HEADER HYDROLASE 25-MAR-20 6YEN TITLE CRYSTAL STRUCTURE OF AMPC FROM E. COLI WITH TANIBORBACTAM (VNRX-5133) 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 K-12; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS BETA LACTAMASE, ANTIBIOTIC RESISTANCE, BICYCLIC BORONATE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.A.LANG,J.BREM,C.J.SCHOFIELD REVDAT 4 24-JAN-24 6YEN 1 REMARK REVDAT 3 30-SEP-20 6YEN 1 JRNL LINK REVDAT 2 01-JUL-20 6YEN 1 JRNL REVDAT 1 24-JUN-20 6YEN 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. 1.42 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) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 97.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 83425 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.144 REMARK 3 FREE R VALUE : 0.169 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 4112 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 97.0360 - 4.3577 1.00 3048 149 0.1671 0.1797 REMARK 3 2 4.3577 - 3.4588 1.00 2839 166 0.1272 0.1337 REMARK 3 3 3.4588 - 3.0215 1.00 2804 149 0.1496 0.1735 REMARK 3 4 3.0215 - 2.7453 1.00 2770 143 0.1457 0.1629 REMARK 3 5 2.7453 - 2.5485 1.00 2782 141 0.1396 0.1706 REMARK 3 6 2.5485 - 2.3982 1.00 2752 149 0.1302 0.1669 REMARK 3 7 2.3982 - 2.2781 1.00 2763 136 0.1203 0.1390 REMARK 3 8 2.2781 - 2.1789 1.00 2733 147 0.1207 0.1435 REMARK 3 9 2.1789 - 2.0950 1.00 2745 152 0.1220 0.1498 REMARK 3 10 2.0950 - 2.0227 1.00 2716 141 0.1221 0.1615 REMARK 3 11 2.0227 - 1.9595 1.00 2742 115 0.1188 0.1349 REMARK 3 12 1.9595 - 1.9035 1.00 2706 159 0.1217 0.1797 REMARK 3 13 1.9035 - 1.8534 1.00 2738 130 0.1220 0.1849 REMARK 3 14 1.8534 - 1.8081 1.00 2693 144 0.1229 0.1877 REMARK 3 15 1.8081 - 1.7670 1.00 2729 153 0.1285 0.1842 REMARK 3 16 1.7670 - 1.7294 1.00 2713 138 0.1306 0.1725 REMARK 3 17 1.7294 - 1.6948 1.00 2682 148 0.1346 0.1925 REMARK 3 18 1.6948 - 1.6628 1.00 2743 127 0.1450 0.2079 REMARK 3 19 1.6628 - 1.6331 1.00 2665 146 0.1458 0.2077 REMARK 3 20 1.6331 - 1.6055 1.00 2711 160 0.1562 0.1990 REMARK 3 21 1.6055 - 1.5796 1.00 2673 153 0.1739 0.1960 REMARK 3 22 1.5796 - 1.5552 1.00 2691 145 0.1785 0.2190 REMARK 3 23 1.5552 - 1.5324 1.00 2684 151 0.1918 0.2272 REMARK 3 24 1.5324 - 1.5108 1.00 2755 103 0.2151 0.2194 REMARK 3 25 1.5108 - 1.4904 1.00 2689 135 0.2281 0.2488 REMARK 3 26 1.4904 - 1.4710 1.00 2682 137 0.2405 0.2828 REMARK 3 27 1.4710 - 1.4526 1.00 2704 133 0.2485 0.3219 REMARK 3 28 1.4526 - 1.4351 1.00 2670 139 0.2712 0.2910 REMARK 3 29 1.4351 - 1.4184 1.00 2691 123 0.2690 0.3254 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.37 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 : 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 6YEN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1292107509. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-FEB-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) : 0.9787 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 83520 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.418 REMARK 200 RESOLUTION RANGE LOW (A) : 97.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 76.80 REMARK 200 R MERGE (I) : 0.13400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 78.60 REMARK 200 R MERGE FOR SHELL (I) : 6.37800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: 1IEM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 6.0, 15 % PEG6000, 0.01 M REMARK 280 ZNCL2, 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 68.61450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 68.61450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 68.61450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 68.61450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 68.61450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 68.61450 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 68.61450 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 68.61450 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 68.61450 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 