HEADER LYASE 07-AUG-12 4B5V TITLE CRYSTAL STRUCTURES OF DIVALENT METAL DEPENDENT PYRUVATE ALDOLASE, TITLE 2 HPAI, IN COMPLEX WITH 4-HYDROXYL-2-KETOHEPTANE-1,7-DIOATE CAVEAT 4B5V CE8U B 1254 HAS WRONG CHIRALITY AT ATOM CAM CE8U A 1253 HAS CAVEAT 2 4B5V WRONG CHIRALITY AT ATOM CAM COMPND MOL_ID: 1; COMPND 2 MOLECULE: 4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 1-251; COMPND 5 SYNONYM: HPAI, 2,4-DIHYDROXYHEPT-2-ENE-1,7-DIOIC ACID ALDOLASE, HHED COMPND 6 ALDOLASE, 4-HYDROXY-2-KETOHEPTANE-1,7-DIOATE ALDOLASE, HKHD ALDOLASE; COMPND 7 EC: 4.1.2.20; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI ATCC 8739; SOURCE 3 ORGANISM_TAXID: 481805; SOURCE 4 ATCC: 8739; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PT7-7 KEYWDS LYASE EXPDTA X-RAY DIFFRACTION AUTHOR M.COINCON,W.WANG,S.Y.K.SEAH,J.SYGUSCH REVDAT 7 20-DEC-23 4B5V 1 REMARK REVDAT 6 15-NOV-23 4B5V 1 REMARK LINK ATOM REVDAT 5 12-JUL-17 4B5V 1 REVDAT 4 06-FEB-13 4B5V 1 HETATM REVDAT 3 31-OCT-12 4B5V 1 JRNL REVDAT 2 05-SEP-12 4B5V 1 JRNL ATOM REVDAT 1 29-AUG-12 4B5V 0 JRNL AUTH M.COINCON,W.WANG,J.SYGUSCH,S.Y.K.SEAH JRNL TITL CRYSTAL STRUCTURE OF REACTION INTERMEDIATES IN PYRUVATE JRNL TITL 2 CLASS II ALDOLASE: SUBSTRATE CLEAVAGE, ENOLATE STABILIZATION JRNL TITL 3 AND SUBSTRATE SPECIFICITY JRNL REF J.BIOL.CHEM. V. 287 36208 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22908224 JRNL DOI 10.1074/JBC.M112.400705 REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 72812 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.700 REMARK 3 FREE R VALUE TEST SET COUNT : 7093 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 37.9415 - 6.3331 1.00 2352 256 0.1818 0.1905 REMARK 3 2 6.3331 - 5.0305 1.00 2281 246 0.1581 0.1802 REMARK 3 3 5.0305 - 4.3957 1.00 2249 244 0.1213 0.1381 REMARK 3 4 4.3957 - 3.9942 1.00 2235 240 0.1166 0.1427 REMARK 3 5 3.9942 - 3.7082 1.00 2261 240 0.1273 0.1475 REMARK 3 6 3.7082 - 3.4897 1.00 2243 248 0.1353 0.1446 REMARK 3 7 3.4897 - 3.3151 1.00 2214 236 0.1434 0.1789 REMARK 3 8 3.3151 - 3.1709 1.00 2217 242 0.1482 0.1813 REMARK 3 9 3.1709 - 3.0488 1.00 2241 242 0.1401 0.1766 REMARK 3 10 3.0488 - 2.9437 1.00 2201 243 0.1473 0.1770 REMARK 3 11 2.9437 - 2.8517 1.00 2212 237 0.1450 0.1842 REMARK 3 12 2.8517 - 2.7702 1.00 2216 242 0.1517 0.1827 REMARK 3 13 2.7702 - 2.6973 1.00 2222 235 0.1537 0.1824 REMARK 3 14 2.6973 - 2.6315 1.00 2218 239 0.1547 0.1768 REMARK 3 15 2.6315 - 2.5717 1.00 2196 236 0.1488 0.1737 REMARK 3 16 2.5717 - 2.5170 1.00 2231 243 0.1529 0.1952 REMARK 3 17 2.5170 - 2.4666 1.00 2205 230 0.1480 0.1819 REMARK 3 18 2.4666 - 2.4201 1.00 2245 241 0.1590 0.1757 REMARK 3 19 2.4201 - 2.3769 1.00 2188 236 0.1636 0.2180 REMARK 3 20 2.3769 - 2.3366 1.00 2204 235 0.1671 0.1916 REMARK 3 21 2.3366 - 2.2989 1.00 2200 238 0.1608 0.2227 REMARK 3 22 2.2989 - 2.2635 1.00 2184 236 0.1702 0.2020 REMARK 3 23 2.2635 - 2.2302 1.00 2247 243 0.1755 0.2281 REMARK 3 24 2.2302 - 2.1988 1.00 2187 238 0.1802 0.1989 REMARK 3 25 2.1988 - 2.1691 1.00 2190 237 0.1819 0.2180 REMARK 3 26 2.1691 - 2.1410 1.00 2228 234 0.2039 0.2225 REMARK 3 27 2.1410 - 2.1142 1.00 2208 237 0.2166 0.2585 