HEADER HYDROLASE 08-FEB-03 1OCL TITLE THE CRYSTAL STRUCTURE OF MALONAMIDASE E2 COMPLEXED WITH MALONATE FROM TITLE 2 BRADYRHIZOBIUM JAPONICUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: MALONAMIDASE E2; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: CIS PEPTIDE BOND BETWEEN GLY 130 AND SER 131 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BRADYRHIZOBIUM JAPONICUM; SOURCE 3 ORGANISM_TAXID: 375; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: AD494 (DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PUC18 KEYWDS AMIDASE, MALONAMIDASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.SHIN,N.-C.HA,T.-H.LEE,B.-H.OH REVDAT 5 06-NOV-19 1OCL 1 REMARK ATOM REVDAT 4 05-JUL-17 1OCL 1 REMARK REVDAT 3 22-APR-15 1OCL 1 HEADER SOURCE KEYWDS REMARK REVDAT 3 2 1 VERSN HETSYN REVDAT 2 24-FEB-09 1OCL 1 VERSN REVDAT 1 25-FEB-03 1OCL 0 SPRSDE 08-FEB-03 1OCL 1GR9 JRNL AUTH S.SHIN,Y.S.YUN,H.M.KOO,Y.S.KIM,K.Y.CHOI,B.-H.OH JRNL TITL CHARACTERIZATION OF A NOVEL SER-CISSER-LYS CATALYTIC TRIAD JRNL TITL 2 IN COMPARISON WITH THE CLASSICAL SER-HIS-ASP TRIAD. JRNL REF J.BIOL.CHEM. V. 278 24937 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12711609 JRNL DOI 10.1074/JBC.M302156200 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 48817 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6124 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 513 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.258 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : CIS_PEP.PARAM REMARK 3 PARAMETER FILE 4 : MAL.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : MAL.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1OCL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-FEB-03. REMARK 100 THE DEPOSITION ID IS D_1290012120. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU ULTRAX 18 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU IMAGE PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48851 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06100 REMARK 200 FOR THE DATA SET : 28.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.15200 REMARK 200 FOR SHELL : 6.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1GR8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG1000, 0.1M TRIS-HCL PH7.0, 15MM REMARK 280 MALONATE, PH 7.