PDB Short entry for 1OJR HEADER LYASE 15-JUL-03 1OJR TITLE L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E192A) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHAMNULOSE-1-PHOSPHATE ALDOLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 4.1.2.19; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: JM105; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PKK223-3 (GEN RHAD) KEYWDS LYASE, ALDOLASE (LYASE), CLASS II, ZINC ENZYME, C4-TETRAMER, KEYWDS 2 BACTERIAL L-RHAMNOSE METABOLISM, CLEAVAGE OF L-RHAMNULOSE-1- KEYWDS 3 PHOSPHATE TO DIHYDROXYACETONEPHOSPHATE AND L-LACTALDEHYDE EXPDTA X-RAY DIFFRACTION AUTHOR M.KROEMER,I.MERKEL,G.E.SCHULZ REVDAT 4 24-JUL-19 1OJR 1 REMARK REVDAT 3 08-MAY-19 1OJR 1 REMARK REVDAT 2 24-FEB-09 1OJR 1 VERSN REVDAT 1 11-SEP-03 1OJR 0 JRNL AUTH M.KROEMER,I.MERKEL,G.E.SCHULZ JRNL TITL STRUCTURE AND CATALYTIC MECHANISM OF JRNL TITL 2 L-RHAMNULOSE-1-PHOSPHATE ALDOLASE. JRNL REF BIOCHEMISTRY V. 42 10560 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 12962479 JRNL DOI 10.1021/BI0349266 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.KROEMER,G.E.SCHULZ REMARK 1 TITL THE STRUCTURE OF L-RHAMNULOSE-1-PHOSPHATE ALDOLASE (CLASS REMARK 1 TITL 2 II) SOLVED BY LOW-RESOLUTION SIR PHASING AND 20-FOLD NCS REMARK 1 TITL 3 AVERAGING REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 58 824 2002 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 11976494 REMARK 1 DOI 10.1107/S0907444902004614 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.C.JOERGER,C.MUELLER-DIECKMANN,G.E.SCHULZ REMARK 1 TITL STRUCTURES OF L-FUCULOSE-1-PHOSPHATE ALDOLASE MUTANTS REMARK 1 TITL 2 OUTLINING MOTIONS DURING CATALYSIS REMARK 1 REF J.MOL.BIOL. V. 303 531 2000 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 11054289 REMARK 1 DOI 10.1006/JMBI.2000.4153 REMARK 1 REFERENCE 3 REMARK 1 AUTH P.MORALEJO,S.M.EGAN,E.HIDALGO,J.AGUILAR REMARK 1 TITL SEQUENCING AND CHARACTERIZATION OF A GENE CLUSTER ENCODING REMARK 1 TITL 2 THE ENZYMES FOR L-RHAMNOSE METABOLISM IN ESCHERICHIA COLI REMARK 1 REF J.BACTERIOL. V. 175 5585 1993 REMARK 1 REFN ISSN 0021-9193 REMARK 1 PMID 8396120 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.43 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 69212 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 + TEST SET) : 0.112 REMARK 3 R VALUE (WORKING SET) : 0.111 REMARK 3 FREE R VALUE : 0.142 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2175 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4849 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2090 REMARK 3 BIN FREE R VALUE SET COUNT : 148 REMARK 3 BIN FREE R VALUE : 0.3060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2120 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 47 REMARK 3 SOLVENT ATOMS : 525 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.27000 REMARK 3 B22 (A**2) : -0.27000 REMARK 3 B33 (A**2) : 0.53000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.039 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.040 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.034 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.647 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.984 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.974 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2338 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2134 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3208 ; 1.252 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5028 ; 1.112 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 294 ; 4.067 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 