REMARK 3 28 2.1142 - 2.0887 0.99 2168 233 0.2318 0.2648 REMARK 3 29 2.0887 - 2.0644 0.97 2124 231 0.2440 0.2756 REMARK 3 30 2.0644 - 2.0412 0.61 1352 155 0.2891 0.2989 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.73 REMARK 3 K_SOL : 0.34 REMARK 3 B_SOL : 80.69 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.270 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.004 3975 REMARK 3 ANGLE : 0.868 5413 REMARK 3 CHIRALITY : 0.050 609 REMARK 3 PLANARITY : 0.003 724 REMARK 3 DIHEDRAL : 18.479 1501 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 4B5V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1290053632. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 72826 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 37.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 19.40 REMARK 200 R MERGE (I) : 0.03000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.29000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 2V5J REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5 M AMMONIUM DIHYDROGEN PHOSPHATE, REMARK 280 30% GLYCEROL, 2 MM COCL2 PH 5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 3 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 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 75.87000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.87000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 75.87000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 75.87000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 75.87000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 75.87000 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 75.87000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 75.87000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 75.87000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 75.87000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 75.87000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 75.87000 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 75.87000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 75.87000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 75.87000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 75.87000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 75.87000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 75.87000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 26560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 46370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -147.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 1.000000 0.000000 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 A2064 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2089 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2134 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2172 LIES ON A SPECIAL POSITION. REMARK 375 HOH B2062 LIES ON A SPECIAL POSITION. REMARK 375 HOH B2087 LIES ON A SPECIAL POSITION. 