68.61450 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 68.61450 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 68.61450 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 68.61450 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 68.61450 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 68.61450 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 68.61450 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 68.61450 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 68.61450 REMARK 290 SMTRY1 13 0.000000 1.000000 0.000000 34.30725 REMARK 290 SMTRY2 13 1.000000 0.000000 0.000000 102.92175 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 102.92175 REMARK 290 SMTRY1 14 0.000000 -1.000000 0.000000 34.30725 REMARK 290 SMTRY2 14 -1.000000 0.000000 0.000000 34.30725 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 34.30725 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 102.92175 REMARK 290 SMTRY2 15 -1.000000 0.000000 0.000000 102.92175 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 34.30725 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 102.92175 REMARK 290 SMTRY2 16 1.000000 0.000000 0.000000 34.30725 REMARK 290 SMTRY3 16 0.000000 0.000000 1.000000 102.92175 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 34.30725 REMARK 290 SMTRY2 17 0.000000 0.000000 1.000000 102.92175 REMARK 290 SMTRY3 17 0.000000 -1.000000 0.000000 102.92175 REMARK 290 SMTRY1 18 -1.000000 0.000000 0.000000 102.92175 REMARK 290 SMTRY2 18 0.000000 0.000000 1.000000 34.30725 REMARK 290 SMTRY3 18 0.000000 1.000000 0.000000 102.92175 REMARK 290 SMTRY1 19 -1.000000 0.000000 0.000000 34.30725 REMARK 290 SMTRY2 19 0.000000 0.000000 -1.000000 34.30725 REMARK 290 SMTRY3 19 0.000000 -1.000000 0.000000 34.30725 REMARK 290 SMTRY1 20 1.000000 0.000000 0.000000 102.92175 REMARK 290 SMTRY2 20 0.000000 0.000000 -1.000000 102.92175 REMARK 290 SMTRY3 20 0.000000 1.000000 0.000000 34.30725 REMARK 290 SMTRY1 21 0.000000 0.000000 1.000000 34.30725 REMARK 290 SMTRY2 21 0.000000 1.000000 0.000000 102.92175 REMARK 290 SMTRY3 21 -1.000000 0.000000 0.000000 102.92175 REMARK 290 SMTRY1 22 0.000000 0.000000 1.000000 102.92175 REMARK 290 SMTRY2 22 0.000000 -1.000000 0.000000 102.92175 REMARK 290 SMTRY3 22 1.000000 0.000000 0.000000 34.30725 REMARK 290 SMTRY1 23 0.000000 0.000000 -1.000000 102.92175 REMARK 290 SMTRY2 23 0.000000 1.000000 0.000000 34.30725 REMARK 290 SMTRY3 23 1.000000 0.000000 0.000000 102.92175 REMARK 290 SMTRY1 24 0.000000 0.000000 -1.000000 34.30725 REMARK 290 SMTRY2 24 0.000000 -1.000000 0.000000 34.30725 REMARK 290 SMTRY3 24 -1.000000 0.000000 0.000000 34.30725 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: 1570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -81.0 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 ZN ZN A 408 LIES ON A SPECIAL POSITION. REMARK 375 CL CL A 410 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 789 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 LYS A 51 CD CE NZ REMARK 470 LYS A 84 CE NZ REMARK 470 LYS A 99 CG CD CE NZ REMARK 470 ASP A 123 OD1 OD2 REMARK 470 GLU A 124 CG CD OE1 OE2 REMARK 470 LYS A 126 CG CD CE NZ REMARK 470 SER A 128 OG REMARK 470 ARG A 133 CZ NH1 NH2 REMARK 470 GLN A 139 CG CD OE1 NE2 REMARK 470 LYS A 164 CE NZ REMARK 470 LYS A 183 CE NZ REMARK 470 LYS A 197 CE NZ REMARK 470 ARG A 204 CZ NH1 NH2 REMARK 470 GLU A 205 CD OE1 OE2 REMARK 470 LYS A 207 CD CE NZ REMARK 470 SER A 212 OG REMARK 470 LYS A 239 NZ REMARK 470 LYS A 246 NZ REMARK 470 LYS A 290 CG CD CE NZ REMARK 470 LYS A 299 NZ REMARK 470 LYS A 332 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 764 O HOH A 785 2.14 REMARK 500 O HOH A 700 O HOH A 766 2.16 REMARK 500 OG SER A 64 O09 KJK A 401 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 757 O HOH A 770 15445 2.19 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 -65.50 -91.03 REMARK 500 VAL A 178 -61.39 -123.46 REMARK 500 TYR A 221 14.81 -158.98 REMARK 500 ASN A 341 40.55 -97.17 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 845 DISTANCE = 5.83 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 KJK A 401 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 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 413 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 217 OD1 REMARK 620 2 HOH A 521 O 90.2 REMARK 620 3 HOH A 646 O 79.7 98.9 REMARK 620 4 HOH A 742 O 92.2 71.2 167.