HEADER HYDROLASE 10-MAY-13 4KNK TITLE CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS HYDROLASE AMIA COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL AUTOLYSIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 198-421; COMPND 5 SYNONYM: N-ACETYLMURAMOYL-L-ALANINE AMIDASE, MANNOSYL-GLYCOPROTEIN COMPND 6 ENDO-BETA-N-ACETYLGLUCOSAMINIDASE, AMIA; COMPND 7 EC: 3.5.1.28, 3.2.1.96; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS; SOURCE 3 ORGANISM_TAXID: 93061; SOURCE 4 STRAIN: NCTC 8325; SOURCE 5 GENE: ATL, NAG, SAOUHSC_00994; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-4T3 KEYWDS PEPTIDOGLYCAN, AUTOLYSIN, AMIDASE, N-ACETYLMURAMOYL-L-ALANINE KEYWDS 2 AMIDASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR F.M.BUETTNER,S.ZOLL,T.STEHLE REVDAT 3 20-SEP-23 4KNK 1 REMARK SEQADV LINK REVDAT 2 03-DEC-14 4KNK 1 JRNL REVDAT 1 12-MAR-14 4KNK 0 JRNL AUTH F.M.BUTTNER,S.ZOLL,M.NEGA,F.GOTZ,T.STEHLE JRNL TITL STRUCTURE-FUNCTION ANALYSIS OF STAPHYLOCOCCUS AUREUS AMIDASE JRNL TITL 2 REVEALS THE DETERMINANTS OF PEPTIDOGLYCAN RECOGNITION AND JRNL TITL 3 CLEAVAGE. JRNL REF J.BIOL.CHEM. V. 289 11083 2014 JRNL REFN ISSN 0021-9258 JRNL PMID 24599952 JRNL DOI 10.1074/JBC.M114.557306 REMARK 2 REMARK 2 RESOLUTION. 1.12 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) 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) : 1.12 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 3 NUMBER OF REFLECTIONS : 146365 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.122 REMARK 3 R VALUE (WORKING SET) : 0.121 REMARK 3 FREE R VALUE : 0.139 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 7319 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 40.8670 - 3.4918 1.00 5098 269 0.1333 0.1398 REMARK 3 2 3.4918 - 2.7718 1.00 5022 264 0.1352 0.1386 REMARK 3 3 2.7718 - 2.4214 1.00 5002 263 0.1353 0.1431 REMARK 3 4 2.4214 - 2.2001 1.00 5025 265 0.1228 0.1282 REMARK 3 5 2.2001 - 2.0424 1.00 4963 261 0.1094 0.1263 REMARK 3 6 2.0424 - 1.9220 1.00 5005 264 0.1094 0.1214 REMARK 3 7 1.9220 - 1.8257 1.00 4986 262 0.1081 0.1339 REMARK 3 8 1.8257 - 1.7462 1.00 4998 263 0.1063 0.1373 REMARK 3 9 1.7462 - 1.6790 1.00 4966 262 0.1032 0.1223 REMARK 3 10 1.6790 - 1.6211 1.00 4968 261 0.0925 0.1092 REMARK 3 11 1.6211 - 1.5704 0.99 4946 260 0.0883 0.1146 REMARK 3 12 1.5704 - 1.5255 0.99 4955 261 0.0885 0.1174 REMARK 3 13 1.5255 - 1.4853 0.99 4942 260 0.0954 0.1220 REMARK 3 14 1.4853 - 1.4491 0.98 4877 257 0.0944 0.1325 REMARK 3 15 1.4491 - 1.4161 0.98 4878 257 0.0987 0.1596 REMARK 3 16 1.4161 - 1.3860 0.97 4770 251 0.1057 0.1444 REMARK 3 17 1.3860 - 1.3583 