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 51.91050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.47000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 51.91050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.47000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.8 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 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 GLY A 330 O HOH A 2214 0.26 REMARK 500 CA ILE A 224 O HOH A 2148 0.37 REMARK 500 O PHE A 333 O HOH A 2217 0.48 REMARK 500 N ALA A 221 O HOH A 2139 0.49 REMARK 500 CG1 ILE A 224 O HOH A 2147 0.54 REMARK 500 ND1 HIS A 398 O HOH A 2278 0.65 REMARK 500 CA PHE A 333 O HOH A 2216 0.74 REMARK 500 CZ ARG A 392 O HOH A 2266 0.76 REMARK 500 CB VAL A 338 O HOH A 2237 0.77 REMARK 500 N ARG A 223 O HOH A 2144 0.78 REMARK 500 CG1 VAL A 336 O HOH A 2230 0.83 REMARK 500 OG SER A 256 O HOH A 2169 0.96 REMARK 500 OD1 ASP A 337 O HOH A 2233 0.99 REMARK 500 CG PRO A 222 O HOH A 2143 1.05 REMARK 500 C GLY A 330 O HOH A 2214 1.05 REMARK 500 O HOH A 2221 O HOH A 2222 1.07 REMARK 500 OD2 ASP A 337 O HOH A 2231 1.07 REMARK 500 O HOH A 2218 O HOH A 2262 1.09 REMARK 500 O HOH A 2048 O HOH A 2274 1.12 REMARK 500 NE2 GLN A 258 O HOH A 2171 1.14 REMARK 500 CD1 ILE A 224 O HOH A 2147 1.14 REMARK 500 O HOH A 2063 O HOH A 2064 1.15 REMARK 500 CA ALA A 221 O HOH A 2139 1.17 REMARK 500 O GLY A 335 O HOH A 2225 1.17 REMARK 500 CE1 HIS A 398 O HOH A 2278 1.18 REMARK 500 CB ARG A 392 O HOH A 2263 1.18 REMARK 500 N PHE A 333 O HOH A 2216 1.23 REMARK 500 CA GLY A 335 O HOH A 2226 1.31 REMARK 500 CA VAL A 338 O HOH A 2237 1.37 REMARK 500 O HOH A 2134 O HOH A 2136 1.37 REMARK 500 C GLY A 335 O HOH A 2228 1.38 REMARK 500 CB PRO A 222 O HOH A 2143 1.40 REMARK 500 CG1 VAL A 338 O HOH A 2237 1.41 REMARK 500 N GLY A 335 O HOH A 2226 1.43 REMARK 500 NE ARG A 392 O HOH A 2266 1.44 REMARK 500 N ILE A 224 O HOH A 2148 1.46 REMARK 500 NH2 ARG A 392 O HOH A 2266 1.46 REMARK 500 CA GLU A 334 O HOH A 2219 1.48 REMARK 500 C PHE A 333 O HOH A 2217 1.50 REMARK 500 CG ASP A 337 O HOH A 2231 1.52 REMARK 500 C ILE A 224 O HOH A 2148 1.54 REMARK 500 CA ARG A 223 O HOH A 2144 1.57 REMARK 500 N VAL A 336 O HOH A 2228 1.58 REMARK 500 O HOH A 2269 O HOH A 2271 1.62 REMARK 500 O HOH A 2267 O HOH A 2269 1.63 REMARK 500 CG2 VAL A 338 O HOH A 2237 1.65 REMARK 500 O HOH A 2274 O HOH A 2277 1.67 REMARK 500 C LYS A 220 O HOH A 2139 1.68 REMARK 500 C PHE A 333 O HOH A 2216 1.69 REMARK 500 NH1 ARG A 392 O HOH A 2266 1.69 REMARK 500 REMARK 500 THIS ENTRY HAS 96 CLOSE CONTACTS 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 2097 O HOH A 2097 2555 0.47 REMARK 500 O HOH A 2265 O HOH A 2265 2555 1.24 REMARK 500 O HOH A 2142 O HOH A 2146 2555 1.52 REMARK 500 O HOH A 2047 O HOH A 2145 2555 1.68 REMARK 500 O HOH A 2218 O HOH A 2223 2555 2.11 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 ASP A 63 28.74 -71.34 REMARK 500 MET A 74 13.11 54.32 REMARK 500 SER A 