HEADER HYDROLASE 01-OCT-15 5E2F TITLE CRYSTAL STRUCTURE OF BETA-LACTAMASE CLASS D FROM BACILLUS SUBTILIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE YBXI; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.5.2.6; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: ACYLATED LYSINE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS (STRAIN 168); SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: YBXI, YBDS, BSU02090; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 GOLD KEYWDS BETA LACTAMASE, STRUCTURAL GENOMICS, PSI-BIOLOGY, MIDWEST CENTER FOR KEYWDS 2 STRUCTURAL GENOMICS, MCSG, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.KIM,G.JOACHIMIAK,M.ENDRES,G.BABNIGG,A.JOACHIMIAK,MCSG,MIDWEST AUTHOR 2 CENTER FOR STRUCTURAL GENOMICS (MCSG) REVDAT 2 30-MAR-22 5E2F 1 REMARK LINK REVDAT 1 14-OCT-15 5E2F 0 JRNL AUTH Y.KIM,G.JOACHIMIAK,M.ENDRES,G.BABNIGG,A.JOACHIMIAK, JRNL AUTH 2 MIDWEST CENTER FOR STRUCTURAL GENOMICS (MCSG) JRNL TITL CRYSTAL STRUCTURE OF BETA-LACTAMASE CLASS D FROM BACILLUS JRNL TITL 2 SUBTILIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10PRE-2104 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 117679 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.126 REMARK 3 R VALUE (WORKING SET) : 0.125 REMARK 3 FREE R VALUE : 0.152 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 5731 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 28.1188 - 4.0361 0.95 4065 217 0.1375 0.1475 REMARK 3 2 4.0361 - 3.2050 0.98 4040 196 0.1348 0.1402 REMARK 3 3 3.2050 - 2.8003 0.99 3982 199 0.1437 0.1718 REMARK 3 4 2.8003 - 2.5444 0.99 4016 191 0.1429 0.1648 REMARK 3 5 2.5444 - 2.3622 0.99 3989 205 0.1357 0.1550 REMARK 3 6 2.3622 - 2.2230 0.99 3998 185 0.1200 0.1508 REMARK 3 7 2.2230 - 2.1117 0.99 3974 184 0.1211 0.1521 REMARK 3 8 2.1117 - 2.0198 0.99 3949 197 0.1081 0.1303 REMARK 3 9 2.0198 - 1.9420 0.99 3925 208 0.1071 0.1326 REMARK 3 10 1.9420 - 1.8750 0.99 3948 188 0.1068 0.1573 REMARK 3 11 1.8750 - 1.8164 0.99 3932 193 0.1038 0.1286 REMARK 3 12 1.8164 - 1.7645 0.99 3895 229 0.1023 0.1452 REMARK 3 13 1.7645 - 1.7181 0.99 3938 200 0.1037 0.1507 REMARK 3 14 1.7181 - 1.6762 0.99 3905 194 0.0961 0.1419 REMARK 3 15 1.6762 - 1.6381 0.99 3880 226 0.0939 0.1359 REMARK 3 16 1.6381 - 1.6032 0.99 3926 216 0.0970 0.1516 REMARK 3 17 1.6032 - 1.5711 0.99 3908 196 0.0971 0.1484 REMARK 3 18 1.5711 - 1.5415 1.00 3955 197 0.1011 0.1298 REMARK 3 19 1.5415 - 1.5140 0.99 3911 218 0.1011 0.1551 REMARK 3 20 1.5140 - 1.4883 0.99 3905 183 0.1036 0.1439 REMARK 3 21 1.4883 - 1.4643 0.99 3898 204 0.1116 0.1489 REMARK 3 22 1.4643 - 1.4418 0.99 3893 207 0.1177 0.1535 REMARK 3 23 1.4418 - 1.4206 0.99 3943 196 0.1258 0.1868 REMARK 3 24 1.4206 - 1.4006 0.98 3806 187 0.1424 0.2132 REMARK 3 25 1.4006 - 1.3816 0.97 3883 195 0.1599 0.1976 REMARK 3 26 1.3816 - 1.3637 