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 OG SER A 126 O HOH A 2267 1.91 REMARK 500 O HOH B 2035 O HOH B 2301 1.92 REMARK 500 O HOH A 2032 O HOH A 2314 1.95 REMARK 500 O HOH A 2361 O HOH A 2362 2.00 REMARK 500 O HOH B 2114 O HOH B 2115 2.02 REMARK 500 O HOH A 2246 O HOH A 2308 2.05 REMARK 500 OD2 ASP B 75 O HOH B 2166 2.06 REMARK 500 O HOH B 2124 O HOH B 2125 2.09 REMARK 500 OD2 ASP A 75 O HOH A 2169 2.10 REMARK 500 O HOH A 2315 O HOH A 2316 2.11 REMARK 500 O HOH B 2287 O HOH B 2332 2.11 REMARK 500 O HOH A 2048 O HOH A 2096 2.13 REMARK 500 OD1 ASN B 185 O HOH B 2314 2.13 REMARK 500 OAD E8U B 1254 O HOH B 2385 2.16 REMARK 500 O HOH A 2189 O HOH A 2360 2.16 REMARK 500 O HOH A 2071 O HOH A 2081 2.16 REMARK 500 O SER A 120 O HOH A 2267 2.16 REMARK 500 O HOH B 2338 O HOH B 2343 2.16 REMARK 500 O HOH B 2145 O HOH B 2146 2.18 REMARK 500 O HOH B 2181 O HOH B 2338 2.18 REMARK 500 O HOH A 2022 O HOH A 2179 2.19 REMARK 500 O HOH A 2077 O HOH A 2156 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 B 2124 O HOH B 2124 5555 1.94 REMARK 500 O HOH A 2076 O HOH B 2009 9555 2.11 REMARK 500 O HOH B 2165 O HOH B 2176 9555 2.14 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 ALA A 183 114.35 -27.95 REMARK 500 ALA B 183 67.79 28.22 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 A2009 DISTANCE = 6.94 ANGSTROMS REMARK 525 HOH A2024 DISTANCE = 7.27 ANGSTROMS REMARK 525 HOH A2042 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH A2056 DISTANCE = 6.51 ANGSTROMS REMARK 525 HOH A2058 DISTANCE = 5.98 ANGSTROMS REMARK 525 HOH A2064 DISTANCE = 6.60 ANGSTROMS REMARK 525 HOH A2076 DISTANCE = 6.67 ANGSTROMS REMARK 525 HOH A2175 DISTANCE = 6.45 ANGSTROMS REMARK 525 HOH A2203 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A2221 DISTANCE = 7.53 ANGSTROMS REMARK 525 HOH B2033 DISTANCE = 6.53 ANGSTROMS REMARK 525 HOH B2055 DISTANCE = 6.45 ANGSTROMS REMARK 525 HOH B2056 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH B2062 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH B2081 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH B2086 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH B2087 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH B2179 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH B2391 DISTANCE = 9.05 ANGSTROMS REMARK 525 HOH B2392 DISTANCE = 6.55 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 PYR, E8U: MICROHETEROGENEITY 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 MG A1255 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 149 OE1 REMARK 620 2 ASP A 175 OD2 72.7 REMARK 620 3 PYR A1252 OXT 95.7 103.6 REMARK 620 4 PYR A1252 O3 105.9 165.2 61.6 REMARK 620 5 E8U A1253 OAB 100.1 95.3 10.9 70.3 REMARK 620 6 E8U A1253 O10 117.6 157.6 57.3 13.0 64.2 REMARK 620 7 E8U A1253 OAE 102.4 96.5 11.5 69.1 2.4 62.6 REMARK 620 8 E8U A1253 O10 112.8 160.3 57.7 8.3 65.4 4.9 64.0 REMARK 620 9 HOH A2123 O 80.5 96.9 157.0 97.4 167.4 104.3 166.5 102.7 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1255 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 149 OE1 REMARK 620 2 ASP B 175 OD2 79.6 REMARK 620 3 PYR B1253 O3 94.4 167.8 REMARK 620 4 PYR B1253 OXT 90.0 106.7 62.4 REMARK 620 5 E8U B1254 O10 105.1 167.1 10.8 61.9 REMARK 620 6 E8U B1254 OAB 100.4 102.9 67.5 11.8 64.7 REMARK 620 7 