HEADER KINASE 04-JUN-03 1OI3 TITLE X-RAY STRUCTURE OF THE DIHYDROXYACETONE KINASE FROM TITLE 2 ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN YCGT; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: DIHYDROXYACETONE BINDING SUBUNIT; COMPND 5 SYNONYM: DIHYDROXYACETONE KINASE; COMPND 6 EC: 2.7.1.29; COMPND 7 ENGINEERED: 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: WA2127; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PMSEH2 KEYWDS KINASE, DIHYDROXYACETONE KINASE, YCGT EXPDTA X-RAY DIFFRACTION AUTHOR C.SIEBOLD,L.-F.GARCIA-ALLES,B.ERNI,U.BAUMANN REVDAT 3 13-JUL-11 1OI3 1 VERSN REVDAT 2 24-FEB-09 1OI3 1 VERSN REVDAT 1 14-JUL-03 1OI3 0 JRNL AUTH C.SIEBOLD,L.-F.GARCIA-ALLES,B.ERNI,U.BAUMANN JRNL TITL A MECHANISM OF COVALENT SUBSTRATE BINDING IN THE X-RAY JRNL TITL 2 STRUCTURE OF SUBUNIT K OF THE ESCHERICHIA COLI JRNL TITL 3 DIHYDROXYACETONE KINASE JRNL REF PROC.NATL.ACAD.SCI.USA V. 100 8188 2003 JRNL REFN ISSN 0027-8424 JRNL PMID 12813127 JRNL DOI 10.1073/PNAS.0932787100 REMARK 2 REMARK 2 RESOLUTION. 2.0 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.19 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 50052 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1443 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 25 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.04 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1857 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1860 REMARK 3 BIN FREE R VALUE SET COUNT : 55 REMARK 3 BIN FREE R VALUE : 0.2210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5040 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 481 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL 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) : -1.60000 REMARK 3 B22 (A**2) : 1.82000 REMARK 3 B33 (A**2) : -0.22000 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): 0.169 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.159 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.094 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5106 ; 0.018 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6942 ; 1.780 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 668 ; 3.891 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 798 ; 0.161 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3878 ; 0.001 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2635 ; 0.238 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 491 ; 0.201 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 46 ; 0.290 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.319 ; 0.200 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): 3306 ; 2.928 ; 2.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5274 ; 3.945 ; 3.500 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1800 ; 4.835 ; 3.500 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1668 ; 6.589 ; 4.500 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 : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 20 A 204 4 REMARK 3 1 B 20 B 204 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 1323 ; 0.11 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 1323 ; 1.54 ; 2.00 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 218 A 368 4 REMARK 3 1 B 218 B 368 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 2 A (A): 1182 ; 0.30 ; 0.50 REMARK 3 MEDIUM THERMAL 2 A (A**2): 1182 ; 1.53 ; 2.