0.95 3710 216 0.1568 0.1969 REMARK 3 27 1.3637 - 1.3466 0.85 3346 185 0.1684 0.2360 REMARK 3 28 1.3466 - 1.3304 0.73 2884 138 0.1718 0.1932 REMARK 3 29 1.3304 - 1.3149 0.55 2170 110 0.1799 0.1981 REMARK 3 30 1.3149 - 1.3002 0.35 1374 71 0.1948 0.2526 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.080 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 : 0.009 4287 REMARK 3 ANGLE : 1.081 5813 REMARK 3 CHIRALITY : 0.090 608 REMARK 3 PLANARITY : 0.008 768 REMARK 3 DIHEDRAL : 19.646 1630 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 5E2F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214228. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97927 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 123708 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 28.112 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05600 REMARK 200 FOR THE DATA SET : 20.2200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.51300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.670 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M CALCIUM CHLORIDE, 0.1 M TRIS:HCL REMARK 280 PH 8.5, 20% (W/V) PEG 4000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K 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 23.84950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 76.98950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.42800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 76.98950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.84950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.42800 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 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 SER A -2 REMARK 465 ASN A -1 REMARK 465 ALA A 0 REMARK 465 MSE A 1 REMARK 465 LYS A 2 REMARK 465 LYS A 3 REMARK 465 TRP A 4 REMARK 465 ILE A 5 REMARK 465 TYR A 6 REMARK 465 VAL A 7 REMARK 465 VAL A 8 REMARK 465 LEU A 9 REMARK 465 VAL A 10 REMARK 465 LEU A 11 REMARK 465 SER A 12 REMARK 465 ILE A 13 REMARK 465 ALA A 14 REMARK 465 GLY A 15 REMARK 465 ILE A 16 REMARK 465 GLY A 17 REMARK 465 GLY A 18 REMARK 465 PHE A 19 REMARK 465 SER A 20 REMARK 465 VAL A 21 REMARK 465 HIS A 22 REMARK 465 ALA A 23 REMARK 465 ALA A 24 REMARK 465 SER A 25 REMARK 465 SER A 26 REMARK 465 ALA A 27 REMARK 465 HIS A 28 REMARK 465 GLU A 29 REMARK 465 LYS A 30 REMARK 465 SER B -2 REMARK 465 ASN B -1 REMARK 465 ALA B 0 REMARK 465 MSE B 1 REMARK 465 LYS B 2 REMARK 465 LYS B 3 REMARK 465 TRP B 4 REMARK 465 ILE B 5 REMARK 465 TYR B 6 REMARK 465 VAL B 7 REMARK 465 VAL B 8 REMARK 465 LEU B 9 REMARK 465 VAL B 10 REMARK 465 LEU B 11 REMARK 465 SER B 12 REMARK 465 ILE B 13 REMARK 465 ALA B 14 REMARK 465 GLY B 15 REMARK 465 ILE B 16 REMARK 465 GLY B 17 REMARK 465 GLY B 18 REMARK 465 PHE B 19 REMARK 465 SER B 20 REMARK 465 VAL B 21 REMARK 465 HIS B 22 REMARK 465 ALA B 23 