0.96 4816 253 0.1072 0.1484 REMARK 3 18 1.3583 - 1.3327 0.96 4765 251 0.1106 0.1426 REMARK 3 19 1.3327 - 1.3088 0.96 4769 251 0.1125 0.1370 REMARK 3 20 1.3088 - 1.2867 0.95 4690 247 0.1178 0.1599 REMARK 3 21 1.2867 - 1.2659 0.94 4636 244 0.1222 0.1417 REMARK 3 22 1.2659 - 1.2464 0.93 4649 245 0.1269 0.1507 REMARK 3 23 1.2464 - 1.2281 0.90 4451 234 0.1260 0.1686 REMARK 3 24 1.2281 - 1.2108 0.89 4435 233 0.1335 0.1606 REMARK 3 25 1.2108 - 1.1944 0.88 4358 230 0.1465 0.1665 REMARK 3 26 1.1944 - 1.1789 0.87 4333 228 0.1501 0.1705 REMARK 3 27 1.1789 - 1.1642 0.83 4108 216 0.1521 0.1888 REMARK 3 28 1.1642 - 1.1502 0.78 3836 202 0.1747 0.2173 REMARK 3 29 1.1502 - 1.1368 0.72 3632 191 0.2109 0.2460 REMARK 3 30 1.1368 - 1.1240 0.44 2167 114 0.2519 0.2511 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) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.490 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.70 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 : 0.009 3457 REMARK 3 ANGLE : 1.328 4718 REMARK 3 CHIRALITY : 0.084 481 REMARK 3 PLANARITY : 0.008 623 REMARK 3 DIHEDRAL : 12.207 1213 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 4KNK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000079561. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : BARTELS SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 146370 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.120 REMARK 200 RESOLUTION RANGE LOW (A) : 48.164 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.12 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 59.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3LAT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES/IMIDAZOLE, PH 6.5, 0.02 M REMARK 280 SODIUM FORMATE, 0.02 M AMMONIUM ACETATE, 0.02 M SODIUM CITRATE, REMARK 280 0.02 M RACEMIC SODIUM/POTASSIUM TARTRATE, 0.02 M SODIUM OXAMATE, REMARK 280 12.5% W/V PEG1000, 12.5% W/V PEG3350, 12.5% W/V MPD, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 48.40000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.84000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 48.40000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 40.84000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 HOH A 858 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 861 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 GLY A 197 REMARK 465 SER A 198 REMARK 465 ALA A 199 REMARK 465 SER A 200 REMARK 465 ALA A 201 REMARK 465 GLN A 202 REMARK 465 PRO A 203 REMARK 465 ARG A 204 REMARK 465 SER A 205 REMARK 465 VAL A 206 REMARK 465 ALA A 207 REMARK 465 ALA A 