PDB Short entry for 1DXF HEADER CLASS II ALDOLASE 05-JAN-00 1DXF TITLE 2-DEHYDRO-3-DEOXY-GALACTARATE ALDOLASE FROM ESCHERICHIA TITLE 2 COLI IN COMPLEX WITH PYRUVATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-DEHYDRO-3-DEOXY-GALACTARATE ALDOLASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 4.1.2.20 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562 KEYWDS CLASS II ALDOLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.IZARD,N.C.BLACKWELL REVDAT 2 24-FEB-09 1DXF 1 VERSN REVDAT 1 25-AUG-00 1DXF 0 JRNL AUTH T.IZARD,N.C.BLACKWELL JRNL TITL CRYSTAL STRUCTURES OF THE METAL-DEPENDENT JRNL TITL 2 2-DEHYDRO-3-DEOXY-GALACTARATE ALDOLASE SUGGEST A JRNL TITL 3 NOVEL REACTION MECHANISM. JRNL REF EMBO J. V. 19 3849 2000 JRNL REFN ISSN 0261-4189 JRNL PMID 10921867 JRNL DOI 10.1093/EMBOJ/19.15.3849 REMARK 2 REMARK 2 RESOLUTION. 2.6 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 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) : 2.6 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.1 REMARK 3 NUMBER OF REFLECTIONS : 15344 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) : 0.173 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.9 REMARK 3 FREE R VALUE TEST SET COUNT : 754 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.6 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1984 REMARK 3 BIN R VALUE (WORKING SET) : 0.24 REMARK 3 BIN FREE R VALUE : 0.322 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.7 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 98 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.033 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3790 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 244 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.7 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.1 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.19 REMARK 3 B22 (A**2) : -3.19 REMARK 3 B33 (A**2) : 6.39 REMARK 3 B12 (A**2) : 3.78 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.28 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.35 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.3 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.9 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.83 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) : 3.31 ; 1.50 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.13 ; 2.00 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.94 ; 2.00 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.95 ; 2.50 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36617 REMARK 3 BSOL : 40.9921 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 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : PYR.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DXF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-JAN-00. REMARK 100 THE PDBE ID CODE IS EBI-4517. 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 : 5.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 232660 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 200 DATA REDUNDANCY : 14.400 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : 0.05900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 63.20000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 36.48854 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 57.33333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 63.20000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 36.48854 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 57.33333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 