REMARK 465 ALA B 24 REMARK 465 SER B 25 REMARK 465 SER B 26 REMARK 465 ALA B 27 REMARK 465 HIS B 28 REMARK 465 GLU B 29 REMARK 465 LYS B 30 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 B 458 O HOH B 587 2.05 REMARK 500 OD1 ASP A 245 O HOH A 401 2.11 REMARK 500 O HOH A 426 O HOH A 637 2.12 REMARK 500 O HOH A 438 O HOH A 671 2.17 REMARK 500 O HOH A 524 O HOH A 655 2.18 REMARK 500 O HOH A 419 O HOH A 443 2.18 REMARK 500 O HOH A 426 O HOH A 651 2.19 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 426 O HOH B 433 3655 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 LEU B 187 C PRO B 188 N 0.116 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 ASN A 64 70.37 64.54 REMARK 500 GLN A 75 -148.61 57.22 REMARK 500 SER A 166 -139.18 -137.44 REMARK 500 ASP A 246 -169.72 -170.42 REMARK 500 THR A 266 -90.95 -123.61 REMARK 500 ASN B 64 67.02 65.60 REMARK 500 GLN B 75 -148.19 55.52 REMARK 500 ASP B 94 -172.69 -174.57 REMARK 500 SER B 166 -140.91 -138.13 REMARK 500 GLU B 186 53.38 -108.10 REMARK 500 ASP B 246 -168.47 -177.67 REMARK 500 THR B 266 -88.21 -122.01 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 679 DISTANCE = 6.60 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 CA A 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 41 OD2 REMARK 620 2 GLU A 42 OE2 98.0 REMARK 620 3 ASP A 135 OD1 113.2 55.4 REMARK 620 4 HOH A 462 O 84.3 92.4 45.5 REMARK 620 5 HOH A 508 O 170.8 87.0 63.4 87.9 REMARK 620 6 HOH A 616 O 86.3 173.3 127.5 93.2 89.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 45 O REMARK 620 2 HOH A 451 O 86.3 REMARK 620 3 HOH A 581 O 76.9 152.9 REMARK 620 4 HOH A 599 O 88.1 78.2 80.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 300 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 47 OD1 REMARK 620 2 ASP B 47 OD2 51.7 REMARK 620 3 HOH B 426 O 157.4 149.8 REMARK 620 4 HOH B 525 O 126.8 75.4 74.5 REMARK 620 5 HOH B 606 O 84.8 79.6 103.7 91.6 REMARK 620 6 HOH B 613 O 86.8 89.4 86.8 87.4 168.8 REMARK 620 7 HOH B 631 O 76.0 127.7 82.2 156.6 96.1 89.1 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 CA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: MCSG-APC115012 RELATED DB: TARGETTRACK DBREF 5E2F A 1 267 UNP P54427 YBXI_BACSU 1 267 DBREF 5E2F B 1 267 UNP P54427 YBXI_BACSU 1 267 SEQADV 5E2F SER A -2 UNP P54427 EXPRESSION TAG SEQADV 5E2F ASN A -1 UNP P54427 EXPRESSION TAG SEQADV 5E2F ALA A 0 UNP P54427 EXPRESSION TAG SEQADV 5E2F SER B -2 UNP P54427 EXPRESSION TAG SEQADV 5E2F ASN B -1 UNP P54427 EXPRESSION TAG SEQADV 5E2F ALA B 0 UNP P54427 EXPRESSION TAG SEQRES 1 A 270 SER ASN ALA MSE LYS LYS TRP ILE TYR VAL VAL LEU VAL SEQRES 2 A 270 LEU SER ILE ALA GLY ILE GLY GLY PHE SER VAL HIS ALA SEQRES 3 A 270 ALA SER SER ALA HIS GLU LYS HIS LEU ASN VAL SER LYS SEQRES 4 A 270 MSE ASN VAL ASP ASP GLU PHE LYS ASP THR ASP GLY