HEADER HYDROLASE 25-NOV-14 4RVA TITLE A TRIPLE MUTANT IN THE OMEGA-LOOP OF TEM-1 BETA-LACTAMASE CHANGES THE TITLE 2 SUBSTRATE PROFILE VIA A LARGE CONFORMATIONAL CHANGE AND AN ALTERED TITLE 3 GENERAL BASE FOR DEACYLATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE TEM; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TEM-1; COMPND 5 SYNONYM: IRT-4, PENICILLINASE, TEM-1, TEM-16/CAZ-7, TEM-2, TEM- COMPND 6 24/CAZ-6, TEM-3, TEM-4, TEM-5, TEM-6, TEM-8/CAZ-2; COMPND 7 EC: 3.5.2.6; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: BLA, BLAT-3, BLAT-4, BLAT-5, BLAT-6; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLOBULAR, BETA-LACTAMASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR V.STOJANOSKI,D.-C.CHOW,L.HU,B.SANKARAN,H.GILBERT,B.V.V.PRASAD, AUTHOR 2 T.PALZKILL REVDAT 5 06-NOV-24 4RVA 1 REMARK REVDAT 4 20-SEP-23 4RVA 1 REMARK SEQADV REVDAT 3 06-MAY-15 4RVA 1 JRNL REVDAT 2 11-MAR-15 4RVA 1 JRNL REVDAT 1 04-MAR-15 4RVA 0 JRNL AUTH V.STOJANOSKI,D.C.CHOW,L.HU,B.SANKARAN,H.F.GILBERT, JRNL AUTH 2 B.V.PRASAD,T.PALZKILL JRNL TITL A TRIPLE MUTANT IN THE OMEGA-LOOP OF TEM-1 BETA-LACTAMASE JRNL TITL 2 CHANGES THE SUBSTRATE PROFILE VIA A LARGE CONFORMATIONAL JRNL TITL 3 CHANGE AND AN ALTERED GENERAL BASE FOR CATALYSIS. JRNL REF J.BIOL.CHEM. V. 290 10382 2015 JRNL REFN ISSN 0021-9258 JRNL PMID 25713062 JRNL DOI 10.1074/JBC.M114.633438 REMARK 2 REMARK 2 RESOLUTION. 1.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1819) 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) : 1.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.910 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 106104 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.180 REMARK 3 FREE R VALUE TEST SET COUNT : 5491 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 49.0096 - 4.4723 1.00 3341 208 0.1435 0.1569 REMARK 3 2 4.4723 - 3.5501 1.00 3375 182 0.1333 0.1488 REMARK 3 3 3.5501 - 3.1014 1.00 3364 154 0.1582 0.1570 REMARK 3 4 3.1014 - 2.8179 1.00 3332 206 0.1727 0.2118 REMARK 3 5 2.8179 - 2.6159 1.00 3386 146 0.1704 0.2377 REMARK 3 6 2.6159 - 2.4617 1.00 3345 198 0.1728 0.1829 REMARK 3 7 2.4617 - 2.3384 1.00 3445 140 0.1665 0.1895 REMARK 3 8 2.3384 - 2.2366 1.00 3384 172 0.1602 0.1977 REMARK 3 9 2.2366 - 2.1505 1.00 3329 206 0.1548 0.1755 REMARK 3 10 2.1505 - 2.0763 1.00 3358 172 0.1647 0.2021 REMARK 3 11 2.0763 - 2.0114 1.00 3420 134 0.1662 0.2133 REMARK 3 12 2.0114 - 1.9539 1.00 3388 157 0.1671 0.2125 REMARK 3 13 1.9539 - 1.9025 1.00 3346 165 0.1724 0.1908 REMARK 3 14 1.9025 - 1.8560 1.00 3356 195 0.1752 0.1968 REMARK 3 15 1.8560 - 1.8138 1.00 3378 170 0.1815 0.2154 REMARK 3 16 1.8138 - 1.7752 1.00 3303 219 0.1778 0.2268 REMARK 3 17 1.7752 - 1.7397 1.00 3347 177 0.1755 0.2297 REMARK 3 18 1.7397 - 1.7069 1.00 3361 223 0.1786 0.1995 REMARK 3 19 1.7069 - 1.6764 1.00 3331 179 0.1877 0.1939 REMARK 3 20 1.6764 - 1.6480 1.00 3314 193 0.1942 0.2447 REMARK 3 21 1.6480 - 1.6214 1.00 3395 187 0.1778 0.2447 REMARK 3 22 1.6214 - 1.5965 1.00 3345 173 0.1902 0.2143 REMARK 3 23 1.5965 - 1.5730 1.00 3375 160 0.1952 0.2136 REMARK 3 24 1.5730 - 1.5508 1.00 3336 201 0.1987 0.2042 REMARK 3 25 1.5508 - 1.5299 1.00 3345 199 0.2128 0.2322 REMARK 3 26 1.5299 - 1.5100 1.00 3286 218 0.2162 0.2276 REMARK 3 27 1.5100 - 1.4911 1.00 3338 201 0.2271 0.2502 REMARK 3 28 1.4911 - 1.4731 0.99 3332 200 0.2245 0.2384 REMARK 3 29 1.4731 - 1.4560 0.99 3387 169 0.2364 0.2550 REMARK 3 30 1.4560 - 1.4397 0.99 3271 187 0.2508 0.2840 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.380 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 : 0.007 2100 REMARK 3 ANGLE : 1.087 2851 REMARK 3 CHIRALITY : 0.043 323 REMARK 3 PLANARITY : 0.005 373 REMARK 3 DIHEDRAL : 13.017 793 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 4RVA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1000087839. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JAN-14 REMARK 200 TEMPERATURE (KELVIN) : 200.0 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.997 REMARK 200 MONOCHROMATOR : ASYMMETRIC CURVED CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55742 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.440 REMARK 200 RESOLUTION RANGE LOW (A) : 59.