112 -147.75 -110.96 REMARK 500 ASN A 123 101.91 -171.72 REMARK 500 PRO A 170 174.27 -56.75 REMARK 500 ASP A 188 121.05 -38.36 REMARK 500 HIS A 292 44.64 -141.13 REMARK 500 ASN A 395 50.31 -110.21 REMARK 500 ASP B 63 31.22 -74.08 REMARK 500 MET B 74 18.31 54.74 REMARK 500 SER B 112 -145.38 -110.54 REMARK 500 ASN B 123 101.63 -170.03 REMARK 500 THR B 124 -0.35 -58.67 REMARK 500 SER B 155 -9.27 -58.95 REMARK 500 ALA B 221 61.13 27.35 REMARK 500 HIS B 292 41.89 -143.45 REMARK 500 VAL B 377 -61.68 -102.07 REMARK 500 ASN B 395 48.77 -105.42 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 A2014 DISTANCE = 7.83 ANGSTROMS REMARK 525 HOH A2049 DISTANCE = 6.02 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MLA A 1413 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MLA B 1413 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1O9N RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE K62A MUTANT OF MALONAMIDASE E2 FROM REMARK 900 BRADYRHIZOBIUM JAPONICUM REMARK 900 RELATED ID: 1O9O RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE S131A MUTANT OF MALONAMIDASE E2 COMPLEXED REMARK 900 WITH MALONAMATE FROM BRADYRHIZOBIUM JAPONICUM REMARK 900 RELATED ID: 1O9P RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE S131A MUTANT OF MALONAMIDASE E2 COMPLEXED REMARK 900 WITH MALONATE FROM BRADYRHIZOBIUM JAPONICUM REMARK 900 RELATED ID: 1O9Q RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE S155C MUTANT OF MALONAMIDASE E2 FROM REMARK 900 BRADYRHIZOBIUM JAPONICUM REMARK 900 RELATED ID: 1OBI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE G130A MUTANT OF MALONAMIDASE E2 FROM REMARK 900 BRADYRHIZOBIUM JAPONICUM REMARK 900 RELATED ID: 1OBJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE T150A MUTANT OF MALONAMIDASE E2 FROM REMARK 900 BRADYRHIZOBIUM JAPONICUM REMARK 900 RELATED ID: 1OBK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE R158Q MUTANT OF MALONAMIDASE E2 FROM REMARK 900 BRADYRHIZOBIUM JAPONICUM REMARK 900 RELATED ID: 1OBL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE S133A MUTANT OF MALONAMIDASE E2 COMPLEXED REMARK 900 WITH MALONATE FROM BRADYRHIZOBIUM JAPONICUM REMARK 900 RELATED ID: 1OCH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE S155C MUTANT OF MALONAMIDASE E2 REMARK 900 RELATED ID: 1OCK RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF MALONAMIDASE E2 FROM BRADYRHIZOBIUM REMARK 900 JAPONICUM REMARK 900 RELATED ID: 1OCM RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF MALONAMIDASE E2 FROM BRADYRHIZOBIUM REMARK 900 JAPONICUM DBREF 1OCL A 1 400 UNP Q9ZIV5 Q9ZIV5 1 400 DBREF 1OCL A 401 412 PDB 1OCL 1OCL 401 