THR SEQRES 5 A 270 PHE ILE LEU HIS ASP LEU GLN LYS ASP GLN THR PHE VAL SEQRES 6 A 270 TYR ASN ARG LYS ARG ALA ASN GLN ARG GLN THR PRO GLN SEQRES 7 A 270 SER THR PHE ALY VAL VAL ASN ALA LEU ILE GLY LEU GLN SEQRES 8 A 270 VAL LYS ALA VAL ARG ASP GLU TYR ASP VAL LYS ARG TRP SEQRES 9 A 270 ASP GLY VAL LYS ARG GLU PHE GLU SER TRP ASN ARG ASP SEQRES 10 A 270 HIS THR LEU GLY SER ALA MSE ARG GLU SER ALA ILE TRP SEQRES 11 A 270 TYR TYR GLN ALA LEU ALA ARG ASP ILE GLY GLU GLU ARG SEQRES 12 A 270 MSE LYS THR TRP LEU HIS THR LEU SER TYR GLY ASN GLU SEQRES 13 A 270 ASP ILE SER GLY GLY ILE ASP GLN PHE TRP LEU GLN SER SEQRES 14 A 270 SER LEU THR ILE SER PRO LEU GLU GLN GLU THR PHE LEU SEQRES 15 A 270 GLU LYS LEU ALA LYS GLU GLU LEU PRO PHE ASP LYS PRO SEQRES 16 A 270 VAL MSE LYS ILE VAL LYS ARG MSE MSE ILE GLN GLU GLU SEQRES 17 A 270 GLY ASP HIS TYR THR LEU TYR GLY LYS THR GLY THR ARG SEQRES 18 A 270 LEU THR ASP MSE GLY LEU GLY TRP PHE VAL GLY PHE ILE SEQRES 19 A 270 LYS THR GLU HIS GLY SER TYR VAL PHE VAL THR ASN VAL SEQRES 20 A 270 ASP ASP SER GLY THR LYS ALA LYS ASN ILE THR VAL ASP SEQRES 21 A 270 ILE LEU LYS LYS TYR GLY LEU ILE THR SER SEQRES 1 B 270 SER ASN ALA MSE LYS LYS TRP ILE TYR VAL VAL LEU VAL SEQRES 2 B 270 LEU SER ILE ALA GLY ILE GLY GLY PHE SER VAL HIS ALA SEQRES 3 B 270 ALA SER SER ALA HIS GLU LYS HIS LEU ASN VAL SER LYS SEQRES 4 B 270 MSE ASN VAL ASP ASP GLU PHE LYS ASP THR ASP GLY THR SEQRES 5 B 270 PHE ILE LEU HIS ASP LEU GLN LYS ASP GLN THR PHE VAL SEQRES 6 B 270 TYR ASN ARG LYS ARG ALA ASN GLN ARG GLN THR PRO GLN SEQRES 7 B 270 SER THR PHE ALY VAL VAL ASN ALA LEU ILE GLY LEU GLN SEQRES 8 B 270 VAL LYS ALA VAL ARG ASP GLU TYR ASP VAL LYS ARG TRP SEQRES 9 B 270 ASP GLY VAL LYS ARG GLU PHE GLU SER TRP ASN ARG ASP SEQRES 10 B 270 HIS THR LEU GLY SER ALA MSE ARG GLU SER ALA ILE TRP SEQRES 11 B 270 TYR TYR GLN ALA LEU ALA ARG ASP ILE GLY GLU GLU ARG SEQRES 12 B 270 MSE LYS THR TRP LEU HIS THR LEU SER TYR GLY ASN GLU SEQRES 13 B 270 ASP ILE SER GLY GLY ILE ASP GLN PHE TRP LEU GLN SER SEQRES 14 B 270 SER LEU THR ILE SER PRO LEU GLU GLN GLU THR PHE LEU SEQRES 15 B 270 GLU LYS LEU ALA LYS GLU GLU LEU PRO PHE ASP LYS PRO SEQRES 16 B 270 VAL MSE LYS ILE VAL LYS ARG MSE MSE ILE GLN GLU GLU SEQRES 17 B 270 GLY ASP HIS TYR THR LEU TYR GLY LYS THR GLY THR ARG SEQRES 18 B 270 LEU THR ASP MSE GLY LEU GLY TRP PHE VAL GLY PHE ILE SEQRES 19 B 270 LYS THR GLU HIS GLY SER TYR VAL PHE VAL THR ASN VAL SEQRES 20 B 270 ASP ASP SER GLY THR LYS ALA LYS ASN ILE THR VAL ASP SEQRES 21 B 270 ILE LEU LYS LYS TYR GLY LEU ILE THR SER MODRES 5E2F MSE A 37 MET MODIFIED RESIDUE MODRES 5E2F ALY A 79 LYS MODIFIED RESIDUE MODRES 5E2F MSE A 121 MET MODIFIED RESIDUE MODRES 5E2F MSE A 141 MET MODIFIED RESIDUE MODRES 5E2F MSE A 194 MET MODIFIED RESIDUE MODRES 5E2F MSE A 200 MET MODIFIED RESIDUE MODRES 5E2F