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 20 A 368 REMARK 3 ORIGIN FOR THE GROUP (A): 63.3420 18.1530 58.7880 REMARK 3 T TENSOR REMARK 3 T11: 0.0139 T22: 0.0399 REMARK 3 T33: 0.0223 T12: 0.0183 REMARK 3 T13: -0.0038 T23: 0.0110 REMARK 3 L TENSOR REMARK 3 L11: 0.5520 L22: -0.0069 REMARK 3 L33: 0.6907 L12: 0.0640 REMARK 3 L13: -0.2680 L23: -0.0077 REMARK 3 S TENSOR REMARK 3 S11: 0.0480 S12: 0.0775 S13: 0.0559 REMARK 3 S21: 0.0065 S22: -0.0145 S23: 0.0008 REMARK 3 S31: -0.0222 S32: -0.1431 S33: -0.0335 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 20 B 368 REMARK 3 ORIGIN FOR THE GROUP (A): 101.2720 18.5810 70.5060 REMARK 3 T TENSOR REMARK 3 T11: 0.0175 T22: 0.0463 REMARK 3 T33: 0.0251 T12: -0.0179 REMARK 3 T13: 0.0004 T23: -0.0267 REMARK 3 L TENSOR REMARK 3 L11: 0.5784 L22: -0.0021 REMARK 3 L33: 0.3655 L12: 0.0211 REMARK 3 L13: -0.2697 L23: 0.0511 REMARK 3 S TENSOR REMARK 3 S11: 0.0327 S12: -0.1219 S13: 0.0582 REMARK 3 S21: -0.0167 S22: 0.0100 S23: -0.0150 REMARK 3 S31: -0.0291 S32: 0.1047 S33: -0.0427 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: RESIDUES 218 TO 222 WERE MODELED AS REMARK 3 POLY-ALANINES DUE TO INSUFFICEIENT ELECTRON DENSITY FOR THE REMARK 3 SIDE-CHAINS FOR THESE RESIDUES. REMARK 4 REMARK 4 1OI3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-JUN-03. REMARK 100 THE PDBE ID CODE IS EBI-12834. 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) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51496 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.7000 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) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 60.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.10000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER 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 (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 48.23250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.68200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 48.23250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.68200 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: PQS 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 400 REMARK 400 COMPOUND REMARK 400 BELONGS TO THE DIHYDROXYACETONE KINASE FAMILY 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 PRO A 2 REMARK 465 TYR A 3 REMARK 465 ARG A 4 REMARK 465 ASN A 5 REMARK 465 CYS A 6 REMARK 465 TRP A 7 REMARK 465 SER A 8 REMARK 465 LYS A 9 REMARK 465 ILE A 10 REMARK 465 MET A 11 REMARK 465 LYS A 12 REMARK 465 LYS A 13 REMARK 465 LEU A 14 REMARK 465 ILE A 15 REMARK 465 ASN A 16 REMARK 465 ASP A 17 REMARK 465 VAL A 18 REMARK 465 GLN A 19 REMARK 465 THR A 205 REMARK 465 VAL A 206 REMARK 465 PRO A 207 REMARK 465 ALA A 208 REMARK 465 ALA A 209 REMARK 465 GLY A 210 REMARK 465 LYS A 211 REMARK 465 PRO A 212 REMARK 465 SER A 213 REMARK 465 PHE A 214 REMARK 465 THR A 215 REMARK 465 MET B 1 REMARK 