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue KJK A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG 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 EDO 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 K9K 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 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 413 DBREF 6YEN 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 KJK A 401 24 HET MES A 402 12 HET PEG A 403 7 HET EDO A 404 4 HET EDO A 405 4 HET EDO A 406 4 HET K9K A 407 28 HET ZN A 408 1 HET ZN A 409 1 HET CL A 410 1 HET CL A 411 1 HET CL A 412 1 HET NA A 413 1 HETNAM KJK (3~{R})-3-[2-[4-(2-AZANYLETHYLAMINO) HETNAM 2 KJK CYCLOHEXYL]ETHANOYLAMINO]-2-OXIDANYL-3,4-DIHYDRO-1,2- HETNAM 3 KJK BENZOXABORININE-8-CARBOXYLIC ACID HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM EDO 1,2-ETHANEDIOL HETNAM K9K (10AR)-2-(((1R,4R)-4-((2-AMINOETHYL)AMINO)CYCLOHEXYL) HETNAM 2 K9K METHYL)-6-CARBOXY-4-HYDROXY-4,10A-DIHYDRO-10H-BENZO[5, HETNAM 3 K9K 6][1,2]OXABORININO[2,3-B][1,4,2]OXAZABOROL-4-UIDE HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 KJK C19 H28 B N3 O5 FORMUL 3 MES C6 H13 N O4 S FORMUL 4 PEG C4 H10 O3 FORMUL 5 EDO 3(C2 H6 O2) FORMUL 8 K9K C19 H27 B N3 O5 1- FORMUL 9 ZN 2(ZN 2+) FORMUL 11 CL 3(CL 1-) FORMUL 14 NA NA 1+ FORMUL 15 HOH *345(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 LYS A 164 GLY A 167 5 4 HELIX 9 AA9 SER A 169 VAL A 178 1 10 HELIX 10 AB1 PRO A 192 TYR A 199 5 8 HELIX 11 AB2 LEU A 216 TYR A 221 1 6 HELIX 12 AB3 THR A 226 LYS A 239 1 14 HELIX 13 AB4 PRO A 240 ILE A 243 5 4 HELIX 14 AB5 GLU A 245 GLN A 256 1 12 HELIX 15 AB6 ASN A 279 SER A 287 1 9 HELIX 16 AB7 ASP A 288 LEU A 293 1 6 HELIX 17 AB8 PRO A 330 GLU A 333 5 4 HELIX 18 AB9 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 GLY A 323 ILE A 329 -1 N ILE A 329 O LEU A 334 SHEET 6 AA110 SER A 311 ALA A 318 -1 N VAL A 313 O PHE A 328 SHEET 7 AA110 GLU A 272 ASP A 275 -1 N GLU A 272 O HIS A 314 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 THR A 262 O MET A 265 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 B07 KJK A 401 1555 1555 1.39 LINK NE2 HIS A 13 ZN ZN A 408 1555 1555 2.05 LINK NE2 HIS A 13 ZN ZN A 408 1555 5555 2.05 LINK OE1 GLU A 21 ZN ZN A 409 1555 1555 2.20 LINK OD1 ASP A 217 NA NA A 413 1555 1555 2.16 LINK NA NA A 413 O HOH A 521 1555 1555 2.54 LINK NA NA A 413 O HOH A 646 1555 1555 2.25 LINK NA NA A 413 O HOH A 742 1555 1555 2.20 CISPEP 1 TRP A 276 PRO A 277 0 3.05 CISPEP 2 THR A 302 PRO A 303 0 -4.32 SITE 1 AC1 13 SER A 64 GLN A 120 TYR A 150 ASN A 152 SITE 2 AC1 13 ASN A 289 LYS A 315 THR A 316 ALA A 318 SITE 3 AC1 13 THR A 319 GLY A 320 ASN A 346 HOH A 524 SITE 4 AC1 13 HOH A 711 SITE 1 AC2 7 GLN A 22 GLN A 23 LYS A 24 TYR A 40 SITE 2 AC2 7 THR A 42 GLN A 56 HOH A 506 SITE 1 AC3 1 TRP A 93 SITE 1 AC4 5 PRO A 5 LEU A 241 GLN A 249 HOH A 548 SITE 2 AC4 5 HOH A 671 SITE 1 AC5 3 GLY A 36 LYS A 37 GLN A 235 SITE 1 AC6 4 LYS A 50 GLY A 206 LYS A 207 ALA A 208 SITE 1 AC7 11 THR A 97 GLN A 136 ASN A 137 PRO A 140 SITE 2 AC7 11 ALA A 141 TRP A 142 HOH A 509 HOH A 513 SITE 3 AC7 11 HOH A 593 HOH A 597 HOH A 658 SITE 1 AC8 2 HIS A 13 CL A 410 SITE 1 AC9 3 THR A 17 GLU A 21 HOH A 775 SITE 1 AD1 2 HIS A 13 ZN A 408 SITE 1 AD2 2 GLY A 320 HOH A 727 SITE 1 AD3 4 GLU A 171 GLN A 175 ILE A 189 ASN A 190 SITE 1 AD4 4 ASP A 217 HOH A 521 HOH A 646 HOH A 742 CRYST1 137.229 137.229 137.229 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 0.007287 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007287 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007287 0.00000