MSE A 201 MET MODIFIED RESIDUE MODRES 5E2F MSE A 222 MET MODIFIED RESIDUE MODRES 5E2F MSE B 37 MET MODIFIED RESIDUE MODRES 5E2F ALY B 79 LYS MODIFIED RESIDUE MODRES 5E2F MSE B 121 MET MODIFIED RESIDUE MODRES 5E2F MSE B 141 MET MODIFIED RESIDUE MODRES 5E2F MSE B 194 MET MODIFIED RESIDUE MODRES 5E2F MSE B 200 MET MODIFIED RESIDUE MODRES 5E2F MSE B 201 MET MODIFIED RESIDUE MODRES 5E2F MSE B 222 MET MODIFIED RESIDUE HET MSE A 37 8 HET ALY A 79 24 HET MSE A 121 8 HET MSE A 141 8 HET MSE A 194 8 HET MSE A 200 8 HET MSE A 201 8 HET MSE A 222 8 HET MSE B 37 8 HET ALY B 79 24 HET MSE B 121 8 HET MSE B 141 8 HET MSE B 194 8 HET MSE B 200 8 HET MSE B 201 8 HET MSE B 222 8 HET CA A 301 1 HET CA A 302 1 HET EDO A 303 4 HET EDO A 304 4 HET CA B 300 1 HET EDO B 301 4 HETNAM MSE SELENOMETHIONINE HETNAM ALY N(6)-ACETYLLYSINE HETNAM CA CALCIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 14(C5 H11 N O2 SE) FORMUL 1 ALY 2(C8 H16 N2 O3) FORMUL 3 CA 3(CA 2+) FORMUL 5 EDO 3(C2 H6 O2) FORMUL 9 HOH *520(H2 O) HELIX 1 AA1 ASN A 33 MSE A 37 5 5 HELIX 2 AA2 VAL A 39 LYS A 44 5 6 HELIX 3 AA3 ASN A 64 ASN A 69 1 6 HELIX 4 AA4 PRO A 74 SER A 76 5 3 HELIX 5 AA5 THR A 77 VAL A 89 1 13 HELIX 6 AA6 PHE A 108 ASN A 112 5 5 HELIX 7 AA7 LEU A 117 GLU A 123 1 7 HELIX 8 AA8 ALA A 125 GLY A 137 1 13 HELIX 9 AA9 GLY A 137 LEU A 148 1 12 HELIX 10 AB1 SER A 171 LYS A 184 1 14 HELIX 11 AB2 ASP A 190 MSE A 201 1 12 HELIX 12 AB3 SER A 247 TYR A 262 1 16 HELIX 13 AB4 ASN B 33 MSE B 37 5 5 HELIX 14 AB5 ASN B 64 ASN B 69 1 6 HELIX 15 AB6 PRO B 74 THR B 77 5 4 HELIX 16 AB7 PHE B 78 VAL B 89 1 12 HELIX 17 AB8 PHE B 108 ASN B 112 5 5 HELIX 18 AB9 LEU B 117 GLU B 123 1 7 HELIX 19 AC1 ALA B 125 GLY B 137 1 13 HELIX 20 AC2 GLY B 137 LEU B 148 1 12 HELIX 21 AC3 SER B 171 LYS B 184 1 14 HELIX 22 AC4 ASP B 190 MSE B 201 1 12 HELIX 23 AC5 SER B 247 TYR B 262 1 16 SHEET 1 AA1 6 GLN A 59 TYR A 63 0 SHEET 2 AA1 6 GLY A 48 ASP A 54 -1 N ASP A 54 O GLN A 59 SHEET 3 AA1 6 GLY A 236 VAL A 244 -1 O VAL A 239 N HIS A 53 SHEET 4 AA1 6 GLY A 225 THR A 233 -1 N THR A 233 O GLY A 236 SHEET 5 AA1 6 TYR A 209 THR A 217 -1 N TYR A 212 O PHE A 230 SHEET 6 AA1 6 ILE A 202 GLU A 205 -1 N GLN A 203 O LEU A 211 SHEET 1 AA2 2 VAL A 98 LYS A 99 0 SHEET 2 AA2 2 HIS A 115 THR A 116 -1 O HIS A 115 N LYS A 99 SHEET 1 AA3 6 GLN B 59 TYR B 63 0 SHEET 2 AA3 6 GLY B 48 ASP B 54 -1 N PHE B 50 O TYR B 63 SHEET 3 AA3 6 GLY B 236 VAL B 244 -1 O VAL B 239 N HIS B 53 SHEET 4 AA3 6 GLY B 225 THR B 233 -1 N ILE B 231 O TYR B 238 SHEET 5 AA3 6 TYR B 209 THR B 217 -1 N TYR B 212 O PHE B 230 SHEET 6 AA3 6 ILE B 202 GLU B 205 -1 N GLN B 203 O LEU B 211 SHEET 1 AA4 2 VAL B 98 LYS B 99 0 SHEET 2 AA4 2 HIS B 115 THR B 116 -1 O HIS B 115 N LYS B 99 LINK C LYS A 36 N MSE A 37 1555 1555 1.32 LINK C MSE A 37 N ASN A 38 1555 1555 1.33 LINK C PHE A 78 N AALY A 79 1555 