465 PRO B 2 REMARK 465 TYR B 3 REMARK 465 ARG B 4 REMARK 465 ASN B 5 REMARK 465 CYS B 6 REMARK 465 TRP B 7 REMARK 465 SER B 8 REMARK 465 LYS B 9 REMARK 465 ILE B 10 REMARK 465 MET B 11 REMARK 465 LYS B 12 REMARK 465 LYS B 13 REMARK 465 LEU B 14 REMARK 465 ILE B 15 REMARK 465 ASN B 16 REMARK 465 ASP B 17 REMARK 465 VAL B 18 REMARK 465 GLN B 19 REMARK 465 THR B 205 REMARK 465 VAL B 206 REMARK 465 PRO B 207 REMARK 465 ALA B 208 REMARK 465 ALA B 209 REMARK 465 GLY B 210 REMARK 465 LYS B 211 REMARK 465 PRO B 212 REMARK 465 SER B 213 REMARK 465 PHE B 214 REMARK 465 THR B 215 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 218 CG CD1 CD2 REMARK 470 ASP A 220 CG OD1 OD2 REMARK 470 ASN A 221 CG OD1 ND2 REMARK 470 GLU A 222 CG CD OE1 OE2 REMARK 470 LEU B 218 CG CD1 CD2 REMARK 470 ASP B 220 CG OD1 OD2 REMARK 470 ASN B 221 CG OD1 ND2 REMARK 470 GLU B 222 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 2010 O HOH B 2026 2.14 REMARK 500 O HOH B 2092 O HOH B 2151 2.13 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 NZ LYS B 55 NZ LYS B 55 2755 1.16 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 49 CB - CG - OD2 ANGL. DEV. = 7.1 DEGREES REMARK 500 ASP A 181 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 244 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP A 248 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP B 150 CB - CG - OD2 ANGL. DEV. = 5.4 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 MET A 78 -132.53 -147.62 REMARK 500 PHE A 88 27.77 49.78 REMARK 500 SER A 151 -164.64 -67.39 REMARK 500 VAL A 160 -138.18 -136.71 REMARK 500 ASP A 236 -179.52 -170.66 REMARK 500 LEU A 335 -124.98 40.83 REMARK 500 GLU B 67 135.77 -39.82 REMARK 500 MET B 78 -130.43 -147.01 REMARK 500 PHE B 88 28.44 49.37 REMARK 500 ASP B 150 62.25 65.19 REMARK 500 SER B 151 -167.68 -77.55 REMARK 500 VAL B 160 -137.36 -135.82 REMARK 500 ASN B 221 22.69 46.14 REMARK 500 LEU B 335 -123.56 43.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1369 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B1369 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OI2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DIHYDROXYACETONE KINASE REMARK 900 FROM ESCHERICHIA COLI DBREF 1OI3 A 1 215 UNP P76015 YCGT_ECOLI 1 215 DBREF 1OI3 A 218 368 UNP P76015 YCGT_ECOLI 216 366 DBREF 1OI3 B 1 215 UNP P76015 YCGT_ECOLI 1 215 DBREF 1OI3 B 218 368 UNP P76015 YCGT_ECOLI 216 366 SEQRES 1 A 366 MET PRO TYR ARG ASN CYS TRP SER LYS ILE MET LYS LYS SEQRES 2 A 366 LEU ILE ASN ASP VAL GLN ASP VAL LEU ASP GLU GLN LEU SEQRES 3 A 366 ALA GLY LEU ALA LYS ALA HIS PRO SER LEU THR LEU HIS SEQRES 4 A 366 GLN ASP PRO VAL TYR VAL THR ARG ALA ASP ALA PRO VAL SEQRES 5 A 366 ALA GLY LYS VAL ALA LEU LEU SER GLY GLY GLY SER GLY SEQRES 6 A 366 HIS GLU PRO MET HIS CYS GLY TYR ILE GLY GLN GLY MET SEQRES 7 A 366 LEU SER GLY ALA CYS PRO GLY GLU ILE PHE THR SER PRO SEQRES 8 A 366 THR PRO ASP LYS ILE PHE GLU CYS ALA MET GLN VAL ASP SEQRES 9 A 366 GLY GLY GLU GLY VAL LEU LEU ILE ILE LYS ASN TYR THR SEQRES 10 A 366 GLY ASP ILE LEU ASN PHE GLU THR ALA THR GLU LEU LEU SEQRES 11 A 366 HIS ASP SER GLY VAL LYS VAL THR THR VAL VAL ILE ASP SEQRES 