63.20000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 36.48854 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 57.33333 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 63.20000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 36.48854 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 57.33333 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 63.20000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 36.48854 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 57.33333 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 63.20000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 36.48854 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 57.33333 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 72.97707 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 114.66667 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 72.97707 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 114.66667 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 72.97707 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 114.66667 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 72.97707 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 114.66667 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 72.97707 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 114.66667 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 72.97707 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 114.66667 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 300 REMARK 300 DETAILS:BIOLOGICAL_UNIT: HEXAMER REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 24650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 58520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -185.7 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 -0.500000 -0.866025 0.000000 126.40000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 63.20000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 109.46561 REMARK 350 BIOMT3 3 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 MET A 1 REMARK 465 ASN A 2 REMARK 465 ASN A 3 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 ASN B 3 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 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 8 98.81 -64.97 REMARK 500 PRO A 52 55.30 -64.80 REMARK 500 PHE A 99 72.71 41.64 REMARK 500 MSE A 131 54.87 37.61 REMARK 500 TYR A 138 -70.00 -55.48 REMARK 500 GLU A 153 34.85 -144.93 REMARK 500 VAL A 170 109.82 -59.40 REMARK 500 GLU B 153 33.02 -142.12 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 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 A 901 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PYR A 501 O3 REMARK 620 2 HOH A2073 O 86.8 REMARK 620 3 GLU A 153 OE1 82.0 145.9 REMARK 620 4 GLU A 153 OE2 102.0 165.0 48.6 REMARK 620 5 ASP A 179 OD2 142.9 82.0 87.8 97.5 REMARK 620 6 PYR A 501 O1 65.5 76.8 69.3 117.8 77.5 REMARK 620 7 HOH A2027 O 96.3 109.5 103.6 57.9 120.8 160.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 901 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 153 OE1 REMARK 620 2 PYR B 501 O1 93.7 REMARK 620 3 PYR B 501 O3 89.3 65.1 REMARK 620 4 HOH B2079 O 168.2 75.7 81.5 REMARK 620 5 ASP B 179 OD2 99.4 85.7 150.1 85.3 REMARK 620 6 HOH B2034 O 83.5 163.6 98.7 105.2 110.