412 DBREF 1OCL B 1 400 UNP Q9ZIV5 Q9ZIV5 1 400 DBREF 1OCL B 401 412 PDB 1OCL 1OCL 401 412 SEQRES 1 A 412 MET ILE SER LEU ALA ASP LEU GLN ARG ARG ILE GLU THR SEQRES 2 A 412 GLY GLU LEU SER PRO ASN ALA ALA ILE ALA GLN SER HIS SEQRES 3 A 412 ALA ALA ILE GLU ALA ARG GLU LYS GLU VAL HIS ALA PHE SEQRES 4 A 412 VAL ARG HIS ASP LYS SER ALA ARG ALA GLN ALA SER GLY SEQRES 5 A 412 PRO LEU ARG GLY ILE ALA VAL GLY ILE LYS ASP ILE ILE SEQRES 6 A 412 ASP THR ALA ASN MET PRO THR GLU MET GLY SER GLU ILE SEQRES 7 A 412 TYR ARG GLY TRP GLN PRO ARG SER ASP ALA PRO VAL VAL SEQRES 8 A 412 MET MET LEU LYS ARG ALA GLY ALA THR ILE ILE GLY LYS SEQRES 9 A 412 THR THR THR THR ALA PHE ALA SER ARG ASP PRO THR ALA SEQRES 10 A 412 THR LEU ASN PRO HIS ASN THR GLY HIS SER PRO GLY GLY SEQRES 11 A 412 SER SER SER GLY SER ALA ALA ALA VAL GLY ALA GLY MET SEQRES 12 A 412 ILE PRO LEU ALA LEU GLY THR GLN THR GLY GLY SER VAL SEQRES 13 A 412 ILE ARG PRO ALA ALA TYR CYS GLY THR ALA ALA ILE LYS SEQRES 14 A 412 PRO SER PHE ARG MET LEU PRO THR VAL GLY VAL LYS CYS SEQRES 15 A 412 TYR SER TRP ALA LEU ASP THR VAL GLY LEU PHE GLY ALA SEQRES 16 A 412 ARG ALA GLU ASP LEU ALA ARG GLY LEU LEU ALA MET THR SEQRES 17 A 412 GLY ARG SER GLU PHE SER GLY ILE VAL PRO ALA LYS ALA SEQRES 18 A 412 PRO ARG ILE GLY VAL VAL ARG GLN GLU PHE ALA GLY ALA SEQRES 19 A 412 VAL GLU PRO ALA ALA GLU GLN GLY LEU GLN ALA ALA ILE SEQRES 20 A 412 LYS ALA ALA GLU ARG ALA GLY ALA SER VAL GLN ALA ILE SEQRES 21 A 412 ASP LEU PRO GLU ALA VAL HIS GLU ALA TRP ARG ILE HIS SEQRES 22 A 412 PRO ILE ILE GLN ASP PHE GLU ALA HIS ARG ALA LEU ALA SEQRES 23 A 412 TRP GLU PHE SER GLU HIS HIS ASP GLU ILE ALA PRO MET SEQRES 24 A 412 LEU ARG ALA SER LEU ASP ALA THR VAL GLY LEU THR PRO SEQRES 25 A 412 LYS GLU TYR ASP GLU ALA ARG ARG ILE GLY ARG ARG GLY SEQRES 26 A 412 ARG ARG GLU LEU GLY GLU VAL PHE GLU GLY VAL ASP VAL SEQRES 27 A 412 LEU LEU THR TYR SER ALA PRO GLY THR ALA PRO ALA LYS SEQRES 28 A 412 ALA LEU ALA SER THR GLY ASP PRO ARG TYR ASN ARG LEU SEQRES 29 A 412 TRP THR LEU MET GLY ASN PRO CYS VAL ASN VAL PRO VAL SEQRES 30 A 412 LEU LYS VAL GLY GLY LEU PRO ILE GLY VAL GLN VAL ILE SEQRES 31 A 412 ALA ARG PHE GLY ASN ASP ALA HIS ALA LEU ALA THR ALA SEQRES 32 A 412 TRP PHE LEU GLU ASP ALA LEU ALA LYS SEQRES 1 B 412 MET ILE SER LEU ALA ASP LEU GLN ARG ARG ILE GLU THR SEQRES 2 B 412 GLY GLU LEU SER PRO ASN ALA ALA ILE ALA GLN SER HIS SEQRES 3 B 412 ALA ALA ILE GLU ALA ARG GLU LYS GLU VAL HIS ALA PHE SEQRES 4 B 412 VAL ARG HIS ASP LYS SER ALA ARG ALA GLN ALA SER GLY SEQRES 5 B 412 PRO LEU ARG GLY ILE ALA VAL GLY ILE LYS ASP ILE ILE SEQRES 6 B 412 ASP THR ALA ASN MET PRO THR