12 A 366 ASP ASP VAL ALA VAL LYS ASP SER LEU TYR THR ALA GLY SEQRES 13 A 366 ARG ARG GLY VAL ALA ASN THR VAL LEU ILE GLU LYS LEU SEQRES 14 A 366 VAL GLY ALA ALA ALA GLU ARG GLY ASP SER LEU ASP ALA SEQRES 15 A 366 CYS ALA GLU LEU GLY ARG LYS LEU ASN ASN GLN GLY HIS SEQRES 16 A 366 SER ILE GLY ILE ALA LEU GLY ALA CYS THR VAL PRO ALA SEQRES 17 A 366 ALA GLY LYS PRO SER PHE THR LEU ALA ASP ASN GLU MET SEQRES 18 A 366 GLU PHE GLY VAL GLY ILE HIS GLY GLU PRO GLY ILE ASP SEQRES 19 A 366 ARG ARG PRO PHE SER SER LEU ASP GLN THR VAL ASP GLU SEQRES 20 A 366 MET PHE ASP THR LEU LEU VAL ASN GLY SER TYR HIS ARG SEQRES 21 A 366 THR LEU ARG PHE TRP ASP TYR GLN GLN GLY SER TRP GLN SEQRES 22 A 366 GLU GLU GLN GLN THR LYS GLN PRO LEU GLN SER GLY ASP SEQRES 23 A 366 ARG VAL ILE ALA LEU VAL ASN ASN LEU GLY ALA THR PRO SEQRES 24 A 366 LEU SER GLU LEU TYR GLY VAL TYR ASN ARG LEU THR THR SEQRES 25 A 366 ARG CYS GLN GLN ALA GLY LEU THR ILE GLU ARG ASN LEU SEQRES 26 A 366 ILE GLY ALA TYR CYS THR SER LEU ASP MET THR GLY PHE SEQRES 27 A 366 SER ILE THR LEU LEU LYS VAL ASP ASP GLU THR LEU ALA SEQRES 28 A 366 LEU TRP ASP ALA PRO VAL HIS THR PRO ALA LEU ASN TRP SEQRES 29 A 366 GLY LYS SEQRES 1 B 366 MET PRO TYR ARG ASN CYS TRP SER LYS ILE MET LYS LYS SEQRES 2 B 366 LEU ILE ASN ASP VAL GLN ASP VAL LEU ASP GLU GLN LEU SEQRES 3 B 366 ALA GLY LEU ALA LYS ALA HIS PRO SER LEU THR LEU HIS SEQRES 4 B 366 GLN ASP PRO VAL TYR VAL THR ARG ALA ASP ALA PRO VAL SEQRES 5 B 366 ALA GLY LYS VAL ALA LEU LEU SER GLY GLY GLY SER GLY SEQRES 6 B 366 HIS GLU PRO MET HIS CYS GLY TYR ILE GLY GLN GLY MET SEQRES 7 B 366 LEU SER GLY ALA CYS PRO GLY GLU ILE PHE THR SER PRO SEQRES 8 B 366 THR PRO ASP LYS ILE PHE GLU CYS ALA MET GLN VAL ASP SEQRES 9 B 366 GLY GLY GLU GLY VAL LEU LEU ILE ILE LYS ASN TYR THR SEQRES 10 B 366 GLY ASP ILE LEU ASN PHE GLU THR ALA THR GLU LEU LEU SEQRES 11 B 366 HIS ASP SER GLY VAL LYS VAL THR THR VAL VAL ILE ASP SEQRES 12 B 366 ASP ASP VAL ALA VAL LYS ASP SER LEU TYR THR ALA GLY SEQRES 13 B 366 ARG ARG GLY VAL ALA ASN THR VAL LEU ILE GLU LYS LEU SEQRES 14 B 366 VAL GLY ALA ALA ALA GLU ARG GLY ASP SER LEU ASP ALA SEQRES 15 B 366 CYS ALA GLU LEU GLY ARG LYS LEU ASN ASN GLN GLY HIS SEQRES 16 B 366 SER ILE GLY ILE ALA LEU GLY ALA CYS THR VAL PRO ALA SEQRES 17 B 366 ALA GLY LYS PRO SER PHE THR LEU ALA ASP ASN GLU MET SEQRES 18 B 366 GLU PHE GLY VAL GLY ILE HIS GLY GLU PRO GLY ILE ASP SEQRES 19 B 366 ARG ARG PRO PHE SER SER LEU ASP GLN THR VAL ASP GLU SEQRES 20 B 366 MET PHE ASP THR LEU LEU VAL ASN GLY SER TYR HIS ARG SEQRES 21 B 366 THR LEU ARG PHE TRP ASP TYR GLN GLN GLY SER TRP GLN SEQRES 22 B 366 GLU GLU GLN GLN THR LYS GLN PRO LEU GLN SER GLY ASP SEQRES 23 B 366 ARG VAL ILE ALA LEU VAL ASN ASN LEU GLY ALA THR PRO SEQRES 24 B 366 LEU SER GLU LEU TYR GLY VAL TYR ASN ARG LEU THR THR SEQRES 25 B 366 ARG CYS GLN GLN ALA GLY LEU THR ILE GLU ARG ASN LEU SEQRES 26 B 366 ILE GLY ALA TYR CYS THR SER LEU ASP MET THR GLY PHE SEQRES 27 B 366 SER ILE THR LEU LEU LYS VAL ASP ASP GLU THR LEU ALA SEQRES 28 B 366 LEU TRP ASP ALA PRO VAL HIS THR PRO ALA LEU ASN TRP SEQRES 29 B 366 GLY LYS HET SO4 A1369 5 HET SO4 B1369 