1555 1.34 LINK C PHE A 78 N BALY A 79 1555 1555 1.33 LINK C AALY A 79 N VAL A 80 1555 1555 1.33 LINK C BALY A 79 N VAL A 80 1555 1555 1.34 LINK C ALA A 120 N MSE A 121 1555 1555 1.33 LINK C MSE A 121 N ARG A 122 1555 1555 1.34 LINK C ARG A 140 N MSE A 141 1555 1555 1.34 LINK C MSE A 141 N LYS A 142 1555 1555 1.34 LINK C VAL A 193 N MSE A 194 1555 1555 1.33 LINK C MSE A 194 N LYS A 195 1555 1555 1.33 LINK C AARG A 199 N MSE A 200 1555 1555 1.33 LINK C BARG A 199 N MSE A 200 1555 1555 1.33 LINK C MSE A 200 N MSE A 201 1555 1555 1.34 LINK C MSE A 201 N ILE A 202 1555 1555 1.34 LINK C ASP A 221 N MSE A 222 1555 1555 1.34 LINK C MSE A 222 N GLY A 223 1555 1555 1.33 LINK C LYS B 36 N MSE B 37 1555 1555 1.33 LINK C MSE B 37 N ASN B 38 1555 1555 1.33 LINK C PHE B 78 N AALY B 79 1555 1555 1.33 LINK C PHE B 78 N BALY B 79 1555 1555 1.33 LINK C AALY B 79 N VAL B 80 1555 1555 1.34 LINK C BALY B 79 N VAL B 80 1555 1555 1.34 LINK C ALA B 120 N MSE B 121 1555 1555 1.33 LINK C MSE B 121 N ARG B 122 1555 1555 1.35 LINK C ARG B 140 N MSE B 141 1555 1555 1.33 LINK C MSE B 141 N LYS B 142 1555 1555 1.33 LINK C VAL B 193 N MSE B 194 1555 1555 1.33 LINK C MSE B 194 N LYS B 195 1555 1555 1.33 LINK C ARG B 199 N MSE B 200 1555 1555 1.34 LINK C MSE B 200 N MSE B 201 1555 1555 1.33 LINK C MSE B 201 N ILE B 202 1555 1555 1.33 LINK C ASP B 221 N MSE B 222 1555 1555 1.34 LINK C MSE B 222 N GLY B 223 1555 1555 1.33 LINK OD2 ASP A 41 CA CA A 301 1555 1555 2.41 LINK OE2 GLU A 42 CA CA A 301 1555 1555 2.30 LINK O ASP A 45 CA CA A 302 1555 1555 2.36 LINK OD1 ASP A 135 CA CA A 301 1555 1655 2.38 LINK CA CA A 301 O HOH A 462 1555 1555 2.38 LINK CA CA A 301 O HOH A 508 1555 1555 2.25 LINK CA CA A 301 O HOH A 616 1555 1555 2.29 LINK CA CA A 302 O HOH A 451 1555 1555 2.55 LINK CA CA A 302 O HOH A 581 1555 1555 2.38 LINK CA CA A 302 O HOH A 599 1555 1555 2.34 LINK OD1 ASP B 47 CA CA B 300 1555 1555 2.53 LINK OD2 ASP B 47 CA CA B 300 1555 1555 2.47 LINK CA CA B 300 O HOH B 426 1555 4545 2.47 LINK CA CA B 300 O HOH B 525 1555 4545 2.43 LINK CA CA B 300 O HOH B 606 1555 4545 2.29 LINK CA CA B 300 O HOH B 613 1555 4545 2.40 LINK CA CA B 300 O HOH B 631 1555 4545 2.35 SITE 1 AC1 6 ASP A 41 GLU A 42 ASP A 135 HOH A 462 SITE 2 AC1 6 HOH A 508 HOH A 616 SITE 1 AC2 4 ASP A 45 HOH A 451 HOH A 581 HOH A 599 SITE 1 AC3 5 SER A 124 THR A 215 GLY A 216 THR A 217 SITE 2 AC3 5 HOH A 403 SITE 1 AC4 5 ARG A 71 GLY A 151 HOH A 432 ARG B 71 SITE 2 AC4 5 HOH B 496 SITE 1 AC5 6 ASP B 47 HOH B 426 HOH B 525 HOH B 606 SITE 2 AC5 6 HOH B 613 HOH B 631 SITE 1 AC6 2 ASN B 64 HOH B 497 CRYST1 47.699 68.856 153.979 90.00 90.00 90.00 P 21 21 21 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 0.020965 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014523 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006494 0.00000