E8U B1254 O10 102.9 175.0 10.6 69.2 8.0 72.5 REMARK 620 8 E8U B1254 OAE 107.1 107.9 63.4 17.1 59.3 7.9 67.3 REMARK 620 9 HOH B2113 O 82.5 92.2 97.6 158.1 100.2 164.8 92.3 158.8 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 700 THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1252 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PYR B 1253 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE E8U B 1254 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PYR A 1252 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE E8U A 1253 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1254 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1255 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1255 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4B5S RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF DIVALENT METAL DEPENDENT PYRUVATE ALDOLASE, REMARK 900 HPAI, IN COMPLEX WITH PYRUVATE REMARK 900 RELATED ID: 4B5T RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF DIVALENT METAL DEPENDENT PYRUVATE ALDOLASE, REMARK 900 HPAI, IN COMPLEX WITH KETOBUTYRATE REMARK 900 RELATED ID: 4B5U RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF DIVALENT METAL DEPENDENT PYRUVATE ALDOLASE, REMARK 900 HPAI, IN COMPLEX WITH PYRUVATE AND SUCCINIC SEMIALDEHYDE REMARK 900 RELATED ID: 4B5W RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF DIVALENT METAL DEPENDENT PYRUVATE ALDOLASE REMARK 900 R70A MUTANT, HPAI, IN COMPLEX WITH PYRUVATE REMARK 900 RELATED ID: 4B5X RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF DIVALENT METAL DEPENDENT PYRUVATE ALDOLASE REMARK 900 (HPAI), MUTANT D42A DBREF 4B5V A 1 251 UNP B1IS70 HPCH_ECOLC 1 251 DBREF 4B5V B 1 251 UNP B1IS70 HPCH_ECOLC 1 251 SEQRES 1 A 251 MET GLU ASN SER PHE LYS ALA ALA LEU LYS ALA GLY ARG SEQRES 2 A 251 PRO GLN ILE GLY LEU TRP LEU GLY LEU SER SER SER TYR SEQRES 3 A 251 SER ALA GLU LEU LEU ALA GLY ALA GLY PHE ASP TRP LEU SEQRES 4 A 251 LEU ILE ASP GLY GLU HIS ALA PRO ASN ASN VAL GLN THR SEQRES 5 A 251 VAL LEU THR GLN LEU GLN ALA ILE ALA PRO TYR PRO SER SEQRES 6 A 251 GLN PRO VAL VAL ARG PRO SER TRP ASN ASP PRO VAL GLN SEQRES 7 A 251 ILE LYS GLN LEU LEU ASP VAL GLY THR GLN THR LEU LEU SEQRES 8 A 251 VAL PRO MET VAL GLN ASN ALA ASP GLU ALA ARG GLU ALA SEQRES 9 A 251 VAL ARG ALA THR ARG TYR PRO PRO ALA GLY ILE ARG GLY SEQRES 10 A 251 VAL GLY SER ALA LEU ALA ARG ALA SER ARG TRP ASN ARG SEQRES 11 A 251 ILE PRO ASP TYR LEU GLN LYS ALA ASN ASP GLN MET CYS SEQRES 12 A 251 VAL LEU VAL GLN ILE GLU THR ARG GLU ALA MET LYS ASN SEQRES 13 A 251 LEU PRO GLN ILE LEU ASP VAL GLU GLY VAL ASP GLY VAL SEQRES 14 A 251 PHE ILE GLY PRO ALA ASP LEU SER ALA ASP MET GLY TYR SEQRES 15 A 251 ALA GLY ASN PRO GLN HIS PRO GLU VAL GLN ALA ALA ILE SEQRES 16 A 251 GLU GLN ALA ILE VAL GLN ILE ARG GLU SER GLY LYS ALA SEQRES 17 A 251 PRO GLY ILE LEU ILE ALA ASN GLU GLN LEU ALA LYS ARG SEQRES 18 A 251 TYR LEU GLU LEU GLY ALA LEU PHE VAL ALA VAL GLY VAL SEQRES 19 A 251 ASP THR THR LEU LEU ALA ARG ALA ALA GLU ALA LEU ALA SEQRES 20 A 251 ALA ARG PHE GLY SEQRES 1 B 251 MET GLU ASN SER PHE LYS ALA ALA LEU LYS ALA GLY