GLU MET GLY SER GLU ILE SEQRES 7 B 412 TYR ARG GLY TRP GLN PRO ARG SER ASP ALA PRO VAL VAL SEQRES 8 B 412 MET MET LEU LYS ARG ALA GLY ALA THR ILE ILE GLY LYS SEQRES 9 B 412 THR THR THR THR ALA PHE ALA SER ARG ASP PRO THR ALA SEQRES 10 B 412 THR LEU ASN PRO HIS ASN THR GLY HIS SER PRO GLY GLY SEQRES 11 B 412 SER SER SER GLY SER ALA ALA ALA VAL GLY ALA GLY MET SEQRES 12 B 412 ILE PRO LEU ALA LEU GLY THR GLN THR GLY GLY SER VAL SEQRES 13 B 412 ILE ARG PRO ALA ALA TYR CYS GLY THR ALA ALA ILE LYS SEQRES 14 B 412 PRO SER PHE ARG MET LEU PRO THR VAL GLY VAL LYS CYS SEQRES 15 B 412 TYR SER TRP ALA LEU ASP THR VAL GLY LEU PHE GLY ALA SEQRES 16 B 412 ARG ALA GLU ASP LEU ALA ARG GLY LEU LEU ALA MET THR SEQRES 17 B 412 GLY ARG SER GLU PHE SER GLY ILE VAL PRO ALA LYS ALA SEQRES 18 B 412 PRO ARG ILE GLY VAL VAL ARG GLN GLU PHE ALA GLY ALA SEQRES 19 B 412 VAL GLU PRO ALA ALA GLU GLN GLY LEU GLN ALA ALA ILE SEQRES 20 B 412 LYS ALA ALA GLU ARG ALA GLY ALA SER VAL GLN ALA ILE SEQRES 21 B 412 ASP LEU PRO GLU ALA VAL HIS GLU ALA TRP ARG ILE HIS SEQRES 22 B 412 PRO ILE ILE GLN ASP PHE GLU ALA HIS ARG ALA LEU ALA SEQRES 23 B 412 TRP GLU PHE SER GLU HIS HIS ASP GLU ILE ALA PRO MET SEQRES 24 B 412 LEU ARG ALA SER LEU ASP ALA THR VAL GLY LEU THR PRO SEQRES 25 B 412 LYS GLU TYR ASP GLU ALA ARG ARG ILE GLY ARG ARG GLY SEQRES 26 B 412 ARG ARG GLU LEU GLY GLU VAL PHE GLU GLY VAL ASP VAL SEQRES 27 B 412 LEU LEU THR TYR SER ALA PRO GLY THR ALA PRO ALA LYS SEQRES 28 B 412 ALA LEU ALA SER THR GLY ASP PRO ARG TYR ASN ARG LEU SEQRES 29 B 412 TRP THR LEU MET GLY ASN PRO CYS VAL ASN VAL PRO VAL SEQRES 30 B 412 LEU LYS VAL GLY GLY LEU PRO ILE GLY VAL GLN VAL ILE SEQRES 31 B 412 ALA ARG PHE GLY ASN ASP ALA HIS ALA LEU ALA THR ALA SEQRES 32 B 412 TRP PHE LEU GLU ASP ALA LEU ALA LYS HET MLA A1413 7 HET MLA B1413 7 HETNAM MLA MALONIC ACID HETSYN MLA DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; HETSYN 2 MLA METHANEDICARBOXYLIC ACID FORMUL 3 MLA 2(C3 H4 O4) FORMUL 5 HOH *513(H2 O) HELIX 1 1 SER A 3 THR A 13 1 11 HELIX 2 2 SER A 17 HIS A 37 1 21 HELIX 3 3 SER A 76 ARG A 80 5 5 HELIX 4 4 ALA A 88 ALA A 97 1 10 HELIX 5 5 THR A 108 SER A 112 5 5 HELIX 6 6 SER A 132 ALA A 141 1 10 HELIX 7 7 VAL A 156 GLY A 164 1 9 HELIX 8 8 ARG A 196 GLY A 209 1 14 HELIX 9 9 ARG A 210 SER A 214 5 5 HELIX 10 10 GLN A 229 GLY A 233 5 5 HELIX 11 11 GLU A 236 ALA A 253 1 18 HELIX 12 12 PRO A 263 ILE A 272 1 10 HELIX 13 13 ILE A 272 LEU A 285 1 14 HELIX 14 14 LEU A 285 HIS A 292 1 8 HELIX 15 15 HIS A 293 ILE A 296 5 4 HELIX 16 16 ALA A 297 ALA A 306 1 10 HELIX 17 17 THR A 311 PHE A 333 1 23 HELIX 18 18 LYS A 351 ALA A 354 5 4 HELIX 