 NE2 REMARK 620 2 HIS A 13 NE2 0.0 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue KL8 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 408 DBREF 6YPD A 4 361 UNP P00811 AMPC_ECOLI 20 377 SEQRES 1 A 358 ALA PRO GLN GLN ILE ASN ASP ILE VAL HIS ARG THR ILE SEQRES 2 A 358 THR PRO LEU ILE GLU GLN GLN LYS ILE PRO GLY MET ALA SEQRES 3 A 358 VAL ALA VAL ILE TYR GLN GLY LYS PRO TYR TYR PHE THR SEQRES 4 A 358 TRP GLY TYR ALA ASP ILE ALA LYS LYS GLN PRO VAL THR SEQRES 5 A 358 GLN GLN THR LEU PHE GLU LEU GLY SER VAL SER LYS THR SEQRES 6 A 358 PHE THR GLY VAL LEU GLY GLY ASP ALA ILE ALA ARG GLY SEQRES 7 A 358 GLU ILE LYS LEU SER ASP PRO THR THR LYS TYR TRP PRO SEQRES 8 A 358 GLU LEU THR ALA LYS GLN TRP ASN GLY ILE THR LEU LEU SEQRES 9 A 358 HIS LEU ALA THR TYR THR ALA GLY GLY LEU PRO LEU GLN SEQRES 10 A 358 VAL PRO ASP GLU VAL LYS SER SER SER ASP LEU LEU ARG SEQRES 11 A 358 PHE TYR GLN ASN TRP GLN PRO ALA TRP ALA PRO GLY THR SEQRES 12 A 358 GLN ARG LEU TYR ALA ASN SER SER ILE GLY LEU PHE GLY SEQRES 13 A 358 ALA LEU ALA VAL LYS PRO SER GLY LEU SER PHE GLU GLN SEQRES 14 A 358 ALA MET GLN THR ARG VAL PHE GLN PRO LEU LYS LEU ASN SEQRES 15 A 358 HIS THR TRP ILE ASN VAL PRO PRO ALA GLU GLU LYS ASN SEQRES 16 A 358 TYR ALA TRP GLY TYR ARG GLU GLY LYS ALA VAL HIS VAL SEQRES 17 A 358 SER PRO GLY ALA LEU ASP ALA GLU ALA TYR GLY VAL LYS SEQRES 18 A 358 SER THR ILE GLU ASP MET ALA ARG TRP VAL GLN SER ASN SEQRES 19 A 358 LEU LYS PRO LEU ASP ILE ASN GLU LYS THR LEU GLN GLN SEQRES 20 A 358 GLY ILE GLN LEU ALA GLN SER ARG TYR TRP GLN THR GLY SEQRES 21 A 358 ASP MET TYR GLN GLY LEU GLY TRP GLU MET LEU ASP TRP SEQRES 22 A 358 PRO VAL ASN PRO ASP SER ILE ILE ASN GLY SER ASP ASN SEQRES 23 A 358 LYS ILE ALA LEU ALA ALA ARG PRO VAL LYS ALA ILE THR SEQRES 24 A 358 PRO PRO THR PRO ALA VAL ARG ALA SER TRP VAL HIS LYS SEQRES 25 A 358 THR GLY ALA THR GLY GLY PHE GLY SER TYR VAL ALA PHE SEQRES 26 A 358 ILE PRO GLU LYS GLU LEU GLY ILE VAL MET LEU ALA ASN SEQRES 27 A 358 LYS ASN TYR PRO ASN PRO ALA ARG VAL ASP ALA ALA TRP SEQRES 28 A 358 GLN ILE LEU ASN ALA LEU GLN HET KL8 A 401 22 HET PEG A 402 7 HET DMS A 403 4 HET EDO A 404 4 HET PEG A 405 7 HET EDO A 406 4 HET CL A 407 1 HET ZN A 408 1 HETNAM KL8 (3~{S})-2,2-BIS(OXIDANYL)-3-(PHENYLMETHYLSULFANYL)-3,4- HETNAM 2 KL8 DIHYDRO-1,2-BENZOXABORININ-2-IUM-8-CARBOXYLIC ACID HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM DMS DIMETHYL SULFOXIDE HETNAM EDO 1,2-ETHANEDIOL HETNAM CL CHLORIDE ION HETNAM ZN ZINC ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 KL8 C16 H16 B O5 S 1- FORMUL 3 PEG 2(C4 H10 O3) FORMUL 4 DMS C2 H6 O S FORMUL 5 EDO 