208 REMARK 465 THR A 209 REMARK 465 PRO A 210 REMARK 465 LYS A 211 REMARK 465 GLY A 418 REMARK 465 THR A 419 REMARK 465 GLN A 420 REMARK 465 SER A 421 REMARK 465 GLY B 197 REMARK 465 SER B 198 REMARK 465 ALA B 199 REMARK 465 SER B 200 REMARK 465 ALA B 201 REMARK 465 GLN B 202 REMARK 465 PRO B 203 REMARK 465 ARG B 204 REMARK 465 SER B 205 REMARK 465 VAL B 206 REMARK 465 ALA B 207 REMARK 465 ALA B 208 REMARK 465 THR B 209 REMARK 465 PRO B 210 REMARK 465 LYS B 211 REMARK 465 THR B 212 REMARK 465 SER B 421 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 216 CD CE NZ REMARK 470 LYS A 231 CG CD CE NZ REMARK 470 LYS A 235 CE NZ REMARK 470 LYS A 238 CG CD CE NZ REMARK 470 ARG A 271 CD NE CZ NH1 NH2 REMARK 470 LYS A 355 CD CE NZ REMARK 470 LYS A 413 CE NZ REMARK 470 LYS B 216 CD CE NZ REMARK 470 LYS B 231 CG CD CE NZ REMARK 470 LYS B 235 CE NZ REMARK 470 LYS B 238 CG CD CE NZ REMARK 470 ARG B 271 CD NE CZ NH1 NH2 REMARK 470 LYS B 355 CD CE NZ REMARK 470 LYS B 413 CE NZ REMARK 470 GLN B 420 CG CD OE1 NE2 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 869 O HOH A 870 1.96 REMARK 500 O HOH A 659 O HOH A 671 2.10 REMARK 500 O HOH A 708 O HOH A 770 2.13 REMARK 500 O HOH A 769 O HOH A 786 2.17 REMARK 500 O HOH B 642 O HOH B 814 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 TRP A 310 72.28 -101.40 REMARK 500 VAL A 312 19.47 -146.61 REMARK 500 ASP B 295 -159.70 -130.68 REMARK 500 VAL B 312 22.79 -149.84 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 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 265 ND1 REMARK 620 2 HIS A 370 ND1 93.3 REMARK 620 3 ASP A 384 OD2 105.3 118.6 REMARK 620 4 HOH A 604 O 155.8 91.8 92.9 REMARK 620 5 HOH A 605 O 94.4 146.4 90.6 69.1 REMARK 620 6 HOH A 811 O 81.9 87.3 152.0 74.8 61.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 503 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 357 OD1 REMARK 620 2 SER A 358 O 86.6 REMARK 620 3 ASP A 362 OD2 143.5 119.5 REMARK 620 4 ASP A 362 OD1 166.7 86.0 49.5 REMARK 620 5 ASN A 364 O 94.4 91.2 108.9 74.7 REMARK 620 6 HOH A 729 O 75.7 162.0 77.9 110.6 86.8 REMARK 620 7 HOH A 731 O 77.4 81.2 81.7 112.3 169.1 98.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 265 ND1 REMARK 620 2 HIS B 370 ND1 93.1 REMARK 620 3 ASP B 384 OD2 106.4 118.9 REMARK 620 4 HOH B 605 O 159.6 86.9 91.3 REMARK 620 5 HOH B 606 O 94.7 144.3 92.1 74.2 REMARK 620 6 HOH B 796 O 85.8 84.1 152.4 73.9 61.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 504 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 305 OG1 REMARK 620 2 HOH B 607 O 97.9 REMARK 620 3 HOH B 609 O 85.7 93.7 REMARK 620 4 HOH B 610 O 112.8 149.3 87.4 REMARK 620 5 HOH B 616 O 97.1 95.0 170.4 83.