19 19 ASP A 358 TYR A 361 5 4 HELIX 20 20 ASN A 362 GLY A 369 1 8 HELIX 21 21 ASN A 395 ALA A 411 1 17 HELIX 22 22 SER B 3 THR B 13 1 11 HELIX 23 23 SER B 17 HIS B 37 1 21 HELIX 24 24 SER B 76 ARG B 80 5 5 HELIX 25 25 ALA B 88 ALA B 97 1 10 HELIX 26 26 THR B 108 SER B 112 5 5 HELIX 27 27 SER B 132 ALA B 141 1 10 HELIX 28 28 VAL B 156 GLY B 164 1 9 HELIX 29 29 ARG B 196 GLY B 209 1 14 HELIX 30 30 ARG B 210 SER B 214 5 5 HELIX 31 31 GLN B 229 GLY B 233 5 5 HELIX 32 32 GLU B 236 ARG B 252 1 17 HELIX 33 33 PRO B 263 HIS B 292 1 30 HELIX 34 34 HIS B 293 ILE B 296 5 4 HELIX 35 35 ALA B 297 VAL B 308 1 12 HELIX 36 36 THR B 311 PHE B 333 1 23 HELIX 37 37 LYS B 351 ALA B 354 5 4 HELIX 38 38 ASN B 362 GLY B 369 1 8 HELIX 39 39 ASN B 395 LYS B 412 1 18 SHEET 1 AA11 PHE A 39 HIS A 42 0 SHEET 2 AA11 THR A 100 THR A 105 -1 O LYS A 104 N VAL A 40 SHEET 3 AA11 ALA A 58 LYS A 62 1 O VAL A 59 N GLY A 103 SHEET 4 AA11 LEU A 146 GLN A 151 1 O LEU A 146 N GLY A 60 SHEET 5 AA11 THR A 189 GLY A 194 -1 O THR A 189 N GLN A 151 SHEET 6 AA11 ALA A 166 LYS A 169 -1 O ALA A 166 N GLY A 194 SHEET 7 AA11 CYS A 372 VAL A 380 -1 O CYS A 372 N LYS A 169 SHEET 8 AA11 LEU A 383 ALA A 391 -1 O LEU A 383 N VAL A 380 SHEET 9 AA11 VAL A 338 TYR A 342 -1 O LEU A 339 N ILE A 390 SHEET 10 AA11 ARG A 223 VAL A 226 1 O GLY A 225 N LEU A 340 SHEET 11 AA11 SER A 256 ALA A 259 1 O SER A 256 N ILE A 224 SHEET 1 BA11 PHE B 39 HIS B 42 0 SHEET 2 BA11 THR B 100 THR B 105 -1 O LYS B 104 N VAL B 40 SHEET 3 BA11 ALA B 58 LYS B 62 1 O VAL B 59 N ILE B 102 SHEET 4 BA11 LEU B 146 GLN B 151 1 O LEU B 146 N GLY B 60 SHEET 5 BA11 THR B 189 GLY B 194 -1 O THR B 189 N GLN B 151 SHEET 6 BA11 ALA B 166 LYS B 169 -1 O ALA B 166 N GLY B 194 SHEET 7 BA11 CYS B 372 VAL B 380 -1 O CYS B 372 N LYS B 169 SHEET 8 BA11 LEU B 383 ALA B 391 -1 O LEU B 383 N VAL B 380 SHEET 9 BA11 VAL B 338 TYR B 342 -1 O LEU B 339 N ILE B 390 SHEET 10 BA11 ARG B 223 VAL B 226 1 O GLY B 225 N LEU B 340 SHEET 11 BA11 SER B 256 ALA B 259 1 O SER B 256 N ILE B 224 CISPEP 1 GLY A 130 SER A 131 0 3.86 CISPEP 2 GLY B 130 SER B 131 0 5.53 SITE 1 AC1 10 GLY A 130 SER A 131 THR A 152 GLY A 153 SITE 2 AC1 10 GLY A 154 SER A 155 ARG A 158 GLN A 277 SITE 3 AC1 10 PRO A 359 HOH A2283 SITE 1 AC2 11 GLY B 130 SER B 131 THR B 152 GLY B 153 SITE 2 AC2 11 GLY B 154 SER B 155 ARG B 158 GLN B 277 SITE 3 AC2 11 PRO B 359 HOH B2096 HOH B2229 CRYST1 103.821 94.940 74.783 90.00 90.00 90.00 P 21 21 2 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 0.009632 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010533 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013372 0.00000