2(C2 H6 O2) FORMUL 8 CL CL 1- FORMUL 9 ZN ZN 2+ FORMUL 10 HOH *356(H2 O) HELIX 1 AA1 PRO A 5 LYS A 24 1 20 HELIX 2 AA2 VAL A 65 ARG A 80 1 16 HELIX 3 AA3 PRO A 88 TRP A 93 1 6 HELIX 4 AA4 ALA A 98 ASN A 102 5 5 HELIX 5 AA5 THR A 105 THR A 111 1 7 HELIX 6 AA6 SER A 127 TRP A 138 1 12 HELIX 7 AA7 ALA A 151 VAL A 163 1 13 HELIX 8 AA8 SER A 169 VAL A 178 1 10 HELIX 9 AA9 PRO A 192 TYR A 199 5 8 HELIX 10 AB1 LEU A 216 TYR A 221 1 6 HELIX 11 AB2 THR A 226 LYS A 239 1 14 HELIX 12 AB3 PRO A 240 ILE A 243 5 4 HELIX 13 AB4 GLU A 245 GLN A 256 1 12 HELIX 14 AB5 ASN A 279 ASP A 288 1 10 HELIX 15 AB6 ASP A 288 LEU A 293 1 6 HELIX 16 AB7 PRO A 330 GLU A 333 5 4 HELIX 17 AB8 PRO A 345 GLN A 361 1 17 SHEET 1 AA110 GLN A 52 PRO A 53 0 SHEET 2 AA110 LYS A 37 ASP A 47 -1 N ALA A 46 O GLN A 52 SHEET 3 AA110 GLY A 27 TYR A 34 -1 N VAL A 30 O PHE A 41 SHEET 4 AA110 LEU A 334 ALA A 340 -1 O LEU A 339 N ALA A 29 SHEET 5 AA110 PHE A 322 ILE A 329 -1 N ILE A 329 O LEU A 334 SHEET 6 AA110 SER A 311 THR A 319 -1 N GLY A 317 O SER A 324 SHEET 7 AA110 GLU A 272 ASP A 275 -1 N LEU A 274 O TRP A 312 SHEET 8 AA110 MET A 265 GLN A 267 -1 N TYR A 266 O MET A 273 SHEET 9 AA110 ARG A 258 THR A 262 -1 N TYR A 259 O GLN A 267 SHEET 10 AA110 LYS A 299 THR A 305 -1 O LYS A 299 N GLN A 261 SHEET 1 AA2 3 PHE A 60 GLU A 61 0 SHEET 2 AA2 3 LYS A 224 SER A 225 -1 O SER A 225 N PHE A 60 SHEET 3 AA2 3 THR A 187 TRP A 188 -1 N TRP A 188 O LYS A 224 SHEET 1 AA3 2 GLN A 147 ARG A 148 0 SHEET 2 AA3 2 ARG A 296 PRO A 297 -1 O ARG A 296 N ARG A 148 SHEET 1 AA4 2 GLY A 202 ARG A 204 0 SHEET 2 AA4 2 LYS A 207 VAL A 209 -1 O VAL A 209 N GLY A 202 LINK OG SER A 64 B02 KL8 A 401 1555 1555 1.40 LINK NE2 HIS A 13 ZN ZN A 408 1555 1555 2.06 LINK NE2 HIS A 13 ZN ZN A 408 1555 5555 2.06 CISPEP 1 TRP A 276 PRO A 277 0 4.89 CISPEP 2 THR A 302 PRO A 303 0 -2.72 SITE 1 AC1 15 SER A 64 GLN A 120 TYR A 150 ASN A 152 SITE 2 AC1 15 VAL A 211 TYR A 221 ASN A 289 LYS A 315 SITE 3 AC1 15 THR A 316 GLY A 317 ALA A 318 ASN A 346 SITE 4 AC1 15 HOH A 502 HOH A 703 HOH A 745 SITE 1 AC2 1 LEU A 131 SITE 1 AC3 6 ASP A 281 ILE A 284 ASP A 351 GLN A 355 SITE 2 AC3 6 EDO A 404 HOH A 802 SITE 1 AC4 3 LYS A 246 GLN A 250 DMS A 403 SITE 1 AC5 6 LYS A 24 TYR A 40 THR A 42 THR A 55 SITE 2 AC5 6 GLN A 56 HOH A 538 SITE 1 AC6 2 ASN A 343 PRO A 345 SITE 1 AC7 2 HIS A 13 ZN A 408 SITE 1 AC8 2 HIS A 13 CL A 407 CRYST1 138.971 138.971 138.971 90.00 90.00 90.00 P 43 3 2 24 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 0.007196 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007196 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007196 0.00000