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 503 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 357 OD1 REMARK 620 2 SER B 358 O 86.9 REMARK 620 3 ASP B 362 OD2 140.9 121.7 REMARK 620 4 ASP B 362 OD1 170.3 86.7 48.7 REMARK 620 5 ASN B 364 O 97.3 90.5 107.5 75.4 REMARK 620 6 HOH B 707 O 76.5 82.8 81.1 110.0 171.1 REMARK 620 7 HOH B 709 O 75.9 161.4 76.9 109.3 84.7 99.8 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 ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMD A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMD B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG B 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMD B 506 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3LAT RELATED DB: PDB REMARK 900 STRUCTURE OF HOMOLOGOUS PROTEIN AMIE FROM S. EPIDERMIDIS REMARK 900 RELATED ID: 4KNL RELATED DB: PDB REMARK 900 STRUCTURE OF AMIA WITH LIGAND DBREF 4KNK A 198 421 UNP Q2FZK7 ATL_STAA8 198 421 DBREF 4KNK B 198 421 UNP Q2FZK7 ATL_STAA8 198 421 SEQADV 4KNK GLY A 197 UNP Q2FZK7 EXPRESSION TAG SEQADV 4KNK GLY B 197 UNP Q2FZK7 EXPRESSION TAG SEQRES 1 A 225 GLY SER ALA SER ALA GLN PRO ARG SER VAL ALA ALA THR SEQRES 2 A 225 PRO LYS THR SER LEU PRO LYS TYR LYS PRO GLN VAL ASN SEQRES 3 A 225 SER SER ILE ASN ASP TYR ILE CYS LYS ASN ASN LEU LYS SEQRES 4 A 225 ALA PRO LYS ILE GLU GLU ASP TYR THR SER TYR PHE PRO SEQRES 5 A 225 LYS TYR ALA TYR ARG ASN GLY VAL GLY ARG PRO GLU GLY SEQRES 6 A 225 ILE VAL VAL HIS ASP THR ALA ASN ASP ARG SER THR ILE SEQRES 7 A 225 ASN GLY GLU ILE SER TYR MET LYS ASN ASN TYR GLN ASN SEQRES 8 A 225 ALA PHE VAL HIS ALA PHE VAL ASP GLY ASP ARG ILE ILE SEQRES 9 A 225 GLU THR ALA PRO THR ASP TYR LEU SER TRP GLY VAL GLY SEQRES 10 A 225 ALA VAL GLY ASN PRO ARG PHE ILE ASN VAL GLU ILE VAL SEQRES 11 A 225 HIS THR HIS ASP TYR ALA SER PHE ALA ARG SER MET ASN SEQRES 12 A 225 ASN TYR ALA ASP TYR ALA ALA THR GLN LEU GLN TYR TYR SEQRES 13 A 225 GLY LEU LYS PRO ASP SER ALA GLU TYR ASP GLY ASN GLY SEQRES 14 A 225 THR VAL TRP THR HIS TYR ALA VAL SER LYS TYR LEU GLY SEQRES 15 A 225 GLY THR ASP HIS ALA ASP PRO HIS GLY TYR LEU ARG SER SEQRES 16 A 225 HIS ASN TYR SER TYR ASP GLN LEU TYR ASP LEU ILE ASN SEQRES 17 A 225 GLU LYS TYR LEU ILE LYS MET GLY LYS VAL ALA PRO TRP SEQRES 18 A 225 GLY THR GLN SER SEQRES 1 B 225 GLY SER ALA SER ALA GLN PRO ARG SER VAL ALA ALA THR SEQRES 2 B 225 PRO LYS THR SER LEU PRO LYS TYR LYS PRO GLN VAL ASN SEQRES 3 B 225 SER SER ILE ASN ASP TYR ILE CYS LYS ASN ASN LEU LYS SEQRES 4 B 225 ALA PRO LYS ILE