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *481(H2 O) HELIX 1 1 ASP A 20 HIS A 33 1 14 HELIX 2 2 HIS A 70 TYR A 73 5 4 HELIX 3 3 THR A 92 ASP A 104 1 13 HELIX 4 4 TYR A 116 SER A 133 1 18 HELIX 5 5 ALA A 161 GLY A 177 1 17 HELIX 6 6 SER A 179 ASN A 192 1 14 HELIX 7 7 SER A 242 ASN A 257 1 16 HELIX 8 8 PRO A 301 GLY A 320 1 20 HELIX 9 9 ASP A 348 ALA A 357 1 10 HELIX 10 10 ASP B 20 HIS B 33 1 14 HELIX 11 11 HIS B 70 TYR B 73 5 4 HELIX 12 12 THR B 92 ASP B 104 1 13 HELIX 13 13 TYR B 116 SER B 133 1 18 HELIX 14 14 ALA B 161 GLY B 177 1 17 HELIX 15 15 SER B 179 ASN B 192 1 14 HELIX 16 16 SER B 242 ASN B 257 1 16 HELIX 17 17 PRO B 301 GLY B 320 1 20 HELIX 18 18 ASP B 348 ALA B 357 1 10 SHEET 1 AA 6 LEU A 36 HIS A 39 0 SHEET 2 AA 6 TYR A 44 ARG A 47 -1 O TYR A 44 N HIS A 39 SHEET 3 AA 6 GLY A 81 ILE A 87 -1 O ALA A 82 N VAL A 45 SHEET 4 AA 6 ALA A 57 SER A 64 1 O SER A 60 N CYS A 83 SHEET 5 AA 6 VAL A 109 LYS A 114 1 O LEU A 110 N LEU A 59 SHEET 6 AA 6 VAL A 137 ILE A 142 1 O THR A 138 N LEU A 111 SHEET 1 AB 6 ASP A 236 PRO A 239 0 SHEET 2 AB 6 GLU A 222 PHE A 225 -1 O MET A 223 N ARG A 238 SHEET 3 AB 6 GLY A 194 GLY A 202 -1 O ALA A 200 N GLU A 224 SHEET 4 AB 6 THR A 338 LYS A 346 -1 O THR A 338 N LEU A 201 SHEET 5 AB 6 ARG A 289 ASN A 296 -1 O ILE A 291 N LEU A 345 SHEET 6 AB 6 THR A 322 GLY A 329 1 O THR A 322 N VAL A 290 SHEET 1 AC 2 TYR A 260 ASP A 268 0 SHEET 2 AC 2 SER A 273 LYS A 281 -1 O SER A 273 N ASP A 268 SHEET 1 AD 2 VAL A 359 HIS A 360 0 SHEET 2 AD 2 ASN A 365 TRP A 366 -1 O TRP A 366 N VAL A 359 SHEET 1 BA 6 LEU B 36 HIS B 39 0 SHEET 2 BA 6 TYR B 44 ARG B 47 -1 O TYR B 44 N HIS B 39 SHEET 3 BA 6 GLY B 81 ILE B 87 -1 O ALA B 82 N VAL B 45 SHEET 4 BA 6 ALA B 57 SER B 64 1 O SER B 60 N CYS B 83 SHEET 5 BA 6 VAL B 109 LYS B 114 1 O LEU B 110 N LEU B 59 SHEET 6 BA 6 VAL B 137 ILE B 142 1 O THR B 138 N LEU B 111 SHEET 1 BB 6 ASP B 236 PRO B 239 0 SHEET 2 BB 6 GLU B 222 PHE B 225 -1 O MET B 223 N ARG B 238 SHEET 3 BB 6 GLY B 194 GLY B 202 -1 O ALA B 200 N GLU B 224 SHEET 4 BB 6 THR B 338 VAL B 347 -1 O THR B 338 N LEU B 201 SHEET 5 BB 6 ARG B 289 ASN B 296 -1 O ARG B 289 N VAL B 347 SHEET 6 BB 6 THR B 322 GLY B 329 1 O THR B 322 N VAL B 290 SHEET 1 BC 2 TYR B 260 ASP B 268 0 SHEET 2 BC 2 SER B 273 LYS B 281 -1 O SER B 273 N ASP B 268 SHEET 1 BD 2 VAL B 359 HIS B 360 0 SHEET 2 BD 2 ASN B 365 TRP B 366 -1 O TRP B 366 N VAL B 359 CISPEP 1 ASP A 41 PRO A 42 0 -1.04 CISPEP 2 ALA A 50 PRO A 51 0 -0.16 CISPEP 3 GLU A 67 PRO A 68 0 8.25 CISPEP 4 MET A 69 HIS A 70 0 0.52 CISPEP 5 ASP B 41 PRO B 42 0 -0.51 CISPEP 6 ALA B 50 PRO B 51 0 -2.02 CISPEP 7 GLU B 67 PRO B 68 0 8.47 CISPEP 8 MET B 69 HIS B 70 0 -0.13 SITE 1 AC1 5 HIS A 33 PRO A 34 SER A 35 HOH A2234 SITE 2 AC1 5 HOH A2235 SITE 1 AC2 5 HIS B 33 PRO B 34 SER B 35 HOH B2245 SITE 2 AC2 5 HOH B2246 CRYST1 96.465 97.364 86.213 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 0.010366 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010271 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011599 0.00000 MTRIX1 1 -0.999620 -0.027330 0.004260 164.82719 1 MTRIX2 1 -0.027350 0.999620 -0.003560 2.59917 1 MTRIX3 1 -0.004160 -0.003670 -0.999980 129.23039 1