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PYR A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PYR B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DXE RELATED DB: PDB REMARK 900 2-DEHYDRO-3-DEOXY-GALACTARATE ALDOLASE FROM ESCHERICHIA COLI DBREF 1DXF A 1 256 UNP P23522 YHAF_ECOLI 1 256 DBREF 1DXF B 1 256 UNP P23522 YHAF_ECOLI 1 256 SEQADV 1DXF MSE A 63 UNP P23522 MET 63 MODIFIED RESIDUE SEQADV 1DXF MSE A 131 UNP P23522 MET 131 MODIFIED RESIDUE SEQADV 1DXF MSE B 63 UNP P23522 MET 63 MODIFIED RESIDUE SEQADV 1DXF MSE B 131 UNP P23522 MET 131 MODIFIED RESIDUE SEQRES 1 A 256 MET ASN ASN ASP VAL PHE PRO ASN LYS PHE LYS ALA ALA SEQRES 2 A 256 LEU ALA ALA LYS GLN VAL GLN ILE GLY CYS TRP SER ALA SEQRES 3 A 256 LEU SER ASN PRO ILE SER THR GLU VAL LEU GLY LEU ALA SEQRES 4 A 256 GLY PHE ASP TRP LEU VAL LEU ASP GLY GLU HIS ALA PRO SEQRES 5 A 256 ASN ASP ILE SER THR PHE ILE PRO GLN LEU MSE ALA LEU SEQRES 6 A 256 LYS GLY SER ALA SER ALA PRO VAL VAL ARG VAL PRO THR SEQRES 7 A 256 ASN GLU PRO VAL ILE ILE LYS ARG LEU LEU ASP ILE GLY SEQRES 8 A 256 PHE TYR ASN PHE LEU ILE PRO PHE VAL GLU THR LYS GLU SEQRES 9 A 256 GLU ALA GLU LEU ALA VAL ALA SER THR ARG TYR PRO PRO SEQRES 10 A 256 GLU GLY ILE ARG GLY VAL SER VAL SER HIS ARG ALA ASN SEQRES 11 A 256 MSE PHE GLY THR VAL ALA ASP TYR PHE ALA GLN SER ASN SEQRES 12 A 256 LYS ASN ILE THR ILE LEU VAL GLN ILE GLU SER GLN GLN SEQRES 13 A 256 GLY VAL ASP ASN VAL ASP ALA ILE ALA ALA THR GLU GLY SEQRES 14 A 256 VAL ASP GLY ILE PHE VAL GLY PRO SER ASP LEU ALA ALA SEQRES 15 A 256 ALA LEU GLY HIS LEU GLY ASN ALA SER HIS PRO ASP VAL SEQRES 16 A 256 GLN LYS ALA ILE GLN HIS ILE PHE ASN ARG ALA SER ALA SEQRES 17 A 256 HIS GLY LYS PRO SER GLY ILE LEU ALA PRO VAL GLU ALA SEQRES 18 A 256 ASP ALA ARG ARG TYR LEU GLU TRP GLY ALA THR PHE VAL SEQRES 19 A 256 ALA VAL GLY SER ASP LEU GLY VAL PHE ARG SER ALA THR SEQRES 20 A 256 GLN LYS LEU ALA ASP THR PHE LYS LYS SEQRES 1 B 256 MET ASN ASN ASP VAL PHE PRO ASN LYS PHE LYS ALA ALA SEQRES 2 B 256 LEU ALA ALA LYS GLN VAL GLN ILE GLY CYS TRP SER ALA SEQRES 3 B 256 LEU SER ASN PRO ILE SER THR GLU VAL LEU GLY LEU ALA SEQRES 4 B 256 GLY PHE ASP TRP LEU VAL LEU ASP GLY GLU HIS ALA PRO SEQRES 5 B 256 ASN ASP ILE SER THR PHE ILE PRO GLN LEU MSE ALA LEU SEQRES 6 B 256 LYS GLY SER ALA SER ALA PRO VAL VAL ARG VAL PRO THR SEQRES 7 B 256 ASN GLU PRO VAL ILE ILE LYS ARG LEU LEU ASP ILE GLY SEQRES 8 B 256 PHE TYR ASN PHE LEU ILE PRO PHE VAL GLU THR LYS GLU SEQRES 9 B 256 GLU ALA GLU LEU ALA VAL ALA SER THR ARG TYR PRO PRO SEQRES 10 B 256 GLU GLY ILE ARG GLY VAL SER VAL SER HIS ARG ALA ASN SEQRES 11 B 256 MSE PHE GLY THR VAL ALA ASP TYR PHE ALA GLN SER ASN SEQRES 12 B 256 LYS ASN ILE THR ILE LEU VAL GLN ILE GLU SER GLN GLN SEQRES 13 B 256 GLY VAL ASP ASN VAL ASP ALA ILE ALA ALA THR GLU GLY SEQRES 14 B 256 VAL ASP GLY ILE PHE VAL GLY PRO SER ASP LEU ALA ALA SEQRES 15 B 256 ALA LEU GLY HIS LEU GLY ASN ALA SER HIS PRO ASP VAL SEQRES 16 B 256 GLN LYS ALA ILE GLN HIS ILE PHE ASN ARG ALA SER ALA SEQRES 17 B 256 HIS GLY LYS PRO SER GLY ILE LEU ALA PRO VAL GLU ALA SEQRES 18 B 256 ASP ALA ARG ARG TYR LEU GLU TRP GLY ALA THR PHE VAL SEQRES 19 B 256 ALA VAL GLY SER ASP LEU GLY VAL PHE ARG SER ALA THR SEQRES 20 B 256 GLN LYS LEU ALA ASP THR PHE LYS LYS MODRES 1DXF MSE A 63 MET SELENOMETHIONINE MODRES 1DXF MSE A 131 MET SELENOMETHIONINE MODRES 1DXF MSE B 63 MET SELENOMETHIONINE MODRES 1DXF MSE B 131 MET SELENOMETHIONINE HET MSE A 63 8 HET MSE A 131 8 HET MSE B 63 8 HET MSE B 131 8 HET MG A 901 1 HET MG B 901 1 HET PYR A 501 6 HET PYR B 501 6 HETNAM MSE SELENOMETHIONINE HETNAM MG MAGNESIUM ION HETNAM PYR PYRUVIC ACID FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 3 MG 2(MG 2+) FORMUL 5 PYR 2(C3 H4 O3) FORMUL 7 HOH *244(H2 O1) HELIX 1 1 ASN A 8 ALA A 16 1 9 