GLU GLU ASP TYR THR SER TYR PHE PRO SEQRES 5 B 225 LYS TYR ALA TYR ARG ASN GLY VAL GLY ARG PRO GLU GLY SEQRES 6 B 225 ILE VAL VAL HIS ASP THR ALA ASN ASP ARG SER THR ILE SEQRES 7 B 225 ASN GLY GLU ILE SER TYR MET LYS ASN ASN TYR GLN ASN SEQRES 8 B 225 ALA PHE VAL HIS ALA PHE VAL ASP GLY ASP ARG ILE ILE SEQRES 9 B 225 GLU THR ALA PRO THR ASP TYR LEU SER TRP GLY VAL GLY SEQRES 10 B 225 ALA VAL GLY ASN PRO ARG PHE ILE ASN VAL GLU ILE VAL SEQRES 11 B 225 HIS THR HIS ASP TYR ALA SER PHE ALA ARG SER MET ASN SEQRES 12 B 225 ASN TYR ALA ASP TYR ALA ALA THR GLN LEU GLN TYR TYR SEQRES 13 B 225 GLY LEU LYS PRO ASP SER ALA GLU TYR ASP GLY ASN GLY SEQRES 14 B 225 THR VAL TRP THR HIS TYR ALA VAL SER LYS TYR LEU GLY SEQRES 15 B 225 GLY THR ASP HIS ALA ASP PRO HIS GLY TYR LEU ARG SER SEQRES 16 B 225 HIS ASN TYR SER TYR ASP GLN LEU TYR ASP LEU ILE ASN SEQRES 17 B 225 GLU LYS TYR LEU ILE LYS MET GLY LYS VAL ALA PRO TRP SEQRES 18 B 225 GLY THR GLN SER HET ZN A 501 1 HET IMD A 502 5 HET NA A 503 1 HET FMT A 504 3 HET PEG A 505 7 HET EDO A 506 4 HET ZN B 501 1 HET IMD B 502 5 HET NA B 503 1 HET NA B 504 1 HET PEG B 505 7 HET IMD B 506 5 HETNAM ZN ZINC ION HETNAM IMD IMIDAZOLE HETNAM NA SODIUM ION HETNAM FMT FORMIC ACID HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ZN 2(ZN 2+) FORMUL 4 IMD 3(C3 H5 N2 1+) FORMUL 5 NA 3(NA 1+) FORMUL 6 FMT C H2 O2 FORMUL 7 PEG 2(C4 H10 O3) FORMUL 8 EDO C2 H6 O2 FORMUL 15 HOH *535(H2 O) HELIX 1 1 SER A 223 ASN A 232 1 10 HELIX 2 2 THR A 273 TYR A 285 1 13 HELIX 3 3 VAL A 312 ASN A 317 1 6 HELIX 4 4 ASP A 330 GLY A 353 1 24 HELIX 5 5 HIS A 370 LEU A 377 1 8 HELIX 6 6 PRO A 385 HIS A 392 1 8 HELIX 7 7 SER A 395 MET A 411 1 17 HELIX 8 8 SER B 223 ASN B 232 1 10 HELIX 9 9 THR B 273 ASN B 284 1 12 HELIX 10 10 VAL B 312 ASN B 317 1 6 HELIX 11 11 ASP B 330 GLY B 353 1 24 HELIX 12 12 HIS B 370 LEU B 377 1 8 HELIX 13 13 PRO B 385 HIS B 392 1 8 HELIX 14 14 SER B 395 MET B 411 1 17 SHEET 1 A 6 ILE A 239 GLU A 241 0 SHEET 2 A 6 ILE A 299 GLU A 301 1 O GLU A 301 N GLU A 240 SHEET 3 A 6 ALA A 292 VAL A 294 -1 N PHE A 293 O ILE A 300 SHEET 4 A 6 PHE A 320 ILE A 325 1 O GLU A 324 N ALA A 292 SHEET 5 A 6 GLY A 261 ASP A 266 1 N VAL A 263 O ILE A 321 SHEET 6 A 6 VAL A 367 THR A 369 1 O TRP A 368 N ILE A 262 SHEET 1 B 6 ILE B 239 GLU B 241 0 SHEET 2 B 6 ILE B 299 GLU B 301 1 O GLU B 301 N GLU B 240 SHEET 3 B 6 ALA B 292 VAL B 294 -1 N PHE B 293 O ILE B 300 SHEET 4 B 6 PHE B 320 ILE B 325 1 O GLU B 324 N ALA B 292 SHEET 5 B 6 GLY B 261 ASP B 266 1 N VAL B 263 O ILE B 321 SHEET 6 B 6 VAL B 367 THR B 369 1 O TRP B 368 N ILE B 262 LINK ND1 HIS A 265 