435 ;15.776 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 381 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2544 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 441 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 553 ; 0.229 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2103 ; 0.188 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2 ; 0.229 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 425 ; 0.191 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): 2 ; 0.179 ; 0.500 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.101 ; 0.500 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 19 ; 0.278 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 60 ; 0.196 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 67 ; 0.283 ; 0.500 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1407 ; 2.842 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2322 ; 3.696 ; 4.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 931 ; 4.896 ; 4.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 877 ; 5.990 ; 6.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. TWO ADDITIONAL DENSITY REGIONS IN THE ACTIVE CENTER REMARK 3 WERE FITTED BY A 1:1 MIXTURE OF DIHYDROXYACETONE AND PHOSPHATE REMARK 3 AND A 1:1 MIXTURE OF PHOSPHATE AND FIVE WATER MOLECULES, REMARK 3 RESPECTIVELY. DIHYDROXYACETONE WAS AN 0.2% (V/V) IMPURITY IN THE REMARK 3 AUTOCLAVED CRYO PROTECTANT GLYCEROL. THE PHOSPHATE WAS FROM THE REMARK 3 LAST PURIFICATION BUFFER AND HAD ESCAPED DIALYSIS. REMARK 4 REMARK 4 1OJR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-JUL-03. REMARK 100 THE DEPOSITION ID IS D_1290013068. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-99 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8468 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 71387 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 30.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.38000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1GT7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP WITH 5 MG/ML PROTEIN AND REMARK 280 18% (V/V) DIOXANE. RESERVOIR WITH 35% (V/V) DIOXANE. HAMPTON REMARK 280 CRYSTAL SCREEN-2 NO.4, PH 4.00, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 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 -Y+1/2,X+1/2,Z REMARK 290 4555 Y+1/2,-X+1/2,Z REMARK 290 5555 -X+1/2,Y+1/2,-Z REMARK 290 6555 X+1/2,-Y+1/2,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 54.01200 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 54.01200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 54.01200 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 54.01200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 54.01200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 54.01200 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 54.01200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 54.01200 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PQS 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 BIOMT1 2 0.000000 -1.000000 0.000000 54.01200 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 54.01200 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 -54.01200 REMARK 350 BIOMT2 3 -1.000000 0.000000 0.000000 54.01200 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 108.02400 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 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 A2113 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2253 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2439 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUES GLU 192 ALA (SURFACE MUTATION) 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 NE2 GLN A 60 O HOH A 2218 1.73 REMARK 500 O HOH A 2115 O HOH A 2507 2.15 REMARK 500 O HOH A 2371 O HOH A 2495 2.15 REMARK 500 O HOH A 2046 O HOH A 2047 2.18 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 2028 O HOH A 2028 4455 2.06 REMARK 500 O HOH A 2017 O HOH A 2447 4456 2.11 REMARK 500 O HOH A 2250 O HOH A 2250 3555 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ASP A 38 CB - CG - OD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 CYS A 142 CA - CB - SG ANGL. DEV. = 8.9 DEGREES 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 GLN A 2 166.41 -44.71 REMARK 500 GLN A 2 166.41 -47.46 REMARK 500 ARG A 28 -128.08 50.38 REMARK 500 ARG A 28 -130.50 54.60 REMARK 500 ASP A 85 80.23 -157.04 REMARK 500 HIS A 143 68.47 -100.51 REMARK 500 HIS A 212 -64.76 -146.30 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 A2008 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH A2015 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH A2035 DISTANCE = 6.39 ANGSTROMS REMARK 525 HOH A2046 DISTANCE = 6.84 ANGSTROMS REMARK 525 HOH A2047 DISTANCE = 7.61 ANGSTROMS REMARK 525 HOH A2073 DISTANCE = 6.74 ANGSTROMS REMARK 525 HOH A2114 DISTANCE = 7.72 ANGSTROMS REMARK 525 HOH A2117 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A2119 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH A2126 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH A2129 DISTANCE = 7.18 ANGSTROMS REMARK 525 HOH A2140 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH A2216 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH A2253 DISTANCE = 7.05 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 ZN A1275 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 141 NE2 REMARK 620 2 HIS A 143 NE2 101.4 REMARK 620 3 HIS A 212 NE2 102.3 99.7 REMARK 620 4 2HA A1277 O2 98.0 92.4 153.8 REMARK 620 5 PO4 A1278 O3 100.1 106.3 141.3 15.0 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1275 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A1276 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A1278 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2HA A1277 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DIO A1283 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1279 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1280 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1281 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1282 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1GT7 RELATED DB: PDB REMARK 900 L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI DBREF 1OJR A 1 274 UNP P32169 RHAD_ECOLI 1 274 SEQADV 1OJR ALA A 192 UNP P32169 GLU 192 ENGINEERED MUTATION SEQRES 1 A 274 MET GLN ASN ILE THR GLN SER TRP PHE VAL GLN GLY MET SEQRES 2 A 274 ILE LYS ALA THR THR ASP ALA TRP LEU LYS GLY TRP ASP SEQRES 3 A 274 GLU ARG ASN GLY GLY ASN LEU THR LEU ARG LEU ASP ASP SEQRES 4 A 274 ALA ASP ILE ALA PRO TYR HIS ASP ASN PHE HIS GLN GLN SEQRES 5 A 274 PRO ARG TYR ILE PRO LEU SER GLN PRO MET PRO LEU LEU SEQRES 6 A 274 ALA ASN THR PRO PHE ILE VAL THR GLY SER GLY LYS PHE SEQRES 7 A 274 PHE ARG ASN VAL GLN LEU ASP PRO ALA ALA ASN LEU GLY SEQRES 8 A 274 ILE VAL LYS VAL ASP SER ASP GLY ALA GLY TYR HIS ILE SEQRES 9 A 274 LEU TRP GLY LEU THR ASN GLU ALA VAL PRO THR SER GLU SEQRES 10 A 274 LEU PRO ALA HIS PHE LEU SER HIS CYS GLU ARG ILE LYS SEQRES 11 A 274 ALA THR ASN GLY LYS ASP ARG VAL ILE MET HIS CYS HIS SEQRES 12 A 274 ALA THR ASN LEU ILE ALA LEU THR TYR VAL LEU GLU ASN SEQRES 13 A 274 ASP THR ALA VAL PHE THR ARG GLN LEU TRP GLU GLY SER