HELIX 2 2 ASN A 29 GLY A 37 1 9 HELIX 3 3 ASP A 54 LEU A 62 1 9 HELIX 4 4 GLU A 80 ILE A 90 1 11 HELIX 5 5 THR A 102 THR A 113 1 12 HELIX 6 6 ASP A 137 ASN A 143 1 7 HELIX 7 7 SER A 154 ASN A 160 1 7 HELIX 8 8 ASN A 160 THR A 167 1 8 HELIX 9 9 GLY A 176 LEU A 184 1 9 HELIX 10 10 HIS A 192 HIS A 209 1 18 HELIX 11 11 VAL A 219 TRP A 229 1 11 HELIX 12 12 ASP A 239 LYS A 256 1 18 HELIX 13 13 ASN B 8 ALA B 16 1 9 HELIX 14 14 ASN B 29 GLY B 37 1 9 HELIX 15 15 ASP B 54 LEU B 62 1 9 HELIX 16 16 GLU B 80 ILE B 90 1 11 HELIX 17 17 THR B 102 THR B 113 1 12 HELIX 18 18 ASP B 137 ASN B 143 1 7 HELIX 19 19 SER B 154 ASN B 160 1 7 HELIX 20 20 ASN B 160 ALA B 166 1 7 HELIX 21 21 GLY B 176 LEU B 184 1 9 HELIX 22 22 HIS B 192 HIS B 209 1 18 HELIX 23 23 VAL B 219 TRP B 229 1 11 HELIX 24 24 ASP B 239 THR B 253 1 15 SHEET 1 A 8 ALA A 71 ARG A 75 0 SHEET 2 A 8 TRP A 43 ASP A 47 1 N LEU A 44 O ALA A 71 SHEET 3 A 8 GLN A 20 SER A 25 1 N CYS A 23 O TRP A 43 SHEET 4 A 8 PHE A 233 ALA A 235 1 N VAL A 234 O GLN A 20 SHEET 5 A 8 PRO A 212 LEU A 216 1 N ILE A 215 O PHE A 233 SHEET 6 A 8 VAL A 170 VAL A 175 1 N ILE A 173 O PRO A 212 SHEET 7 A 8 THR A 147 ILE A 152 1 N ILE A 148 O ASP A 171 SHEET 8 A 8 ASN A 94 ILE A 97 1 N PHE A 95 O THR A 147 SHEET 1 B 8 ALA B 71 ARG B 75 0 SHEET 2 B 8 TRP B 43 ASP B 47 1 N LEU B 44 O ALA B 71 SHEET 3 B 8 GLN B 20 SER B 25 1 N CYS B 23 O TRP B 43 SHEET 4 B 8 PHE B 233 ALA B 235 1 N VAL B 234 O GLN B 20 SHEET 5 B 8 PRO B 212 LEU B 216 1 N ILE B 215 O PHE B 233 SHEET 6 B 8 VAL B 170 VAL B 175 1 N ILE B 173 O PRO B 212 SHEET 7 B 8 THR B 147 ILE B 152 1 N ILE B 148 O ASP B 171 SHEET 8 B 8 ASN B 94 ILE B 97 1 N PHE B 95 O THR B 147 LINK C LEU A 62 N MSE A 63 1555 1555 1.33 LINK C MSE A 63 N ALA A 64 1555 1555 1.33 LINK C ASN A 130 N MSE A 131 1555 1555 1.34 LINK C MSE A 131 N PHE A 132 1555 1555 1.33 LINK MG MG A 901 O3 PYR A 501 1555 1555 2.54 LINK MG MG A 901 O HOH A2073 1555 2655 2.62 LINK MG MG A 901 OE1 GLU A 153 1555 1555 2.28 LINK MG MG A 901 O HOH A2027 1555 1555 2.44 LINK MG MG A 901 O1 PYR A 501 1555 1555 2.59 LINK MG MG A 901 OD2 ASP A 179 1555 1555 2.28 LINK MG MG A 901 OE2 GLU A 153 1555 1555 2.90 LINK C LEU B 62 N MSE B 63 1555 1555 1.33 LINK C MSE B 63 N ALA B 64 1555 1555 1.33 LINK C ASN B 130 N MSE B 131 1555 1555 1.33 LINK C MSE B 131 N PHE B 132 1555 1555 1.33 LINK MG MG B 901 O1 PYR B 501 1555 1555 2.66 LINK MG MG B 901 O3 PYR B 501 1555 1555 2.51 LINK MG MG B 901 O HOH B2079 1555 3665 2.47 LINK MG MG B 901 OD2 ASP B 179 1555 1555 2.29 LINK MG MG B 901 O HOH B2034 1555 1555 2.29 LINK MG MG B 901 OE1 GLU B 153 1555 1555 2.30 CISPEP 1 PHE A 6 PRO A 7 0 0.40 CISPEP 2 PRO A 116 PRO A 117 0 0.09 CISPEP 3 PHE B 6 PRO B 7 0 0.05 CISPEP 4 PRO B 116 PRO B 117 0 -0.21 SITE 1 AC1 5 GLU A 153 ASP A 179 PYR A 501 HOH A2027 SITE 2 AC1 5 HOH A2073 SITE 1 AC2 5 GLU B 153 ASP B 179 PYR B 501 HOH B2034 SITE 2 AC2 5 HOH B2079 SITE 1 AC3 9 ARG A 75 GLN A 151 GLU A 153 GLY A 176 SITE 2 AC3 9 PRO A 177 SER A 178 ASP A 179 LEU A 216 SITE 3 AC3 9 MG A 901 SITE 1 AC4 10 ARG B 75 GLN B 151 GLU B 153 PHE B 174 SITE 2 AC4 10 GLY B 176 PRO B 177 SER B 178 ASP B 179 SITE 3 AC4 10 LEU B 216 MG B 901 CRYST1 126.400 126.400 172.000 90.00 90.00 120.00 H 3 2 36 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 0.007911 0.004568 0.000000 0.00000 SCALE2 0.000000 0.009135 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005814 0.00000 MTRIX1 1 0.997800 0.066500 -0.001700 -2.28630 1 MTRIX2 1 0.066500 -0.997800 0.001200 68.68410 1 MTRIX3 1 -0.001600 -0.001300 -1.000000 21.18270 1