ZN ZN A 501 1555 1555 2.15 LINK OD1 ASP A 357 NA NA A 503 1555 1555 2.50 LINK O SER A 358 NA NA A 503 1555 1555 2.42 LINK OD2 ASP A 362 NA NA A 503 1555 1555 2.53 LINK OD1 ASP A 362 NA NA A 503 1555 1555 2.65 LINK O ASN A 364 NA NA A 503 1555 1555 2.33 LINK ND1 HIS A 370 ZN ZN A 501 1555 1555 2.06 LINK OD2 ASP A 384 ZN ZN A 501 1555 1555 2.07 LINK ZN ZN A 501 O HOH A 604 1555 1555 2.44 LINK ZN ZN A 501 O HOH A 605 1555 1555 2.22 LINK ZN ZN A 501 O HOH A 811 1555 1555 2.67 LINK NA NA A 503 O HOH A 729 1555 1555 2.49 LINK NA NA A 503 O HOH A 731 1555 1555 2.41 LINK ND1 HIS B 265 ZN ZN B 501 1555 1555 2.16 LINK OG1 THR B 305 NA NA B 504 1555 1555 2.33 LINK OD1 ASP B 357 NA NA B 503 1555 1555 2.56 LINK O SER B 358 NA NA B 503 1555 1555 2.41 LINK OD2 ASP B 362 NA NA B 503 1555 1555 2.59 LINK OD1 ASP B 362 NA NA B 503 1555 1555 2.66 LINK O ASN B 364 NA NA B 503 1555 1555 2.33 LINK ND1 HIS B 370 ZN ZN B 501 1555 1555 2.05 LINK OD2 ASP B 384 ZN ZN B 501 1555 1555 2.05 LINK ZN ZN B 501 O HOH B 605 1555 1555 2.40 LINK ZN ZN B 501 O HOH B 606 1555 1555 2.14 LINK ZN ZN B 501 O HOH B 796 1555 1555 2.64 LINK NA NA B 503 O HOH B 707 1555 1555 2.40 LINK NA NA B 503 O HOH B 709 1555 1555 2.65 LINK NA NA B 504 O HOH B 607 1555 1555 2.36 LINK NA NA B 504 O HOH B 609 1555 1555 2.36 LINK NA NA B 504 O HOH B 610 1555 1555 2.38 LINK NA NA B 504 O HOH B 616 1555 1555 2.35 CISPEP 1 ASP A 384 PRO A 385 0 6.93 CISPEP 2 ASP B 384 PRO B 385 0 8.71 SITE 1 AC1 6 HIS A 265 HIS A 370 ASP A 384 HOH A 604 SITE 2 AC1 6 HOH A 605 HOH A 811 SITE 1 AC2 6 PRO A 219 ASN A 226 ASP A 227 CYS A 230 SITE 2 AC2 6 GLU A 405 HOH A 722 SITE 1 AC3 6 ASP A 357 SER A 358 ASP A 362 ASN A 364 SITE 2 AC3 6 HOH A 729 HOH A 731 SITE 1 AC4 5 THR A 244 SER A 245 HOH A 721 HOH A 740 SITE 2 AC4 5 GLN B 350 SITE 1 AC5 7 ALA A 314 ASN A 317 EDO A 506 HOH A 622 SITE 2 AC5 7 HOH A 652 HOH A 656 HOH A 812 SITE 1 AC6 3 GLN A 286 TRP A 310 PEG A 505 SITE 1 AC7 6 HIS B 265 HIS B 370 ASP B 384 HOH B 605 SITE 2 AC7 6 HOH B 606 HOH B 796 SITE 1 AC8 7 PRO B 219 ASN B 226 ASP B 227 CYS B 230 SITE 2 AC8 7 GLU B 405 HOH B 718 HOH B 843 SITE 1 AC9 6 ASP B 357 SER B 358 ASP B 362 ASN B 364 SITE 2 AC9 6 HOH B 707 HOH B 709 SITE 1 BC1 6 TYR A 243 THR B 305 HOH B 607 HOH B 609 SITE 2 BC1 6 HOH B 610 HOH B 616 SITE 1 BC2 3 TYR B 250 TRP B 310 HOH B 601 SITE 1 BC3 3 GLN B 286 TRP B 310 HOH B 823 CRYST1 96.800 81.680 68.690 90.00 128.84 90.00 C 1 2 1 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 0.010331 0.000000 0.008319 0.00000 SCALE2 0.000000 0.012243 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018691 0.00000