ARG SEQRES 2 B 251 PRO GLN ILE GLY LEU TRP LEU GLY LEU SER SER SER TYR SEQRES 3 B 251 SER ALA GLU LEU LEU ALA GLY ALA GLY PHE ASP TRP LEU SEQRES 4 B 251 LEU ILE ASP GLY GLU HIS ALA PRO ASN ASN VAL GLN THR SEQRES 5 B 251 VAL LEU THR GLN LEU GLN ALA ILE ALA PRO TYR PRO SER SEQRES 6 B 251 GLN PRO VAL VAL ARG PRO SER TRP ASN ASP PRO VAL GLN SEQRES 7 B 251 ILE LYS GLN LEU LEU ASP VAL GLY THR GLN THR LEU LEU SEQRES 8 B 251 VAL PRO MET VAL GLN ASN ALA ASP GLU ALA ARG GLU ALA SEQRES 9 B 251 VAL ARG ALA THR ARG TYR PRO PRO ALA GLY ILE ARG GLY SEQRES 10 B 251 VAL GLY SER ALA LEU ALA ARG ALA SER ARG TRP ASN ARG SEQRES 11 B 251 ILE PRO ASP TYR LEU GLN LYS ALA ASN ASP GLN MET CYS SEQRES 12 B 251 VAL LEU VAL GLN ILE GLU THR ARG GLU ALA MET LYS ASN SEQRES 13 B 251 LEU PRO GLN ILE LEU ASP VAL GLU GLY VAL ASP GLY VAL SEQRES 14 B 251 PHE ILE GLY PRO ALA ASP LEU SER ALA ASP MET GLY TYR SEQRES 15 B 251 ALA GLY ASN PRO GLN HIS PRO GLU VAL GLN ALA ALA ILE SEQRES 16 B 251 GLU GLN ALA ILE VAL GLN ILE ARG GLU SER GLY LYS ALA SEQRES 17 B 251 PRO GLY ILE LEU ILE ALA ASN GLU GLN LEU ALA LYS ARG SEQRES 18 B 251 TYR LEU GLU LEU GLY ALA LEU PHE VAL ALA VAL GLY VAL SEQRES 19 B 251 ASP THR THR LEU LEU ALA ARG ALA ALA GLU ALA LEU ALA SEQRES 20 B 251 ALA ARG PHE GLY HET PYR A1252 9 HET E8U A1253 42 HET GOL A1254 14 HET MG A1255 1 HET GOL B1252 14 HET PYR B1253 9 HET E8U B1254 42 HET MG B1255 1 HETNAM PYR PYRUVIC ACID HETNAM E8U (4R)-4-OXIDANYL-2-OXIDANYLIDENE-HEPTANEDIOIC ACID HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 PYR 2(C3 H4 O3) FORMUL 4 E8U 2(C7 H10 O6) FORMUL 5 GOL 2(C3 H8 O3) FORMUL 6 MG 2(MG 2+) FORMUL 11 HOH *803(H2 O) HELIX 1 1 ASN A 3 ALA A 11 1 9 HELIX 2 2 SER A 24 GLY A 33 1 10 HELIX 3 3 ASN A 49 ALA A 61 1 13 HELIX 4 4 ASP A 75 VAL A 85 1 11 HELIX 5 5 ASN A 97 THR A 108 1 12 HELIX 6 6 GLY A 119 ALA A 123 5 5 HELIX 7 7 ALA A 123 ARG A 127 5 5 HELIX 8 8 ASP A 133 ALA A 138 1 6 HELIX 9 9 ASN A 139 MET A 142 5 4 HELIX 10 10 THR A 150 ASN A 156 1 7 HELIX 11 11 ASN A 156 ASP A 162 1 7 HELIX 12 12 GLY A 172 GLY A 181 1 10 HELIX 13 13 HIS A 188 SER A 205 1 18 HELIX 14 14 ASN A 215 GLY A 226 1 12 HELIX 15 15 ASP A 235 ARG A 249 1 15 HELIX 16 16 ASN B 3 ALA B 11 1 9 HELIX 17 17 SER B 24 GLY B 33 1 10 HELIX 18 18 ASN B 49 ALA B 61 1 13 HELIX 19 19 ASP B 75 VAL B 85 1 11 HELIX 20 20 ASN B 97 ALA B 107 1 11 HELIX 21 21 GLY B 119 ALA B 123 5 5 HELIX 22 22 ALA B 123 ARG B 127 5 5 HELIX 23 23 ASP B 133 ALA B 138 1 6 HELIX 24 24 ASN B 139 MET B 142 5 4 HELIX 25 25 THR B 150 ASN B 156 1 7 HELIX 26 26 ASN B 156 ASP B 162 1 7 HELIX 27 27 GLY B 172 GLY B 181 1 10 HELIX 28 28 HIS B 188 SER B 205 1 18 HELIX 29 29 ASN B 215 LEU B 225 1 11 HELIX 30 30 ASP B 235 ARG B 249 1 15 SHEET 1 AA 9 GLN A 15 LEU A 20 0 SHEET 2 AA 9 PHE A 229 VAL A 234 1 O VAL A 230 N GLY A 17 SHEET 3 AA 9 ALA A 208 LEU A 212 1 O ILE A 211 N ALA A 231 SHEET 4 AA 9 VAL A 166 ILE A 171 1 O ASP A 167 N ALA A 208 SHEET 5 AA 9 CYS A 143 ILE A 148 1 O VAL A 144 N ASP A 167 SHEET 6 AA 9 THR A 89 VAL A 92 1 O LEU A 90 N LEU A 145 SHEET 7 AA 9 GLN A 66 ARG A 70 1 O VAL A 69 N LEU A 91 SHEET 8 AA 9 TRP A 38 ASP A 42 1 O LEU