SEQRES 14 A 274 THR GLU CYS LEU VAL VAL PHE PRO ASP GLY VAL GLY ILE SEQRES 15 A 274 LEU PRO TRP MET VAL PRO GLY THR ASP ALA ILE GLY GLN SEQRES 16 A 274 ALA THR ALA GLN GLU MET GLN LYS HIS SER LEU VAL LEU SEQRES 17 A 274 TRP PRO PHE HIS GLY VAL PHE GLY SER GLY PRO THR LEU SEQRES 18 A 274 ASP GLU THR PHE GLY LEU ILE ASP THR ALA GLU LYS SER SEQRES 19 A 274 ALA GLN VAL LEU VAL LYS VAL TYR SER MET GLY GLY MET SEQRES 20 A 274 LYS GLN THR ILE SER ARG GLU GLU LEU ILE ALA LEU GLY SEQRES 21 A 274 LYS ARG PHE GLY VAL THR PRO LEU ALA SER ALA LEU ALA SEQRES 22 A 274 LEU HET ZN A1275 1 HET PO4 A1276 5 HET PO4 A1278 5 HET 2HA A1277 6 HET DIO A1283 6 HET GOL A1279 6 HET GOL A1280 6 HET GOL A1281 6 HET GOL A1282 6 HETNAM ZN ZINC ION HETNAM PO4 PHOSPHATE ION HETNAM 2HA DIHYDROXYACETONE HETNAM DIO 1,4-DIETHYLENE DIOXIDE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ZN ZN 2+ FORMUL 3 PO4 2(O4 P 3-) FORMUL 5 2HA C3 H6 O3 FORMUL 6 DIO C4 H8 O2 FORMUL 7 GOL 4(C3 H8 O3) FORMUL 11 HOH *525(H2 O) HELIX 1 1 ASN A 3 GLN A 6 5 4 HELIX 2 2 SER A 7 GLY A 24 1 18 HELIX 3 3 ASP A 38 ALA A 43 1 6 HELIX 4 4 PRO A 44 PHE A 49 5 6 HELIX 5 5 MET A 62 ALA A 66 5 5 HELIX 6 6 PHE A 78 VAL A 82 5 5 HELIX 7 7 ASP A 85 ASN A 89 1 5 HELIX 8 8 GLU A 117 THR A 132 1 16 HELIX 9 9 ALA A 144 THR A 151 1 8 HELIX 10 10 ASP A 157 GLY A 168 1 12 HELIX 11 11 GLU A 171 PHE A 176 1 6 HELIX 12 12 THR A 190 GLN A 202 1 13 HELIX 13 13 THR A 220 MET A 244 1 25 HELIX 14 14 SER A 252 GLY A 264 1 13 HELIX 15 15 LEU A 268 ALA A 273 1 6 SHEET 1 AA 9 ARG A 54 PRO A 57 0 SHEET 2 AA 9 GLY A 101 GLY A 107 -1 O TYR A 102 N ILE A 56 SHEET 3 AA 9 LEU A 90 VAL A 95 -1 O ILE A 92 N LEU A 105 SHEET 4 AA 9 PRO A 69 THR A 73 -1 O PHE A 70 N VAL A 93 SHEET 5 AA 9 ASN A 32 ARG A 36 -1 O LEU A 33 N THR A 73 SHEET 6 AA 9 VAL A 138 CYS A 142 -1 O ILE A 139 N THR A 34 SHEET 7 AA 9 GLY A 213 GLY A 218 -1 O VAL A 214 N CYS A 142 SHEET 8 AA 9 LEU A 206 TRP A 209 -1 O VAL A 207 N PHE A 215 SHEET 9 AA 9 VAL A 180 ILE A 182 1 O GLY A 181 N LEU A 208 LINK ZN ZN A1275 NE2 HIS A 141 1555 1555 2.14 LINK ZN ZN A1275 NE2 HIS A 143 1555 1555 2.11 LINK ZN ZN A1275 NE2 HIS A 212 1555 1555 2.05 LINK ZN ZN A1275 O2 A2HA A1277 1555 1555 1.96 LINK ZN ZN A1275 O3 BPO4 A1278 1555 1555 1.86 SITE 1 AC1 6 HIS A 141 HIS A 143 HIS A 212 2HA A1277 SITE 2 AC1 6 PO4 A1278 HOH A2503 SITE 1 AC2 13 ASN A 29 ASN A 32 SER A 75 GLY A 76 SITE 2 AC2 13 THR A 115 SER A 116 PO4 A1278 HOH A2497 SITE 3 AC2 13 HOH A2498 HOH A2499 HOH A2500 HOH A2501 SITE 4 AC2 13 HOH A2502 SITE 1 AC3 12 GLY A 31 ASN A 32 GLU A 117 HIS A 141 SITE 2 AC3 12 HIS A 143 HIS A 212 ZN A1275 PO4 A1276 SITE 3 AC3 12 GOL A1279 HOH A2497 HOH A2502 HOH A2503 SITE 1 AC4 12 ASN A 29 GLY A 30 GLY A 31 ASN A 32 SITE 2 AC4 12 GLU A 117 HIS A 141 HIS A 143 HIS A 212 SITE 3 AC4 12 ZN A1275 GOL A1279 HOH A2502 HOH A2507 SITE 1 AC5 7 HIS A 46 ASP A 47 PHE A 49 GLN A 51 SITE 2 AC5 7 TYR A 55 HOH A2524 HOH A2525 SITE 1 AC6 11 ASN A 29 GLU A 171 PRO A 188 PHE A 263 SITE 2 AC6 11 2HA A1277 PO4 A1278 HOH A2115 HOH A2503 SITE 3 AC6 11 HOH A2504 HOH A2505 HOH A2507 SITE 1 AC7 6 GLY A 76 LYS A 77 ASN A 81 ASP A 222 SITE 2 AC7 6 GLU A 223 HOH A2508 SITE 1 AC8 9 ARG A 80 GLN A 83 HOH A2075 HOH A2510 SITE 2 AC8 9 HOH A2511 HOH A2514 HOH A2517 HOH A2518 SITE 3 AC8 9 HOH A2519 SITE 1 AC9 7 LEU A 154 TYR A 242 MET A 244 LYS A 248 SITE 2 AC9 7 HOH A2520 HOH A2521 HOH A2522 CRYST1 108.024 108.024 57.166 90.00 90.00 90.00 P 4 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 0.009257 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009257 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017493 0.00000