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.59700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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 1BTL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2M SODIUM CITRATE, PH REMARK 280 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 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 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 29.52250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.13000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.75250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.13000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.52250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.75250 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 MET A 69 -147.70 53.62 REMARK 500 TYR A 105 81.22 60.34 REMARK 500 ALA A 172 74.75 54.42 REMARK 500 LEU A 220 -125.51 -102.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BCT A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BTL RELATED DB: PDB DBREF 4RVA A 26 290 UNP P62593 BLAT_ECOLX 24 286 SEQADV 4RVA TYR A 165 UNP P62593 TRP 163 ENGINEERED MUTATION SEQADV 4RVA TYR A 166 UNP P62593 GLU 164 ENGINEERED MUTATION SEQADV 4RVA GLY A 167 UNP P62593 PRO 165 ENGINEERED MUTATION SEQADV 4RVA PRO A 201 UNP P62593 LEU 199 ENGINEERED MUTATION SEQRES 1 A 263 HIS PRO GLU THR LEU VAL LYS VAL LYS ASP ALA GLU ASP SEQRES 2 A 263 GLN LEU GLY ALA ARG VAL GLY TYR ILE GLU LEU ASP LEU SEQRES 3 A 263 ASN SER GLY LYS ILE LEU GLU SER PHE ARG PRO GLU GLU SEQRES 4 A 263 ARG PHE PRO MET MET SER THR PHE LYS VAL LEU LEU CYS SEQRES 5 A 263 GLY ALA VAL LEU SER ARG VAL ASP ALA GLY GLN GLU GLN SEQRES 6 A 263 LEU GLY ARG ARG ILE HIS TYR SER GLN ASN ASP LEU VAL SEQRES 7 A 263 GLU TYR SER PRO VAL THR GLU LYS HIS LEU THR ASP GLY SEQRES 8 A 263 MET THR VAL ARG GLU LEU CYS SER ALA ALA ILE THR MET SEQRES 9 A 263 SER ASP ASN THR ALA ALA ASN LEU LEU LEU THR THR ILE SEQRES 10 A 263 GLY GLY PRO LYS GLU LEU THR ALA PHE LEU HIS ASN MET SEQRES 11 A 263 GLY ASP HIS VAL THR ARG LEU ASP ARG TYR TYR GLY GLU SEQRES 12 A 263 LEU ASN GLU ALA ILE PRO ASN ASP GLU ARG ASP THR THR SEQRES 13 A 263 MET PRO ALA ALA MET ALA THR THR LEU ARG LYS LEU LEU SEQRES 14 A 263 THR GLY GLU LEU LEU THR PRO ALA SER ARG GLN GLN LEU SEQRES 15 A 263 ILE ASP TRP MET GLU ALA ASP LYS VAL ALA GLY PRO LEU SEQRES 16 A 263 LEU ARG SER ALA LEU PRO ALA GLY TRP PHE ILE ALA ASP SEQRES 17 A 263 LYS SER GLY ALA GLY GLU ARG GLY SER ARG GLY ILE ILE SEQRES 18 A 263 ALA ALA LEU GLY PRO ASP GLY LYS PRO SER ARG ILE VAL SEQRES 19 A 263 VAL ILE TYR THR THR GLY SER GLN ALA THR MET ASP GLU SEQRES 20 A 263 ARG ASN ARG GLN ILE ALA GLU ILE GLY ALA SER LEU ILE SEQRES 21 A 263 LYS HIS TRP HET BCT A 301 4 HETNAM BCT BICARBONATE ION FORMUL 2 BCT C H O3 1- FORMUL 3 HOH *435(H2 O) HELIX 1 1 HIS A 26 GLY A 41 1 16 HELIX 2 2 THR A 71 ALA A 86 1 16 HELIX 3 3 SER A 98 LEU A 102 5 5 HELIX 4 4 VAL A 108 HIS A 112 5 5 HELIX 5 5 VAL A 119 MET A 129 1 11 HELIX 6 6 ASP A 131 ILE A 142 1 12 HELIX 7 7 GLY A 144 MET A 155 1 12 HELIX 8 8 MET A 182 GLY A 196 1 15 HELIX 9 9 THR A 200 ALA A 213 1 14 HELIX 10 10 LEU A 220 LEU A 225 5 6 HELIX 11 11 THR A 271 HIS A 289 1 19 SHEET 1 A 5 ILE A 56 PHE A 60 0 SHEET 2 A 5 ARG A 43 ASP A 50 -1 N GLU A 48 O LEU A 57 SHEET 3 A 5 ARG A 259 THR A 266 -1 O TYR A 264 N GLY A 45 SHEET 4 A 5 ARG A 244 GLY A 251 -1 N ILE A 246 O ILE A 263 SHEET 5 A 5 PHE A 230 ALA A 237 -1 N PHE A 230 O GLY A 251 SHEET 1 B 2 PHE A 66 PRO A 67 0 SHEET 2 B 2 THR A 180 THR A 181 -1 O THR A 181 N PHE A 66 SHEET 1 C 2 ARG A 94 ILE A 95 0 SHEET 2 C 2 MET A 117 THR A 118 -1 O MET A 117 N ILE A 95 SSBOND 1 CYS A 77 CYS A 123 1555 1555 2.11 SITE 1 AC1 9 MET A 69 SER A 70 SER A 130 GLY A 236 SITE 2 AC1 9 ALA A 237 HOH A 492 HOH A 615 HOH A 691 SITE 3 AC1 9 HOH A 719 CRYST1 59.045 59.505 86.260 90.00 90.00 90.00 P 21 21 21 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 0.016936 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016805 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011593 0.00000