A 39 N VAL A 68 SHEET 9 AA 9 GLN A 15 LEU A 20 1 O LEU A 18 N LEU A 40 SHEET 1 BA 9 GLN B 15 LEU B 20 0 SHEET 2 BA 9 PHE B 229 VAL B 234 1 O VAL B 230 N GLY B 17 SHEET 3 BA 9 ALA B 208 LEU B 212 1 O ILE B 211 N ALA B 231 SHEET 4 BA 9 VAL B 166 ILE B 171 1 O ASP B 167 N ALA B 208 SHEET 5 BA 9 CYS B 143 ILE B 148 1 O VAL B 144 N ASP B 167 SHEET 6 BA 9 THR B 89 VAL B 92 1 O LEU B 90 N LEU B 145 SHEET 7 BA 9 GLN B 66 ARG B 70 1 O VAL B 69 N LEU B 91 SHEET 8 BA 9 TRP B 38 ASP B 42 1 O LEU B 39 N VAL B 68 SHEET 9 BA 9 GLN B 15 LEU B 20 1 O LEU B 18 N LEU B 40 LINK OE1 GLU A 149 MG MG A1255 1555 1555 2.28 LINK OD2 ASP A 175 MG MG A1255 1555 1555 2.42 LINK OXTBPYR A1252 MG MG A1255 1555 1555 2.71 LINK O3 BPYR A1252 MG MG A1255 1555 1555 2.60 LINK OABCE8U A1253 MG MG A1255 1555 1555 2.70 LINK O10CE8U A1253 MG MG A1255 1555 1555 2.75 LINK OAEAE8U A1253 MG MG A1255 1555 1555 2.82 LINK O10AE8U A1253 MG MG A1255 1555 1555 2.70 LINK MG MG A1255 O HOH A2123 1555 1555 2.58 LINK MG MG A1255 O HOH A2128 1555 1555 2.08 LINK OE1 GLU B 149 MG MG B1255 1555 1555 2.39 LINK OD2 ASP B 175 MG MG B1255 1555 1555 2.49 LINK O3 BPYR B1253 MG MG B1255 1555 1555 2.59 LINK OXTBPYR B1253 MG MG B1255 1555 1555 2.68 LINK O10CE8U B1254 MG MG B1255 1555 1555 2.74 LINK OABCE8U B1254 MG MG B1255 1555 1555 2.68 LINK O10AE8U B1254 MG MG B1255 1555 1555 2.65 LINK OAEAE8U B1254 MG MG B1255 1555 1555 2.77 LINK MG MG B1255 O HOH B2113 1555 1555 2.30 LINK MG MG B1255 O HOH B2121 1555 1555 2.10 CISPEP 1 PRO A 111 PRO A 112 0 2.32 CISPEP 2 PRO B 111 PRO B 112 0 4.52 SITE 1 AC1 8 LEU A 22 SER A 23 LEU A 54 HOH A2130 SITE 2 AC1 8 HOH A2136 HOH A2146 SER B 24 TYR B 26 SITE 1 AC2 13 ARG B 70 GLN B 147 GLU B 149 PHE B 170 SITE 2 AC2 13 GLY B 172 PRO B 173 ALA B 174 ASP B 175 SITE 3 AC2 13 LEU B 212 MG B1255 HOH B2157 HOH B2383 SITE 4 AC2 13 HOH B2384 SITE 1 AC3 21 HIS B 45 ARG B 70 VAL B 118 GLY B 119 SITE 2 AC3 21 SER B 120 ALA B 121 GLN B 147 GLY B 172 SITE 3 AC3 21 PRO B 173 ALA B 174 ASP B 175 LEU B 212 SITE 4 AC3 21 MG B1255 HOH B2121 HOH B2157 HOH B2383 SITE 5 AC3 21 HOH B2384 HOH B2385 HOH B2386 HOH B2387 SITE 6 AC3 21 HOH B2389 SITE 1 AC4 12 ARG A 70 GLN A 147 PHE A 170 GLY A 172 SITE 2 AC4 12 PRO A 173 ALA A 174 ASP A 175 LEU A 212 SITE 3 AC4 12 MG A1255 HOH A2163 HOH A2403 HOH A2404 SITE 1 AC5 21 HIS A 45 ARG A 70 VAL A 118 GLY A 119 SITE 2 AC5 21 SER A 120 GLN A 147 GLY A 172 PRO A 173 SITE 3 AC5 21 ALA A 174 ASP A 175 LEU A 212 MG A1255 SITE 4 AC5 21 HOH A2128 HOH A2163 HOH A2403 HOH A2404 SITE 5 AC5 21 HOH A2405 HOH A2406 HOH A2407 HOH A2408 SITE 6 AC5 21 HOH A2409 SITE 1 AC6 8 SER A 24 TYR A 26 HOH A2082 HOH A2410 SITE 2 AC6 8 LEU B 22 SER B 23 GLN B 51 LEU B 54 SITE 1 AC7 7 GLN A 147 GLU A 149 ASP A 175 PYR A1252 SITE 2 AC7 7 E8U A1253 HOH A2123 HOH A2128 SITE 1 AC8 7 GLN B 147 GLU B 149 ASP B 175 PYR B1253 SITE 2 AC8 7 E8U B1254 HOH B2113 HOH B2121 CRYST1 151.740 151.740 151.740 90.00 90.00 90.00 P 21 3 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 0.006590 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006590 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006590 0.00000